From david.m.groppe at gmail.com  Wed Feb  1 02:53:55 2017
From: david.m.groppe at gmail.com (David Groppe)
Date: Tue, 31 Jan 2017 20:53:55 -0500
Subject: [FieldTrip] preprocessing procedures for ECoG/iEEG data
In-Reply-To: <CAOpyOFXvnSAKNNaS-OmkEoqg0wKhsEUQuXg-LZwNmnT6GbPNUQ@mail.gmail.com>
References: <CAOpyOFXvnSAKNNaS-OmkEoqg0wKhsEUQuXg-LZwNmnT6GbPNUQ@mail.gmail.com>
Message-ID: <CAOgkkom7Oe3nLLAdn8otaP5BPhAHd4fpLa7gd3gdLSWLtKTFdQ@mail.gmail.com>

Hi Tim,
   Regarding re-referencing, the two most common re-referencing schemes in
iEEG are average reference or bipolar (i.e., contiguous neighbors in a
strip, shaft, or grid):

http://www.sciencedirect.com/science/article/pii/S1388245706002616

You can also use a Laplacian for grids or reference against the white
matter signal obtained from depth electrodes:

http://www.sciencedirect.com/science/article/pii/S1053811916304232

Each method has it pros and cons.

If you're interested in using a white matter reference, postimplant brain
shift correction, or some electrode visualization functions not available
in FieldTrip, I recommend trying our new MATLAB electrode localization and
visualization toolbox, iELVis:

http://episurg.pbworks.com

hope this is helpful,
      -David


On Mon, Jan 30, 2017 at 5:10 PM, Tim Meehan <timeehan at gmail.com> wrote:

> Hello all,
>
> I am a new user of fieldtrip and new to analyzing electrophysiological
> data. I have familiarized myself with some basics of preprocessing of EEG
> data, but I would like to know if there are special considerations for
> dealing with ECoG/iEEG data -- our dataset has recordings from both
> subdural surface electrodes and depth electrodes, sampled at 2kHz. We are
> initially most interested in extracting the high-gamma band (70-150 Hz)
> envelope as a measure of local activity.
>
> First a general question: is there anyone who could point me to or provide
> me with a preprocessing procedure in fieldtrip that is tailored for
> ECoG/iEEG? I've perused the ECoG section in the wiki but there is no
> information on preprocessing there.
>
> If this is too vague, some specific questions I have are:
> 1) What cutoffs do people tend to use for low and high-pass filters?
>
> 2) What is your choice for re-referencing, if any? Our initial
> reference/ground are the left and right mastoids. I have seen papers that
> re-reference to the nearest neighbor. I think I need to use
> ft_apply_montage to do this, but beyond that I could use some guidance.
>
> 3) At what point do you epoch into trials? My guess is after high/low-pass
> filtering and re-referencing but before artifact detection and removal?
>
> Any feedback on these would be very much appreciated. If you need more
> details please let me know.
>
> Thanks!
> Tim
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From timeehan at gmail.com  Wed Feb  1 16:41:16 2017
From: timeehan at gmail.com (Tim Meehan)
Date: Wed, 1 Feb 2017 10:41:16 -0500
Subject: [FieldTrip] preprocessing procedures for ECoG/iEEG data
In-Reply-To: <CAOgkkom7Oe3nLLAdn8otaP5BPhAHd4fpLa7gd3gdLSWLtKTFdQ@mail.gmail.com>
References: <CAOpyOFXvnSAKNNaS-OmkEoqg0wKhsEUQuXg-LZwNmnT6GbPNUQ@mail.gmail.com>
 <CAOgkkom7Oe3nLLAdn8otaP5BPhAHd4fpLa7gd3gdLSWLtKTFdQ@mail.gmail.com>
Message-ID: <CAOpyOFUOHeKBE2MgkPJaRM0gdnUC_S52mChtc5UjzHDdyR30mg@mail.gmail.com>

Hi David,

Thanks! This should be helpful indeed.

Tim

On Tue, Jan 31, 2017 at 8:53 PM, David Groppe <david.m.groppe at gmail.com>
wrote:

> Hi Tim,
>    Regarding re-referencing, the two most common re-referencing schemes in
> iEEG are average reference or bipolar (i.e., contiguous neighbors in a
> strip, shaft, or grid):
>
> http://www.sciencedirect.com/science/article/pii/S1388245706002616
>
> You can also use a Laplacian for grids or reference against the white
> matter signal obtained from depth electrodes:
>
> http://www.sciencedirect.com/science/article/pii/S1053811916304232
>
> Each method has it pros and cons.
>
> If you're interested in using a white matter reference, postimplant brain
> shift correction, or some electrode visualization functions not available
> in FieldTrip, I recommend trying our new MATLAB electrode localization and
> visualization toolbox, iELVis:
>
> http://episurg.pbworks.com
>
> hope this is helpful,
>       -David
>
>
> On Mon, Jan 30, 2017 at 5:10 PM, Tim Meehan <timeehan at gmail.com> wrote:
>
>> Hello all,
>>
>> I am a new user of fieldtrip and new to analyzing electrophysiological
>> data. I have familiarized myself with some basics of preprocessing of EEG
>> data, but I would like to know if there are special considerations for
>> dealing with ECoG/iEEG data -- our dataset has recordings from both
>> subdural surface electrodes and depth electrodes, sampled at 2kHz. We are
>> initially most interested in extracting the high-gamma band (70-150 Hz)
>> envelope as a measure of local activity.
>>
>> First a general question: is there anyone who could point me to or
>> provide me with a preprocessing procedure in fieldtrip that is tailored for
>> ECoG/iEEG? I've perused the ECoG section in the wiki but there is no
>> information on preprocessing there.
>>
>> If this is too vague, some specific questions I have are:
>> 1) What cutoffs do people tend to use for low and high-pass filters?
>>
>> 2) What is your choice for re-referencing, if any? Our initial
>> reference/ground are the left and right mastoids. I have seen papers that
>> re-reference to the nearest neighbor. I think I need to use
>> ft_apply_montage to do this, but beyond that I could use some guidance.
>>
>> 3) At what point do you epoch into trials? My guess is after
>> high/low-pass filtering and re-referencing but before artifact detection
>> and removal?
>>
>> Any feedback on these would be very much appreciated. If you need more
>> details please let me know.
>>
>> Thanks!
>> Tim
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From elam4hcp at gmail.com  Wed Feb  1 19:05:18 2017
From: elam4hcp at gmail.com (Jennifer Elam)
Date: Wed, 1 Feb 2017 12:05:18 -0600
Subject: [FieldTrip] Announcing HCP Course 2017 at UBC in Vancouver June
	19-23!
Message-ID: <CAJbMWh49Gy26yLokZCkkn4SN06ZZUNYtAnTaBAppmNCC8sUiiA@mail.gmail.com>

We are pleased to announce the *2017 HCP Course: "Exploring the Human
Connectome"*
<https://store.humanconnectome.org/courses/2017/exploring-the-human-connectome.php>,
to be held *June 19 – 23, 2017* at the University of British Columbia (UBC)
<http://ubcconferences.com/>, in Vancouver, BC, Canada. This is the week
before the Organization of Human Brain Mapping (OHBM) annual meeting
<http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageID=3734> to be
held in downtown Vancouver (about 8 miles away from UBC) June 25-29.
This 5-day intensive course will provide training in acquisition,
processing, analysis and visualization of whole brain imaging and
behavioral data using methods and informatics tools developed by the
WU-Minn-Oxford Human Connectome Project (HCP) consortium.

The course is designed for investigators who are interested in:

   - using data collected and distributed from the HCP young adult study
   - acquiring and analyzing HCP-style imaging and behavioral data at your
   own institution
   - processing your own non-HCP data using HCP pipelines and methods
   - using Connectome Workbench
   <https://www.humanconnectome.org/software/connectome-workbench.html> tools
   and sharing data using the BALSA <https://balsa.wustl.edu/> imaging
   database
   - learning HCP multimodal neuroimaging analysis methods, including those
   that combine MEG and MRI data
   - exploring the HCP MMP 1.0
   <http://humanconnectome.org/about/pressroom/nature-article-cortical-brain-maps-at-the-highest-resolution-to-date/>
    multimodal parcellation brain map and learning about how it can be used
   in your analyses
   - positioning yourself to capitalize on HCP-style data being distributed
   by the Connectome Coordinating Facility (CCF) from forthcoming large-scale
   projects (e.g., Lifespan HCP development and aging and Connectomes
   Related to Human Disease projects)


Participants will learn how to acquire, analyze, visualize, and interpret
data from four major MR modalities (structural MR, resting-state fMRI,
diffusion imaging, task-evoked fMRI) plus magnetoencephalography (MEG) and
extensive behavioral data.  Lectures and labs will provide grounding in
neurobiological as well as methodological issues involved in interpreting
multimodal data, and will span the range from single-voxel/vertex to brain
network analysis approaches.

The course is open to students, postdocs, faculty, and industry
participants.  The course is aimed at both new and current users of HCP
data, methods, and tools, and will cover both basic and advanced topics.
Prior experience in human neuroimaging or in computational analysis of
brain networks is desirable, preferably including some familiarity with FSL
<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki> and Freesurfer
<https://surfer.nmr.mgh.harvard.edu/> software.

For more info and to register visit the HCP Course 2017 website
<https://store.humanconnectome.org/courses/2017/exploring-the-human-connectome.php>.
If you have any questions, please contact us at: hcpcourse at humanconnectome.
org

We look forward to seeing you in Vancouver!

Best,
2017 HCP Course Organizers
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From Elana.Harris at cchmc.org  Wed Feb  1 19:18:30 2017
From: Elana.Harris at cchmc.org (Harris, Elana)
Date: Wed, 1 Feb 2017 18:18:30 +0000
Subject: [FieldTrip] Coordinate of fiducials
In-Reply-To: <CAJbMWh49Gy26yLokZCkkn4SN06ZZUNYtAnTaBAppmNCC8sUiiA@mail.gmail.com>
References: <CAJbMWh49Gy26yLokZCkkn4SN06ZZUNYtAnTaBAppmNCC8sUiiA@mail.gmail.com>
Message-ID: <b44c61175fbc4ecf8c4eb6946d0c7db1@cchmc.org>


Dear community,

Does anyone know the format of the CTF  Hz and Hz2 files so that we can get x,y,z coordinates for each fiducial before and after the recording spit out in MATLAB

Thanks,

Elana
________________________________
From: fieldtrip-bounces at science.ru.nl <fieldtrip-bounces at science.ru.nl> on behalf of Jennifer Elam <elam4hcp at gmail.com>
Sent: Wednesday, February 1, 2017 1:05:18 PM
To: fieldtrip at science.ru.nl
Subject: [FieldTrip] Announcing HCP Course 2017 at UBC in Vancouver June 19-23!

We are pleased to announce the 2017 HCP Course: "Exploring the Human Connectome"<https://urldefense.proofpoint.com/v2/url?u=https-3A__store.humanconnectome.org_courses_2017_exploring-2Dthe-2Dhuman-2Dconnectome.php&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=f7HTPnVFgQflJvHLJvPtv4l7ltCrqxVe294kQW3Nzig&s=IGkMALN3otLOEWVzdpUjTocbRQNr7IE0iD_cCkmKD_Q&e=>, to be held June 19 - 23, 2017 at the University of British Columbia (UBC)<https://urldefense.proofpoint.com/v2/url?u=http-3A__ubcconferences.com_&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=f7HTPnVFgQflJvHLJvPtv4l7ltCrqxVe294kQW3Nzig&s=-kmLOVCkIo8dltPqijaULVPw0H1Wyz01HKX98Omzdj4&e=>, in Vancouver, BC, Canada. This is the week before the Organization of Human Brain Mapping (OHBM) annual meeting<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.humanbrainmapping.org_i4a_pages_index.cfm-3FpageID-3D3734&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=f7HTPnVFgQflJvHLJvPtv4l7ltCrqxVe294kQW3Nzig&s=MfelwGWec8xABgX0eDH_jyHQyUvjpRVuFbodlr3z6ng&e=> to be held in downtown Vancouver (about 8 miles away from UBC) June 25-29.
This 5-day intensive course will provide training in acquisition, processing, analysis and visualization of whole brain imaging and behavioral data using methods and informatics tools developed by the WU-Minn-Oxford Human Connectome Project (HCP) consortium.

The course is designed for investigators who are interested in:

  *   using data collected and distributed from the HCP young adult study
  *   acquiring and analyzing HCP-style imaging and behavioral data at your own institution
  *   processing your own non-HCP data using HCP pipelines and methods
  *   using Connectome Workbench<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.humanconnectome.org_software_connectome-2Dworkbench.html&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=f7HTPnVFgQflJvHLJvPtv4l7ltCrqxVe294kQW3Nzig&s=BCHIIMMvKPOd3xS27XiixhdSgetNJgCKjzdPW376qB8&e=> tools and sharing data using the BALSA<https://urldefense.proofpoint.com/v2/url?u=https-3A__balsa.wustl.edu_&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=f7HTPnVFgQflJvHLJvPtv4l7ltCrqxVe294kQW3Nzig&s=8qytFLTyOC0l47SRu0arNiZmCLwisjV7-dQxlVaT3kE&e=> imaging database
  *   learning HCP multimodal neuroimaging analysis methods, including those that combine MEG and MRI data
  *   exploring the HCP MMP 1.0<https://urldefense.proofpoint.com/v2/url?u=http-3A__humanconnectome.org_about_pressroom_nature-2Darticle-2Dcortical-2Dbrain-2Dmaps-2Dat-2Dthe-2Dhighest-2Dresolution-2Dto-2Ddate_&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=f7HTPnVFgQflJvHLJvPtv4l7ltCrqxVe294kQW3Nzig&s=vv4cDO-r5MliyWsfBan1soQ9uaG4z3nnstwd6IZo0ro&e=> multimodal parcellation brain map and learning about how it can be used in your analyses
  *   positioning yourself to capitalize on HCP-style data being distributed by the Connectome Coordinating Facility (CCF) from forthcoming large-scale projects (e.g., Lifespan HCP development and aging and Connectomes Related to Human Disease projects)

Participants will learn how to acquire, analyze, visualize, and interpret data from four major MR modalities (structural MR, resting-state fMRI, diffusion imaging, task-evoked fMRI) plus magnetoencephalography (MEG) and extensive behavioral data.  Lectures and labs will provide grounding in neurobiological as well as methodological issues involved in interpreting multimodal data, and will span the range from single-voxel/vertex to brain network analysis approaches.

The course is open to students, postdocs, faculty, and industry participants.  The course is aimed at both new and current users of HCP data, methods, and tools, and will cover both basic and advanced topics. Prior experience in human neuroimaging or in computational analysis of brain networks is desirable, preferably including some familiarity with FSL<https://urldefense.proofpoint.com/v2/url?u=https-3A__fsl.fmrib.ox.ac.uk_fsl_fslwiki&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=f7HTPnVFgQflJvHLJvPtv4l7ltCrqxVe294kQW3Nzig&s=FkIJchrO7kxdIGf__-gAWr1fCcydPkfPGfK2xaKss6I&e=> and Freesurfer<https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=f7HTPnVFgQflJvHLJvPtv4l7ltCrqxVe294kQW3Nzig&s=YytSx1Fi1kHubaVRYrSvyxQ15X1f-n3J4KQHFNpARh4&e=> software.

For more info and to register visit the HCP Course 2017 website<https://urldefense.proofpoint.com/v2/url?u=https-3A__store.humanconnectome.org_courses_2017_exploring-2Dthe-2Dhuman-2Dconnectome.php&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=f7HTPnVFgQflJvHLJvPtv4l7ltCrqxVe294kQW3Nzig&s=IGkMALN3otLOEWVzdpUjTocbRQNr7IE0iD_cCkmKD_Q&e=>. If you have any questions, please contact us at: hcpcourse at humanconnectome.org<mailto:hcpcourse at humanconnectome.org>

We look forward to seeing you in Vancouver!

Best,
2017 HCP Course Organizers
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From a.stolk8 at gmail.com  Wed Feb  1 19:38:15 2017
From: a.stolk8 at gmail.com (Arjen Stolk)
Date: Wed, 1 Feb 2017 10:38:15 -0800
Subject: [FieldTrip] Coordinate of fiducials
In-Reply-To: <b44c61175fbc4ecf8c4eb6946d0c7db1@cchmc.org>
References: <CAJbMWh49Gy26yLokZCkkn4SN06ZZUNYtAnTaBAppmNCC8sUiiA@mail.gmail.com>
 <b44c61175fbc4ecf8c4eb6946d0c7db1@cchmc.org>
Message-ID: <CAAiwptQBehJuK6x+Mhp16qR1Fir15ezKZAkfi9uDUbuX3htJfQ@mail.gmail.com>

Hi Elana,

This page describes how to obtain continuous head positions,
http://www.fieldtriptoolbox.org/example/how_to_incorporate_head_movements_in_meg_analysis

>From the top of my head, ft_read_headshape can also get you the fiducial
positions at recording onset (see its help, and/or code in
ft_realtime_headlocalizer), and perhaps also at recording offset.

Best, Arjen


2017-02-01 10:18 GMT-08:00 Harris, Elana <Elana.Harris at cchmc.org>:

>
> Dear community,
>
> Does anyone know the format of the CTF  Hz and Hz2 files so that we can
> get x,y,z coordinates for each fiducial before and after the recording spit
> out in MATLAB
>
> Thanks,
>
> Elana
> ------------------------------
> *From:* fieldtrip-bounces at science.ru.nl <fieldtrip-bounces at science.ru.nl>
> on behalf of Jennifer Elam <elam4hcp at gmail.com>
> *Sent:* Wednesday, February 1, 2017 1:05:18 PM
> *To:* fieldtrip at science.ru.nl
> *Subject:* [FieldTrip] Announcing HCP Course 2017 at UBC in Vancouver
> June 19-23!
>
> We are pleased to announce the *2017 HCP Course: "Exploring the Human
> Connectome"*
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__store.humanconnectome.org_courses_2017_exploring-2Dthe-2Dhuman-2Dconnectome.php&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=f7HTPnVFgQflJvHLJvPtv4l7ltCrqxVe294kQW3Nzig&s=IGkMALN3otLOEWVzdpUjTocbRQNr7IE0iD_cCkmKD_Q&e=>,
> to be held *June 19 – 23, 2017* at the University of British Columbia
> (UBC)
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__ubcconferences.com_&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=f7HTPnVFgQflJvHLJvPtv4l7ltCrqxVe294kQW3Nzig&s=-kmLOVCkIo8dltPqijaULVPw0H1Wyz01HKX98Omzdj4&e=>,
> in Vancouver, BC, Canada. This is the week before the Organization of
> Human Brain Mapping (OHBM) annual meeting
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.humanbrainmapping.org_i4a_pages_index.cfm-3FpageID-3D3734&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=f7HTPnVFgQflJvHLJvPtv4l7ltCrqxVe294kQW3Nzig&s=MfelwGWec8xABgX0eDH_jyHQyUvjpRVuFbodlr3z6ng&e=>
>  to be held in downtown Vancouver (about 8 miles away from UBC) June
> 25-29.
> This 5-day intensive course will provide training in acquisition,
> processing, analysis and visualization of whole brain imaging and
> behavioral data using methods and informatics tools developed by the
> WU-Minn-Oxford Human Connectome Project (HCP) consortium.
>
> The course is designed for investigators who are interested in:
>
>    - using data collected and distributed from the HCP young adult study
>    - acquiring and analyzing HCP-style imaging and behavioral data at
>    your own institution
>    - processing your own non-HCP data using HCP pipelines and methods
>    - using Connectome Workbench
>    <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.humanconnectome.org_software_connectome-2Dworkbench.html&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=f7HTPnVFgQflJvHLJvPtv4l7ltCrqxVe294kQW3Nzig&s=BCHIIMMvKPOd3xS27XiixhdSgetNJgCKjzdPW376qB8&e=>
>     tools and sharing data using the BALSA
>    <https://urldefense.proofpoint.com/v2/url?u=https-3A__balsa.wustl.edu_&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=f7HTPnVFgQflJvHLJvPtv4l7ltCrqxVe294kQW3Nzig&s=8qytFLTyOC0l47SRu0arNiZmCLwisjV7-dQxlVaT3kE&e=>
>     imaging database
>    - learning HCP multimodal neuroimaging analysis methods, including
>    those that combine MEG and MRI data
>    - exploring the HCP MMP 1.0
>    <https://urldefense.proofpoint.com/v2/url?u=http-3A__humanconnectome.org_about_pressroom_nature-2Darticle-2Dcortical-2Dbrain-2Dmaps-2Dat-2Dthe-2Dhighest-2Dresolution-2Dto-2Ddate_&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=f7HTPnVFgQflJvHLJvPtv4l7ltCrqxVe294kQW3Nzig&s=vv4cDO-r5MliyWsfBan1soQ9uaG4z3nnstwd6IZo0ro&e=>
>     multimodal parcellation brain map and learning about how it can be
>    used in your analyses
>    - positioning yourself to capitalize on HCP-style data being distributed
>    by the Connectome Coordinating Facility (CCF) from forthcoming large-scale
>    projects (e.g., Lifespan HCP development and aging and Connectomes
>    Related to Human Disease projects)
>
>
> Participants will learn how to acquire, analyze, visualize, and interpret
> data from four major MR modalities (structural MR, resting-state fMRI,
> diffusion imaging, task-evoked fMRI) plus magnetoencephalography (MEG) and
> extensive behavioral data.  Lectures and labs will provide grounding in
> neurobiological as well as methodological issues involved in interpreting
> multimodal data, and will span the range from single-voxel/vertex to brain
> network analysis approaches.
>
> The course is open to students, postdocs, faculty, and industry
> participants.  The course is aimed at both new and current users of HCP
> data, methods, and tools, and will cover both basic and advanced topics.
> Prior experience in human neuroimaging or in computational analysis of
> brain networks is desirable, preferably including some familiarity with
> FSL
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__fsl.fmrib.ox.ac.uk_fsl_fslwiki&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=f7HTPnVFgQflJvHLJvPtv4l7ltCrqxVe294kQW3Nzig&s=FkIJchrO7kxdIGf__-gAWr1fCcydPkfPGfK2xaKss6I&e=>
>  and Freesurfer
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=f7HTPnVFgQflJvHLJvPtv4l7ltCrqxVe294kQW3Nzig&s=YytSx1Fi1kHubaVRYrSvyxQ15X1f-n3J4KQHFNpARh4&e=>
>  software.
>
> For more info and to register visit the HCP Course 2017 website
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__store.humanconnectome.org_courses_2017_exploring-2Dthe-2Dhuman-2Dconnectome.php&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=f7HTPnVFgQflJvHLJvPtv4l7ltCrqxVe294kQW3Nzig&s=IGkMALN3otLOEWVzdpUjTocbRQNr7IE0iD_cCkmKD_Q&e=>.
> If you have any questions, please contact us at:
> hcpcourse at humanconnectome.org
>
> We look forward to seeing you in Vancouver!
>
> Best,
> 2017 HCP Course Organizers
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From Elana.Harris at cchmc.org  Wed Feb  1 20:07:06 2017
From: Elana.Harris at cchmc.org (Harris, Elana)
Date: Wed, 1 Feb 2017 19:07:06 +0000
Subject: [FieldTrip] Coordinate of fiducials
In-Reply-To: <CAAiwptQBehJuK6x+Mhp16qR1Fir15ezKZAkfi9uDUbuX3htJfQ@mail.gmail.com>
References: <CAJbMWh49Gy26yLokZCkkn4SN06ZZUNYtAnTaBAppmNCC8sUiiA@mail.gmail.com>
 <b44c61175fbc4ecf8c4eb6946d0c7db1@cchmc.org>,
 <CAAiwptQBehJuK6x+Mhp16qR1Fir15ezKZAkfi9uDUbuX3htJfQ@mail.gmail.com>
Message-ID: <958d0fb2fe33417c81890238e7daaaea@cchmc.org>


Thanks

________________________________
From: fieldtrip-bounces at science.ru.nl <fieldtrip-bounces at science.ru.nl> on behalf of Arjen Stolk <a.stolk8 at gmail.com>
Sent: Wednesday, February 1, 2017 1:38 PM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] Coordinate of fiducials

Hi Elana,

This page describes how to obtain continuous head positions, http://www.fieldtriptoolbox.org/example/how_to_incorporate_head_movements_in_meg_analysis<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.fieldtriptoolbox.org_example_how-5Fto-5Fincorporate-5Fhead-5Fmovements-5Fin-5Fmeg-5Fanalysis&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=0iTTbC3sAXF0_EAtEWxzNaxLCDK_W_sOWAaeK8ABL_g&s=JvpFp6yUQcy3NUIvBaN4VOnwuOk0gTll8RiWGivEdNA&e=>

>From the top of my head, ft_read_headshape can also get you the fiducial positions at recording onset (see its help, and/or code in ft_realtime_headlocalizer), and perhaps also at recording offset.

Best, Arjen


2017-02-01 10:18 GMT-08:00 Harris, Elana <Elana.Harris at cchmc.org<mailto:Elana.Harris at cchmc.org>>:

Dear community,

Does anyone know the format of the CTF  Hz and Hz2 files so that we can get x,y,z coordinates for each fiducial before and after the recording spit out in MATLAB

Thanks,

Elana
________________________________
From: fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl> <fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>> on behalf of Jennifer Elam <elam4hcp at gmail.com<mailto:elam4hcp at gmail.com>>
Sent: Wednesday, February 1, 2017 1:05:18 PM
To: fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>
Subject: [FieldTrip] Announcing HCP Course 2017 at UBC in Vancouver June 19-23!

We are pleased to announce the 2017 HCP Course: "Exploring the Human Connectome"<https://urldefense.proofpoint.com/v2/url?u=https-3A__store.humanconnectome.org_courses_2017_exploring-2Dthe-2Dhuman-2Dconnectome.php&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=f7HTPnVFgQflJvHLJvPtv4l7ltCrqxVe294kQW3Nzig&s=IGkMALN3otLOEWVzdpUjTocbRQNr7IE0iD_cCkmKD_Q&e=>, to be held June 19 - 23, 2017 at the University of British Columbia (UBC)<https://urldefense.proofpoint.com/v2/url?u=http-3A__ubcconferences.com_&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=f7HTPnVFgQflJvHLJvPtv4l7ltCrqxVe294kQW3Nzig&s=-kmLOVCkIo8dltPqijaULVPw0H1Wyz01HKX98Omzdj4&e=>, in Vancouver, BC, Canada. This is the week before the Organization of Human Brain Mapping (OHBM) annual meeting<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.humanbrainmapping.org_i4a_pages_index.cfm-3FpageID-3D3734&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=f7HTPnVFgQflJvHLJvPtv4l7ltCrqxVe294kQW3Nzig&s=MfelwGWec8xABgX0eDH_jyHQyUvjpRVuFbodlr3z6ng&e=> to be held in downtown Vancouver (about 8 miles away from UBC) June 25-29.
This 5-day intensive course will provide training in acquisition, processing, analysis and visualization of whole brain imaging and behavioral data using methods and informatics tools developed by the WU-Minn-Oxford Human Connectome Project (HCP) consortium.

The course is designed for investigators who are interested in:

  *   using data collected and distributed from the HCP young adult study
  *   acquiring and analyzing HCP-style imaging and behavioral data at your own institution
  *   processing your own non-HCP data using HCP pipelines and methods
  *   using Connectome Workbench<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.humanconnectome.org_software_connectome-2Dworkbench.html&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=f7HTPnVFgQflJvHLJvPtv4l7ltCrqxVe294kQW3Nzig&s=BCHIIMMvKPOd3xS27XiixhdSgetNJgCKjzdPW376qB8&e=> tools and sharing data using the BALSA<https://urldefense.proofpoint.com/v2/url?u=https-3A__balsa.wustl.edu_&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=f7HTPnVFgQflJvHLJvPtv4l7ltCrqxVe294kQW3Nzig&s=8qytFLTyOC0l47SRu0arNiZmCLwisjV7-dQxlVaT3kE&e=> imaging database
  *   learning HCP multimodal neuroimaging analysis methods, including those that combine MEG and MRI data
  *   exploring the HCP MMP 1.0<https://urldefense.proofpoint.com/v2/url?u=http-3A__humanconnectome.org_about_pressroom_nature-2Darticle-2Dcortical-2Dbrain-2Dmaps-2Dat-2Dthe-2Dhighest-2Dresolution-2Dto-2Ddate_&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=f7HTPnVFgQflJvHLJvPtv4l7ltCrqxVe294kQW3Nzig&s=vv4cDO-r5MliyWsfBan1soQ9uaG4z3nnstwd6IZo0ro&e=> multimodal parcellation brain map and learning about how it can be used in your analyses
  *   positioning yourself to capitalize on HCP-style data being distributed by the Connectome Coordinating Facility (CCF) from forthcoming large-scale projects (e.g., Lifespan HCP development and aging and Connectomes Related to Human Disease projects)

Participants will learn how to acquire, analyze, visualize, and interpret data from four major MR modalities (structural MR, resting-state fMRI, diffusion imaging, task-evoked fMRI) plus magnetoencephalography (MEG) and extensive behavioral data.  Lectures and labs will provide grounding in neurobiological as well as methodological issues involved in interpreting multimodal data, and will span the range from single-voxel/vertex to brain network analysis approaches.

The course is open to students, postdocs, faculty, and industry participants.  The course is aimed at both new and current users of HCP data, methods, and tools, and will cover both basic and advanced topics. Prior experience in human neuroimaging or in computational analysis of brain networks is desirable, preferably including some familiarity with FSL<https://urldefense.proofpoint.com/v2/url?u=https-3A__fsl.fmrib.ox.ac.uk_fsl_fslwiki&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=f7HTPnVFgQflJvHLJvPtv4l7ltCrqxVe294kQW3Nzig&s=FkIJchrO7kxdIGf__-gAWr1fCcydPkfPGfK2xaKss6I&e=> and Freesurfer<https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=f7HTPnVFgQflJvHLJvPtv4l7ltCrqxVe294kQW3Nzig&s=YytSx1Fi1kHubaVRYrSvyxQ15X1f-n3J4KQHFNpARh4&e=> software.

For more info and to register visit the HCP Course 2017 website<https://urldefense.proofpoint.com/v2/url?u=https-3A__store.humanconnectome.org_courses_2017_exploring-2Dthe-2Dhuman-2Dconnectome.php&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=f7HTPnVFgQflJvHLJvPtv4l7ltCrqxVe294kQW3Nzig&s=IGkMALN3otLOEWVzdpUjTocbRQNr7IE0iD_cCkmKD_Q&e=>. If you have any questions, please contact us at: hcpcourse at humanconnectome.org<mailto:hcpcourse at humanconnectome.org>

We look forward to seeing you in Vancouver!

Best,
2017 HCP Course Organizers

_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.science.ru.nl_mailman_listinfo_fieldtrip&d=DwMFaQ&c=P0c35rBvlN7D8BNx7kSJTg&r=0zypa9e5hKKp6Dlr4vDw8BiqKwwEYMFtAcQeKwciN-s&m=0iTTbC3sAXF0_EAtEWxzNaxLCDK_W_sOWAaeK8ABL_g&s=hdj8hFe1OR6unHhaeT6DUZ82338O4hrLJ--wVr2EZQc&e=>

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From stan.vanpelt at donders.ru.nl  Thu Feb  2 08:55:05 2017
From: stan.vanpelt at donders.ru.nl (Pelt, S. van (Stan))
Date: Thu, 2 Feb 2017 07:55:05 +0000
Subject: [FieldTrip] EEG source reconstruction using DICS method
In-Reply-To: <58886FF9.3050904@uni-tuebingen.de>
References: <7cd6ae18b167496c939bc39a69057d44@EXPRD01.hosting.ru.nl>
 <5880823B.2050806@uni-tuebingen.de>
 <CACnpnhQuabYFA3ToZMRBr8s4wQwfj1RZD_fqJs-mksM0ST86Zw@mail.gmail.com>
 <58886FF9.3050904@uni-tuebingen.de>
Message-ID: <7CCA2706D7A4DA45931A892DF3C2894C58ECAC30@exprd02.hosting.ru.nl>

Dear Elena,

A late follow-up to Jens’ reply regarding the greenish colors outside the brain. I think it simply has to do with you colormap settings. Zero-values will be green according to the colormap of your first plot, but black according to the colormap of your second plot. See also http://www.fieldtriptoolbox.org/development/tutorial/plotting (search for ‘colormap’).

Best,
Stan

From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of "Jens Klinzing, Uni Tübingen"
Sent: woensdag 25 januari 2017 10:29
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] EEG source reconstruction using DICS method

Dear Elena,
I'm glad the first problem is solved.

About the second one: Are you referring to the yellowish background outside of the brain? My first guess would be that this is a mere plotting issue. Can you check whether there actually are non-NAN or even non-zero values for grid points marked as 'outside' (before interpolation and before and after contrasting)? If not, you know it is a problem with the plotting.

Best,
Jens


Elena Krugliakova<mailto:krugliakova.es at gmail.com>
Donnerstag, 19. Januar 2017 13:55
Dear Jens,
Thank you for your answer!
1. Indeed, I found where ft_sourceanalysis starts to recompute transfer matrix and just loaded precomputed headmodel and sensors. Now everything is fine, and it takes several seconds to run ft_sourceanalysis.
2. About homogeneous "noise outside the mri scan".
Noise appears after I calculate difference between two sources, following tutorial http://www.fieldtriptoolbox.org/tutorial/beamformer. However, sourceplot for not-contrasted conditions looks good. Maybe you could give me an advice, how to get rid of this background noise.
Kind Regards,
Elena



With difference calculation:

cfg                     = [];
cfg.elec                = elec;
cfg.headmodel           = vol;
cfg.grid                = leadfield;
cfg.keepleadfield       =  'yes'
cfg.projectnoise        = 'yes';
cfg.frequency           = [10 15];
cfg.method              = 'dics';
cfg.dics.projectnoise   = 'yes';
cfg.dics.lambda         = '5%';
cfg.dics.keepfilter     = 'yes';
cfg.dics.realfilter     = 'yes';
sourcePNandBS           = ft_sourceanalysis(cfg, freq_PNandBS);
cfg.grid.filter   = sourcePNandBS.avg.filter;
sourcePN          = ft_sourceanalysis(cfg, freq_PN_Post);
sourceBS          = ft_sourceanalysis(cfg, freq_BS_Post);
sourceDiff.avg.pow      = (sourcePN.avg.pow - sourceBS.avg.pow) ./ sourceBS.avg.pow;

cfg            = [];
cfg.parameter  = 'avg.pow';
sourceDiffInt  = ft_sourceinterpolate(cfg, sourceDiff, mri);

cfg = [];
sourceDiffIntNorm = ft_volumenormalise(cfg, sourceDiffInt);

cfg = [];
cfg.method        = 'ortho';
cfg.funparameter  = 'avg.pow';
cfg.maskparameter = cfg.funparameter;
cfg.opacitymap    = 'rampup';
ft_sourceplot(cfg, sourceDiffIntNorm);
 figure
[Inline images 1]




Without difference calculation:

cfg                     = [];
cfg.elec                = elec;
..........
sourcePNandBS           = ft_sourceanalysis(cfg, freq_PNandBS);

cfg.grid.filter   = sourcePNandBS.avg.filter;

sourcePN          = ft_sourceanalysis(cfg, freq_PN_Post);
sourcePN.avg.pow = sourcePN.avg.pow ./ sourcePN.avg.noise;

cfg            = [];
cfg.parameter  = 'avg.pow';
sourcePN  = ft_sourceinterpolate(cfg, sourcePN, mri);

cfg            = [];
sourcePNIntNorm = ft_volumenormalise(cfg, sourcePNInt);

cfg = [];
cfg.method        = 'ortho';
cfg.funparameter  = 'avg.pow';
cfg.maskparameter = cfg.funparameter;
cfg.opacitymap    = 'rampup';
ft_sourceplot(cfg, sourcePNIntNorm);
figure
[Inline images 2]

_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
Jens Klinzing, Uni Tübingen<mailto:jens.klinzing at uni-tuebingen.de>
Donnerstag, 19. Januar 2017 10:09
Dear Elena,

Question 1:
I assume the reason it takes so long is that you are using a FEM-based headmodel. For FEM, ft_sourceanalysis computes a huge transfer matrix on-the-fly (by calling prepare_headmodel - ft_prepare_vol_sens - sb_transfer) every time you do a source reconstruction. For more information see http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=1967 .

You can circumvent the issue by computing the transfer matrix beforehand and changing the code in a way that it doesnt compute a new transfer matrix if you have already provided one.

Alternatively you could use a BEM headmodel (dipoli if possible since bemcp seems to have issues http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2817).

Question 2:
Did you check your segmentation, the headmodel and the coregistration of electrodes/head every step of the way? If you fill all inside voxels with 1s and plot that, do you see an obvious shift/rotation of the "activity" in relation to the MRI?

Best,
Jens
Elena Krugliakova<mailto:krugliakova.es at gmail.com>
Montag, 9. Januar 2017 12:48
Dear Fieldtrip community,
I have a question regarding source reconstruction using the 'dics' method applied to EEG data.
I have two problems: first, even with 32GB of RAM it takes 9 hours to call one ft_sourceanalysis. Maybe, there is a way to optimise the procedure somehow?

Second, at the end of analysis I obtain a very strange figure, on which I see activity localised outside the mri scan. Mistake on which step of analysis might cause this problem?
As a template I used http://www.fieldtriptoolbox.org/tutorial/beamformer
Please, find my script below.

Thank you in advance!
Kind Regards,
Elena


Script:

% freqanalysis
cfg = [];
cfg.toilim  = [-0.5 -0.1]; % prestimulus
Pre         = ft_redefinetrial(cfg, MyData);
cfg = [];
cfg.toilim  = [0.9 1.3]; % poststimulus
Post        = ft_redefinetrial(cfg,  MyData);
cfg = [];
dataAll     = ft_appenddata([], Pre, Post);

cfg = [];
cfg.method       = 'mtmfft';
cfg.output       = 'powandcsd'
cfg.keeptrials   = 'no';
cfg.taper        = 'dpss';
cfg.foi          = 35;
cfg.tapsmofrq    = 4;

freq_Pre         = ft_freqanalysis(cfg,  Pre);
freq_Post        = ft_freqanalysis(cfg,  Post);
freq_PrePost     = ft_freqanalysis(cfg, dataAll);

%% headmodel preparation --- with standard brain
mri     = ft_read_mri('Subject01.mri');
cfg = [];
cfg.dim = mri.dim;
mri     = ft_volumereslice(cfg,mri);

cfg = [];
cfg.output          = {'gray','white','csf','skull','scalp'}
segmentedmri        = ft_volumesegment(cfg, mri);

cfg = [];
cfg.shift           = 0.3;
cfg.method        = 'hexahedral';
cfg.tissue          = {'gray','white','csf','skull','scalp'}
cfg.numvertices     = [800, 800, 800, 400, 200];
cfg.unit                = segmentedmri.unit
bndFEM              = ft_prepare_mesh(cfg,segmentedmri);

cfg = [];
cfg.method          ='simbio';
cfg.conductivity    = [0.33 0.14 1.79 0.01 0.43];
vol_simbio_lowresol = ft_prepare_headmodel(cfg, bndFEM);
%% loading aligned electrodes
load elec_aligned    % 109 EEG electrodes

%% leadfield preparation
cfg = [];
cfg.elec                = elec_aligned;
cfg.vol                 = vol_simbio_lowresol;
cfg.channel             = 'all';
cfg.reducerank          = 3;     % 3 for eeg
cfg.grid.unit           = 'mm';
cfg.grid.resolution     = 10;
leadfield_FEM_lowresol  = ft_prepare_leadfield(cfg);

%% sourceanalysis
cfg = [];
cfg.frequency           = 35;
cfg.vol                 = vol_simbio_lowresol;
cfg.grid                = leadfield_FEM_lowresol
cfg.projectnoise        = 'yes';
cfg.method              = 'dics';
cfg.dics.projectnoise   = 'yes';
cfg.dics.lambda         = '5%';
cfg.dics.keepfilter     = 'yes';
cfg.dics.realfilter     = 'yes';
sourceAll               = ft_sourceanalysis(cfg, freq_PrePost);
cfg.grid.filter         = sourceAll.avg.filter;

sourcePre_con           = ft_sourceanalysis(cfg, freq_Pre);

sourcePost_con          = ft_sourceanalysis(cfg, freq_Post);

sourceDiff              = sourcePost_con;
sourceDiff.avg.pow      = (sourcePost_con.avg.pow - sourcePre_con.avg.pow) ./ sourcePre_con.avg.pow;

%% sourceplot
cfg = [];
cfg.downsample = 2;
cfg.parameter  = 'pow';
sourceDiffInt  = ft_sourceinterpolate(cfg, sourceDiff, mri);

cfg = [];
sourceDiffIntNorm = ft_volumenormalise(cfg, sourceDiffInt);

cfg = [];
cfg.method        = 'glassbrain';
cfg.funparameter  = 'pow';
cfg.maskparameter = cfg.funparameter;
ft_sourceplot(cfg, sourceDiffIntNorm);

_______________________________________________
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fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From v.piai.research at gmail.com  Thu Feb  2 10:45:18 2017
From: v.piai.research at gmail.com (=?UTF-8?Q?Vit=c3=b3ria_Piai?=)
Date: Thu, 2 Feb 2017 10:45:18 +0100
Subject: [FieldTrip] preprocessing procedures for ECoG/iEEG data
In-Reply-To: <CAOpyOFXvnSAKNNaS-OmkEoqg0wKhsEUQuXg-LZwNmnT6GbPNUQ@mail.gmail.com>
References: <CAOpyOFXvnSAKNNaS-OmkEoqg0wKhsEUQuXg-LZwNmnT6GbPNUQ@mail.gmail.com>
Message-ID: <c11f78d4-78a8-0ff5-3bd0-52bab1487bf2@gmail.com>

Hi Tim,

The answers to your questions will depend a lot on what you're planning 
on doing later.

For 1), again it depends. If you're mainly interested in high gamma, it 
doesn't really matter that much since you'll do spectral decomposition 
later on. You could demean the data and not use any filters (or maybe a 
low-pass if you want to get some help with artifact rejection).

For 2) here some more recent references that may help. The bottom line 
is, as David said, all methods have prons and cons. Choose wisely 
depending on what you want to be able to claim about your data!
Mercier, M. R., Bickel, S., Megevand, P., Groppe, D. M., Schroeder, C. 
E., Mehta, A. D., & Lado, F. A. (2017). Evaluation of cortical local 
field potential diffusion in stereotactic electro-encephalography 
recordings: a glimpse on white matter signal. NeuroImage, 147, 219–232.
Arnulfo, G., Hirvonen, J., Nobili, L., Palva, S., & Palva, J. M. (2015). 
Phase and amplitude correlations in resting-state activity in human 
stereotactical EEG recordings. NeuroImage, 112, 114–127.
Shirhatti, V., Borthakur, A., & Ray, S. (2016). Effect of reference 
scheme on power and phase of the local field potential. Neural 
Computation, 28, 882–913.
Trongnetrpunya, A., Nandi, B., Kang, D., Kocsis, B., Schroeder, C. E., & 
Ding, M. (2016). Assessing granger causality in electrophysiological 
data: removing the adverse effects of Common Signals via Bipolar 
Derivations. Frontiers in Systems Neuroscience, 9: 189.

Since you're mentioning high gamma, I'm assuming you have stimuli being 
presented and you want to look at changes in high gamma as a function of 
those. In that case, I guess you have a good idea what your time windows 
will be like. So for 3) your suggestion would be a good way to go. What 
I usually do is to segment longer chunks of data than my narrow time 
windows of interest, mark the artifacts but do not reject any trials 
yet. I then save the artifacts and once I finally settle on what my time 
windows will be, I exclude trials with artifacts within that time window.
- ft_databrowser will allow you to mark and save artifacts, 
ft_rejectartifact will allow you to remove trials containing the artifacts.


Good luck,
Vitoria



On 1/30/2017 11:10 PM, Tim Meehan wrote:
> Hello all,
>
> I am a new user of fieldtrip and new to analyzing electrophysiological 
> data. I have familiarized myself with some basics of preprocessing of 
> EEG data, but I would like to know if there are special considerations 
> for dealing with ECoG/iEEG data -- our dataset has recordings from 
> both subdural surface electrodes and depth electrodes, sampled at 
> 2kHz. We are initially most interested in extracting the high-gamma 
> band (70-150 Hz) envelope as a measure of local activity.
>
> First a general question: is there anyone who could point me to or 
> provide me with a preprocessing procedure in fieldtrip that is 
> tailored for ECoG/iEEG? I've perused the ECoG section in the wiki but 
> there is no information on preprocessing there.
>
> If this is too vague, some specific questions I have are:
> 1) What cutoffs do people tend to use for low and high-pass filters?
>
> 2) What is your choice for re-referencing, if any? Our initial 
> reference/ground are the left and right mastoids. I have seen papers 
> that re-reference to the nearest neighbor. I think I need to use 
> ft_apply_montage to do this, but beyond that I could use some guidance.
>
> 3) At what point do you epoch into trials? My guess is after 
> high/low-pass filtering and re-referencing but before artifact 
> detection and removal?
>
> Any feedback on these would be very much appreciated. If you need more 
> details please let me know.
>
> Thanks!
> Tim
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From jan.schoffelen at donders.ru.nl  Thu Feb  2 11:08:17 2017
From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Thu, 2 Feb 2017 10:08:17 +0000
Subject: [FieldTrip] Nijmegen FieldTrip course 2017: registration open
Message-ID: <DBCA4BBE-973D-43AC-9DB4-6673948E698B@donders.ru.nl>

Dear all,

We would like to announce that the registration for our yearly FieldTrip toolkit course in Nijmegen has been opened , which will take place between April 3 and April 7. Please follow this link<http://www.ru.nl/donders/agenda-news/tool-kits-cognitive/vm-tool-kits/donders-meg-eeg-tool-kit> for more information.

Note that we typically receive more registration requests than that there are seats in the course (which will be 60). Unfortunately, we always have to disappoint people. The selection of participants will be based on the background experience, the research interest and the expectations on what you will learn (see the questions below). Based on this you will not automatically be selected  if you were not selected for a previous occasion.

Best wishes,

Jan-Mathijs


J.M.Schoffelen, MD PhD
Senior Researcher, VIDI-fellow
Telephone: +31-24-3614793
Physical location: room 00.028
Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands



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From mona at sdsc.edu  Thu Feb  2 19:21:35 2017
From: mona at sdsc.edu (Wong-Barnum, Mona)
Date: Thu, 2 Feb 2017 18:21:35 +0000
Subject: [FieldTrip] ft_selectdata
Message-ID: <47F41F00-2A78-48DA-8D7C-0CC66C6AF5FE@mail.ucsd.edu>


Hi:

I’m trying to do some frequency band filtering on my data using ft_selectdata but it doesn’t seem to be working…the new “filtered” data is the same as the original data.

Here is my code (note the eeg.mat file has been through the ft_preprocessing function):

addpath /path/to/fieldtrip
ft_defaults

disp ( 'Reading eeg.mat...' )
data = importdata ( 'eeg.mat' );

disp ( 'Getting low delta band...' )
cfg = [];
cfg.frequency = [0.1 2];
eeg_low_delta = ft_selectdata ( cfg, data );
disp ( 'Saving eeg_low_delta.mat...' );
save eeg_low_delta.mat eeg_low_delta -v7.3;

What am I doing wrong?  All help is appreciated.

thanks,
Mona

************************************************************
    Mona Wong
    Web & Mobile Application Developer
    San Diego Supercomputer Center

    "When your thoughts are too expensive,
     to ever want to keep."

-- U2's When I Look At The World
************************************************************





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From hallmbh at aston.ac.uk  Thu Feb  2 21:17:12 2017
From: hallmbh at aston.ac.uk (Hall, Michael (Research Student))
Date: Thu, 2 Feb 2017 20:17:12 +0000
Subject: [FieldTrip] ft_selectdata
In-Reply-To: <47F41F00-2A78-48DA-8D7C-0CC66C6AF5FE@mail.ucsd.edu>
References: <47F41F00-2A78-48DA-8D7C-0CC66C6AF5FE@mail.ucsd.edu>
Message-ID: <60BAA83166F3DDF0.1216a9bc-f1de-4343-b94b-ca45fcef42f4@mail.outlook.com>

Hi Mona,

The cfg.frequency parameter in ft_selectdata only works on data with a frequency dimension.

Try using the cfg.bpfilter = 'yes'; cfg.bpfreq = [0.1 2]; in ft_preprocessing.

Best wishes,
Mike

Get Outlook for Android<https://aka.ms/ghei36>


From: Wong-Barnum, Mona
Sent: Thursday, 2 February, 18:22
Subject: [FieldTrip] ft_selectdata
To: FieldTrip discussion list


Hi:

I’m trying to do some frequency band filtering on my data using ft_selectdata but it doesn’t seem to be working…the new “filtered” data is the same as the original data.

Here is my code (note the eeg.mat file has been through the ft_preprocessing function):

addpath /path/to/fieldtrip

ft_defaults

disp ( 'Reading eeg.mat...' )

data = importdata ( 'eeg.mat' );

disp ( 'Getting low delta band...' )

cfg = [];

cfg.frequency = [0.1 2];

eeg_low_delta = ft_selectdata ( cfg, data );

disp ( 'Saving eeg_low_delta.mat...' );

save eeg_low_delta.mat eeg_low_delta -v7.3;

What am I doing wrong?  All help is appreciated.

thanks,

Mona

************************************************************
    Mona Wong
    Web & Mobile Application Developer
    San Diego Supercomputer Center

    "When your thoughts are too expensive,
     to ever want to keep."

-- U2's When I Look At The World
************************************************************





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From marios.philiastides at gmail.com  Fri Feb  3 13:16:27 2017
From: marios.philiastides at gmail.com (Marios Philiastides)
Date: Fri, 3 Feb 2017 12:16:27 +0000
Subject: [FieldTrip] cuttingEEG Symposium
Message-ID: <CANrv7RPyyipeDokx6K9mEhfVFWQjzZfbH1rgTKkHLSG3AJYDmQ@mail.gmail.com>

Dear all,

The 3rd cuttingEEG Symposium will be held in Glasgow between 19-22 June,
2017. The symposium is designed to showcase the most up-to-date
developments in the EEG literature, through a mixture of plenary talks and
hands-on workshops. Participants will have the opportunity to present
posters of their most recent work during the event.

For a complete list of speakers/topics and to register please visit the
event's website:

http://cuttingeeg.ccni.gla.ac.uk/

Looking forward to welcoming you in Glasgow over the summer.

Best regards,

Marios G. Philiastides, Ph.D.
Associate Professor
Institute of Neuroscience and Psychology
Centre for Cognitive Neuroimaging
University of Glasgow
Glasgow, G12 8QB

Web: http://decision.ccni.gla.ac.uk/
Email: marios.philiastides at glasgow.ac.uk
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From timeehan at gmail.com  Fri Feb  3 22:30:03 2017
From: timeehan at gmail.com (Tim Meehan)
Date: Fri, 3 Feb 2017 16:30:03 -0500
Subject: [FieldTrip] combine depth and subdural recordings or treat
	separately?
Message-ID: <CAOpyOFU5WG4vqqu+pKA1HHVkERw69pMYZBVsN4nZvARyOUO4TQ@mail.gmail.com>

Hello everyone,

I have a dataset of intracranial EEG from one patient that was recorded
from both subdural strip and depth electrodes. Can anyone advise on whether
it's appropriate to analyze these together in one combined dataset, or if
the signals are different enough to warrant treating them separately?

Thanks!
Tim
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From timeehan at gmail.com  Fri Feb  3 23:23:48 2017
From: timeehan at gmail.com (Tim Meehan)
Date: Fri, 3 Feb 2017 17:23:48 -0500
Subject: [FieldTrip] way to subset data in cfg structure?
Message-ID: <CAOpyOFUMONNESb_g_oTXPcRHAmSeFB8QdDdJGfDfoze8vojrhQ@mail.gmail.com>

Hello everyone,

I'm trying to preprocess a block of continuous data, but the block is too
long such that I can't hold all the channels in memory together, even after
downsampling. Is there perhaps a setting in ft_preprocessing through which
you can specify a subset of data from a larger block? This would solve my
problem, I think.

Thanks!
Tim
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From michelic72 at gmail.com  Sat Feb  4 12:52:44 2017
From: michelic72 at gmail.com (Cristiano Micheli)
Date: Sat, 4 Feb 2017 12:52:44 +0100
Subject: [FieldTrip] combine depth and subdural recordings or treat
	separately?
In-Reply-To: <CAOpyOFU5WG4vqqu+pKA1HHVkERw69pMYZBVsN4nZvARyOUO4TQ@mail.gmail.com>
References: <CAOpyOFU5WG4vqqu+pKA1HHVkERw69pMYZBVsN4nZvARyOUO4TQ@mail.gmail.com>
Message-ID: <CADW7XCDMQNdZYXCJBGdKAZPiXc1AXBQ25FiPVG8rjOOJo4pYYQ@mail.gmail.com>

Hi Tim,

from what I understand it would be useful to know the noise covariance
matrix of strips and depth electrodes, which, if similar, might provide an
objective criterion for data fusion (or data weighting if different).
However it is difficult to know at what point all contacts are really
'brain silent'.
The information about the manufacturer of the strip/depth electrodes, the
experimental reference and ground, the composition of the conductive
surface, the inter-electrode distance and their location inside the skull
might also provide useful information on the account of data-fusion,
because you might be able to estimate the contacts' impedance.

After that it might be useful to have a look at the raw data, to check for
artifacts (like EKG) and evaluate how they are picked up differently from
strips and depth contacts.

I hope this helps

Kind regards,
Cris



On Fri, Feb 3, 2017 at 10:30 PM, Tim Meehan <timeehan at gmail.com> wrote:

> Hello everyone,
>
> I have a dataset of intracranial EEG from one patient that was recorded
> from both subdural strip and depth electrodes. Can anyone advise on whether
> it's appropriate to analyze these together in one combined dataset, or if
> the signals are different enough to warrant treating them separately?
>
> Thanks!
> Tim
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From stephen.whitmarsh at gmail.com  Sat Feb  4 15:35:31 2017
From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh)
Date: Sat, 4 Feb 2017 15:35:31 +0100
Subject: [FieldTrip] way to subset data in cfg structure?
In-Reply-To: <CAOpyOFUMONNESb_g_oTXPcRHAmSeFB8QdDdJGfDfoze8vojrhQ@mail.gmail.com>
References: <CAOpyOFUMONNESb_g_oTXPcRHAmSeFB8QdDdJGfDfoze8vojrhQ@mail.gmail.com>
Message-ID: <CAFrxm=wBUcj++=p_kJqG_uQFZiciJuwAUmT2WE6SrFJhr=WbAA@mail.gmail.com>

Hi Tim,

You might want to check out the cfg.channel setting in ft_preprocessing, or
use cfg.channel and cfg.trials in ft_selectdata. You can use ft_appenddata
to recombine data over trials or channels at a later point.

Hope this helps,
Stephen


On 3 February 2017 at 23:23, Tim Meehan <timeehan at gmail.com> wrote:

> Hello everyone,
>
> I'm trying to preprocess a block of continuous data, but the block is too
> long such that I can't hold all the channels in memory together, even after
> downsampling. Is there perhaps a setting in ft_preprocessing through which
> you can specify a subset of data from a larger block? This would solve my
> problem, I think.
>
> Thanks!
> Tim
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From danielle.farrar at gmail.com  Mon Feb  6 02:52:34 2017
From: danielle.farrar at gmail.com (Danielle Farrar)
Date: Sun, 5 Feb 2017 20:52:34 -0500
Subject: [FieldTrip] Starting at ft_timelockstatistics
In-Reply-To: <CAN1QL1Pf+5dP7et=00ZDQC8Paho6Z-W6oZmNgc_=bwTEAn3YGQ@mail.gmail.com>
References: <CAN1QL1Pf+5dP7et=00ZDQC8Paho6Z-W6oZmNgc_=bwTEAn3YGQ@mail.gmail.com>
Message-ID: <CAN1QL1O4-1moj846_Ni=DWLzwg39+XCwfsrrt_OXhxgF7Y_Vow@mail.gmail.com>

Hello,

Just a quick question to follow up on this. I've gotten a bit further on
this question, but now am stuck because ft_timelockstatistics requires a
cfg.design field.  I was wondering how to construct this field?  I haven't
been able to find an example in the documentation.

Thanks,
Danielle

On Tue, Jan 31, 2017 at 11:40 AM, Danielle Farrar <danielle.farrar at gmail.com
> wrote:

> Hello,
>
> My apologies if this has been covered before, I just joined the list and
> am having trouble searching the archives.
>
> I have a set of EEG data that was recorded from a Biosemi apparatus using
> a 128-channel cap. The dataset is in text files, is post-processed and is
> the result of filtering, epoching, and averaging, and has been imported
> into matlab.  I created trial structs out of the datasets.  It is a dataset
> of 21 subjects with two conditions.  I'm trying to do some non-parametric
> clustering statistics on the dataset and I don't have access to the
> original bdf files.
>
> I have the electrode names and coordinates saved in matlab matrices.  Now,
> I'd like to do clustering analysis using a monte carlo simulation to
> determine areas of significant differences between the two conditions, but
> am having trouble ensuring that my datasets are structured appropriately
> for input. It seems that the tutorials mostly assume that the data is in a
> raw output format from one of the systems.
>
> I know that for ft_timelockstatistics, the data is supposed to be output
> from the ft_timelockanalysis. I was trying to use ft_timelockanalysis as an
> entry point  However, I am having trouble constructing the data struct
> appropriate for the timelock function.  Can this be done?  Should I be
> starting further upstream? I'm attaching some of the code. I'm know the
> data struct needs additional information but am not sure how to go about
> using it.
>
> The error I get when I run the following code is "Error using ft_checkdata
> (line 480). This function requires raw+comp or raw data as input."
>
> Thanks!
> Danielle
>
> ********************************
>
> for i=size(CD_condition.data,3),
>       CD_trial{i} = CD_condition.data(:,:,i);
> end
>
> CD.trial = CD_trial;
>
> cfg.channel = 'all';
> cfg.trials = 'all';
> cfg.covariance = 'yes';
> cfg.covariancewindow = 'prestim';
> cfg.removemean = 'yes';
> cfg.vartrllength = 0;
>
> CD.type = 'raw+comp';
> ft_timelockanalysis(cfg,CD);
>
>
>
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From maity_winky at yahoo.es  Mon Feb  6 09:28:31 2017
From: maity_winky at yahoo.es (=?UTF-8?Q?Mait=C3=A9_Crespo_Garc=C3=ADa?=)
Date: Mon, 6 Feb 2017 08:28:31 +0000 (UTC)
Subject: [FieldTrip] Starting at ft_timelockstatistics
In-Reply-To: <CAN1QL1O4-1moj846_Ni=DWLzwg39+XCwfsrrt_OXhxgF7Y_Vow@mail.gmail.com>
References: <CAN1QL1Pf+5dP7et=00ZDQC8Paho6Z-W6oZmNgc_=bwTEAn3YGQ@mail.gmail.com>
 <CAN1QL1O4-1moj846_Ni=DWLzwg39+XCwfsrrt_OXhxgF7Y_Vow@mail.gmail.com>
Message-ID: <264055019.2734773.1486369711622@mail.yahoo.com>

Hello Danielle,
the links below may help you to configure the design field. 

Best wishes,Maité

http://www.fieldtriptoolbox.org/development/designhttp://www.fieldtriptoolbox.org/walkthrough#paired_comparison



 

    El Lunes 6 de febrero de 2017 3:10, Danielle Farrar <danielle.farrar at gmail.com> escribió:
 

 Hello,
Just a quick question to follow up on this. I've gotten a bit further on this question, but now am stuck because ft_timelockstatistics requires a cfg.design field.  I was wondering how to construct this field?  I haven't been able to find an example in the documentation.
Thanks,Danielle
On Tue, Jan 31, 2017 at 11:40 AM, Danielle Farrar <danielle.farrar at gmail.com> wrote:

Hello,
My apologies if this has been covered before, I just joined the list and am having trouble searching the archives.
I have a set of EEG data that was recorded from a Biosemi apparatus using a 128-channel cap. The dataset is in text files, is post-processed and is the result of filtering, epoching, and averaging, and has been imported into matlab.  I created trial structs out of the datasets.  It is a dataset of 21 subjects with two conditions.  I'm trying to do some non-parametric clustering statistics on the dataset and I don't have access to the original bdf files.
I have the electrode names and coordinates saved in matlab matrices.  Now, I'd like to do clustering analysis using a monte carlo simulation to determine areas of significant differences between the two conditions, but am having trouble ensuring that my datasets are structured appropriately for input. It seems that the tutorials mostly assume that the data is in a raw output format from one of the systems.  
I know that for ft_timelockstatistics, the data is supposed to be output from the ft_timelockanalysis. I was trying to use ft_timelockanalysis as an entry point  However, I am having trouble constructing the data struct appropriate for the timelock function.  Can this be done?  Should I be starting further upstream? I'm attaching some of the code. I'm know the data struct needs additional information but am not sure how to go about using it.  
The error I get when I run the following code is "Error using ft_checkdata (line 480). This function requires raw+comp or raw data as input."
Thanks!Danielle
****************************** **
for i=size(CD_condition.data,3),      CD_trial{i} = CD_condition.data(:,:,i);end
CD.trial = CD_trial;
cfg.channel = 'all';cfg.trials = 'all';cfg.covariance = 'yes';cfg.covariancewindow = 'prestim';cfg.removemean = 'yes';cfg.vartrllength = 0;
CD.type = 'raw+comp';ft_timelockanalysis(cfg,CD);




_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip

   
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From jan.schoffelen at donders.ru.nl  Mon Feb  6 09:40:04 2017
From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Mon, 6 Feb 2017 08:40:04 +0000
Subject: [FieldTrip] Symmetric Source Reconstruction
In-Reply-To: <CAHcwWFFR7-JrPVNwfovpn1EOVHuAsbTTjME+6OXJndOx=YuNuQ@mail.gmail.com>
References: <CAHcwWFFR7-JrPVNwfovpn1EOVHuAsbTTjME+6OXJndOx=YuNuQ@mail.gmail.com>
Message-ID: <3E18DBC0-CAA4-4C3D-8F6C-AFAC5AB5A21D@donders.ru.nl>

Hi Behzad,

You could try to do the following, before calling ft_sourceinterpolate:

sourceC.pos = sourceC.pos(:,1:3);

Best,
Jan-Mathijs




J.M.Schoffelen, MD PhD
Senior Researcher, VIDI-fellow
Telephone: +31-24-3614793
Physical location: room 00.028
Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands





> On 26 Jan 2017, at 17:36, Behzad Iravani <behzadiravani at gmail.com> wrote:
> 
> 
> Dear FieldTrip experts ,
> 
> I'm interested to perform symmetric source reconstruction on time lock data. However I encountered an error. here is my code:
> 
> cfg                         = [];
> cfg.grid.unit            = 'mm';
> cfg.grid.resolution   = 5;
> cfg.grid.tight           = 'yes';
> cfg.inwardshift        = -2;
> cfg.headmodel        = vol;
> cfg.symmetric        ='y';  % symmetric sources
> 
> grid                = ft_prepare_sourcemodel(cfg);
> 
> 
> % timelock data for two conditions
> 
> load timelockA     %co-variance computed
> load timelockB     %co-variance computed
> load timeloackAB %co-variance computed
> 
> load elecfile.mat   % sensor positions
> load vol.mat         % pre-compute head model
> 
> cfg                     = [];
> cfg.method         = 'lcmv';     
> cfg.grid               = grid;       
> cfg.headmodel     = vol;       
> cfg.elec               = elecfile;
> cfg.keepfilter        = 'yes';
> source                = ft_sourceanalysis(timeloackAB); % compute common filter
> 
> cfg.keepfilter        = 'no';
> cfg.grid.filter         =source.avg.filter
> sourceA               = ft_sourceanalysis(timeloackA); % compute common filter
> 
> sourceB               = ft_sourceanalysis(timeloackA); % compute common filter
> 
> 
> % Contrast Condition A versus B
> cfg           = [];
> cfg.parameter = 'pow';
> cfg.operation = '(x1./x2-1)';
> SourceC= ft_math(cfg,sourceA ,sourceB);
> 
> load mri.mat       % load anatomical image
> 
> cfg            = [];
> cfg.parameter  = 'pow';
> sourcePostInt  = ft_sourceinterpolate(cfg,  SourceC ,mri);
> 
> here I get error in ft_warp_apply because the grid.pos is 6*n which it is supposed to be 3*n, since I chose the symmetric option it turned to 6*n.
> 
> How can I solve this problem?
> 
> Thanks in advance
> Best
> 
> Behzad
> 
> 
>   
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip





From jan.schoffelen at donders.ru.nl  Mon Feb  6 09:57:13 2017
From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Mon, 6 Feb 2017 08:57:13 +0000
Subject: [FieldTrip] Error reading fif file during ft_read_headshape
In-Reply-To: <CO2PR03MB236070B66C42B5D496EEE3B7B24B0@CO2PR03MB2360.namprd03.prod.outlook.com>
References: <CO2PR03MB236070B66C42B5D496EEE3B7B24B0@CO2PR03MB2360.namprd03.prod.outlook.com>
Message-ID: <AA46DD2B-E204-4283-ADAE-41610B9A2DAD@donders.ru.nl>

Hi Alba,

The first error that you report is a low-level reading error, that may have nothing to do with fieldtrip. You may want to check which version of the mne-matlab software you are using.

The workaround you tried out is not going to work, because ft_volumedownsample only works on data that is defined on a volumetric grid of dipole positions, not on a cortical sheet.

Best,
Jan-Mathijs


J.M.Schoffelen, MD PhD
Senior Researcher, VIDI-fellow
Telephone: +31-24-3614793
Physical location: room 00.028
Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands




On 30 Jan 2017, at 22:53, Alba Xifra Porxas, Ms <alba.xifraporxas at mail.mcgill.ca<mailto:alba.xifraporxas at mail.mcgill.ca>> wrote:


Dear FieldTrippers,

My name is Alba Xifra Porxas and I am working in the Biosignals and Systems Analysis Lab at McGill University. Currently I am analyzing MEG data from a motor-task paradigm from young and elderly subjects. I am following the tutorial: Source reconstruction of event-related fields using minimum-norm estimate (http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate).

I am having problems reading the downsampled mesh from MNE suite. When I call FT_READ_HEADSHAPE, I receive the following error message:

>> sourcespace = ft_read_headshape('s003-oct-6-src.fif', 'format', 'mne_source');

Error using fiff_read_tag (line 178)

Only two and three dimensional matrices are supported at this time

Error in mne_read_source_spaces/read_source_space/find_tag (line 288)

                    tag = fiff_read_tag(fid,node.dir(p).pos);

Error in mne_read_source_spaces/read_source_space (line 254)

        tag2 = find_tag(this,FIFF.FIFF_MNE_SOURCE_SPACE_NEAREST_DIST);

Error in mne_read_source_spaces (line 111)

    this = read_source_space(spaces(k));

Error in ft_read_headshape (line 391)

    src = mne_read_source_spaces(filename, 1);

However, I can visualize it correctly in MNE. The command I used to create the source space is:  mne_setup_source_space --ico -6.

Since I have the meshes from FreeSurfer, I tried a workaround. I call FT_READ_HEADSHAPE using lh.orig and rh.orig, which works. I successfully coregister the source space with the sensor-space and compute source reconstruction using minimum-norm estimation. However, when I try to downsample the output of FT_SOURCEANALYSIS calling FT_VOLUMEDOWNSAMPLE before parcellation, I receive the following error:

Reference to non-existent field 'dim'.

Error in ft_volumedownsample (line 100)

xsel = 1:cfg.downsample:source.dim(1);

Even if I manually introduce this missing field ‘dim’, it seems the number of vertices is too big:

>> source.dim(1) = length(source.pos);source.dim(2) = length(source.pos);source.dim(3) = length(source.pos);

>> cfg = [];cfg.downsample = 4;source_down = ft_volumedownsample(cfg,source);

Error using repmat

Maximum variable size allowed by the program is exceeded.

Error in ndgrid (line 73)

        varargout{i} = repmat(x,s);

Error in pos2transform (line 25)

[X,Y,Z] = ndgrid(x, y, z);

Error in ft_checkdata>source2volume (line 1286)

  data.transform = pos2transform(data.pos, data.dim);

Error in ft_checkdata (line 350)

      data = source2volume(data);

Error in ft_volumedownsample (line 69)

source = ft_checkdata(source, 'datatype', 'volume', 'feedback', 'no');

The source I use is as follows:

>> display(source)

source =

      time: [1x3900 double]

    inside: [255462x1 logical]

       pos: [255462x3 double]

    method: 'average'

       avg: [1x1 struct]

       cfg: [1x1 struct]

       dim: [255462 255462 255462]

Therefore, I am back to where I started. I need to read the fif file from MNE suite.

I uploaded my fif file in Dropbox. Here is the link: https://www.dropbox.com/sh/uq181l76353hd8q/AACjTu8KI_rGaXlaDMyw-Diba?dl=0

Could someone tell me if there is something wrong with the file or with my workaround? Any help would be really appreciated. I am using Fieldtrip version 20170118.

Best,

Alba Xifra Porxas
PhD student, Biosignals and Systems Analysis Lab
McGill University, Montréal, Canada
_______________________________________________
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From timeehan at gmail.com  Mon Feb  6 23:53:37 2017
From: timeehan at gmail.com (Tim Meehan)
Date: Mon, 6 Feb 2017 17:53:37 -0500
Subject: [FieldTrip] way to subset data in cfg structure?
In-Reply-To: <CAFrxm=wBUcj++=p_kJqG_uQFZiciJuwAUmT2WE6SrFJhr=WbAA@mail.gmail.com>
References: <CAOpyOFUMONNESb_g_oTXPcRHAmSeFB8QdDdJGfDfoze8vojrhQ@mail.gmail.com>
 <CAFrxm=wBUcj++=p_kJqG_uQFZiciJuwAUmT2WE6SrFJhr=WbAA@mail.gmail.com>
Message-ID: <CAOpyOFWEGwwmcaW5-wdKZ5SChA6rFpnrM8QcNLSvtUyzQyE8jg@mail.gmail.com>

Hi Stephen,

Thanks, I checked out ft_selectdata, but what I really want is a way to
subselect the time dimension, not the channel dimension. I don't see this
as an option in ft_selectdata. I can do this subselection manually by going
into the trials and time fields but it's a little bit clunky and was hoping
there might be a more elegant way...

Thanks,
Tim

On Sat, Feb 4, 2017 at 9:35 AM, Stephen Whitmarsh <
stephen.whitmarsh at gmail.com> wrote:

> Hi Tim,
>
> You might want to check out the cfg.channel setting in ft_preprocessing,
> or use cfg.channel and cfg.trials in ft_selectdata. You can use
> ft_appenddata to recombine data over trials or channels at a later point.
>
> Hope this helps,
> Stephen
>
>
> On 3 February 2017 at 23:23, Tim Meehan <timeehan at gmail.com> wrote:
>
>> Hello everyone,
>>
>> I'm trying to preprocess a block of continuous data, but the block is too
>> long such that I can't hold all the channels in memory together, even after
>> downsampling. Is there perhaps a setting in ft_preprocessing through which
>> you can specify a subset of data from a larger block? This would solve my
>> problem, I think.
>>
>> Thanks!
>> Tim
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From saeedzahran at hotmail.com  Tue Feb  7 10:29:03 2017
From: saeedzahran at hotmail.com (Saeed Zahran)
Date: Tue, 7 Feb 2017 09:29:03 +0000
Subject: [FieldTrip] simulated EEG to simulated MEG
In-Reply-To: <mailman.13.1486378802.14627.fieldtrip@science.ru.nl>
References: <mailman.13.1486378802.14627.fieldtrip@science.ru.nl>
Message-ID: <DM5PR0101MB293725210011563AA620A6E5B7430@DM5PR0101MB2937.prod.exchangelabs.com>



Goodmorning,


How do you convert the simulated EEG to simulated MEG,

Its possible to convert the electrical potential generated at each cells to

magnetic potential? without modelling the MEG


Best regards

 Saeed Zahran

________________________________
From: fieldtrip-bounces at science.ru.nl <fieldtrip-bounces at science.ru.nl> on behalf of fieldtrip-request at science.ru.nl <fieldtrip-request at science.ru.nl>
Sent: Monday, February 6, 2017 1:00 PM
To: fieldtrip at science.ru.nl
Subject: fieldtrip Digest, Vol 75, Issue 7

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        fieldtrip at science.ru.nl

To subscribe or unsubscribe via the World Wide Web, visit
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FieldTrip is the MATLAB software toolbox for MEG and EEG analysis that is being developed by a team of researchers at the Donders Institute for Brain, Cognition and ...


or, via email, send a message with subject or body 'help' to
        fieldtrip-request at science.ru.nl

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When replying, please edit your Subject line so it is more specific
than "Re: Contents of fieldtrip digest..."


Today's Topics:

   1. Re: Starting at ft_timelockstatistics (Danielle Farrar)
   2. Re: Starting at ft_timelockstatistics (Mait? Crespo Garc?a)
   3. Re: Symmetric Source Reconstruction
      (Schoffelen, J.M. (Jan Mathijs))
   4. Re: Error reading fif file during ft_read_headshape
      (Schoffelen, J.M. (Jan Mathijs))


----------------------------------------------------------------------

Message: 1
Date: Sun, 5 Feb 2017 20:52:34 -0500
From: Danielle Farrar <danielle.farrar at gmail.com>
To: fieldtrip at science.ru.nl
Subject: Re: [FieldTrip] Starting at ft_timelockstatistics
Message-ID:
        <CAN1QL1O4-1moj846_Ni=DWLzwg39+XCwfsrrt_OXhxgF7Y_Vow at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hello,

Just a quick question to follow up on this. I've gotten a bit further on
this question, but now am stuck because ft_timelockstatistics requires a
cfg.design field.  I was wondering how to construct this field?  I haven't
been able to find an example in the documentation.

Thanks,
Danielle

On Tue, Jan 31, 2017 at 11:40 AM, Danielle Farrar <danielle.farrar at gmail.com
> wrote:

> Hello,
>
> My apologies if this has been covered before, I just joined the list and
> am having trouble searching the archives.
>
> I have a set of EEG data that was recorded from a Biosemi apparatus using
> a 128-channel cap. The dataset is in text files, is post-processed and is
> the result of filtering, epoching, and averaging, and has been imported
> into matlab.  I created trial structs out of the datasets.  It is a dataset
> of 21 subjects with two conditions.  I'm trying to do some non-parametric
> clustering statistics on the dataset and I don't have access to the
> original bdf files.
>
> I have the electrode names and coordinates saved in matlab matrices.  Now,
> I'd like to do clustering analysis using a monte carlo simulation to
> determine areas of significant differences between the two conditions, but
> am having trouble ensuring that my datasets are structured appropriately
> for input. It seems that the tutorials mostly assume that the data is in a
> raw output format from one of the systems.
>
> I know that for ft_timelockstatistics, the data is supposed to be output
> from the ft_timelockanalysis. I was trying to use ft_timelockanalysis as an
> entry point  However, I am having trouble constructing the data struct
> appropriate for the timelock function.  Can this be done?  Should I be
> starting further upstream? I'm attaching some of the code. I'm know the
> data struct needs additional information but am not sure how to go about
> using it.
>
> The error I get when I run the following code is "Error using ft_checkdata
> (line 480). This function requires raw+comp or raw data as input."
>
> Thanks!
> Danielle
>
> ********************************
>
> for i=size(CD_condition.data,3),
>       CD_trial{i} = CD_condition.data(:,:,i);
> end
>
> CD.trial = CD_trial;
>
> cfg.channel = 'all';
> cfg.trials = 'all';
> cfg.covariance = 'yes';
> cfg.covariancewindow = 'prestim';
> cfg.removemean = 'yes';
> cfg.vartrllength = 0;
>
> CD.type = 'raw+comp';
> ft_timelockanalysis(cfg,CD);
>
>
>
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------------------------------

Message: 2
Date: Mon, 6 Feb 2017 08:28:31 +0000 (UTC)
From: Mait? Crespo Garc?a <maity_winky at yahoo.es>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] Starting at ft_timelockstatistics
Message-ID: <264055019.2734773.1486369711622 at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hello Danielle,
the links below may help you to configure the design field.

Best wishes,Mait?

http://www.fieldtriptoolbox.org/development/designhttp://www.fieldtriptoolbox.org/walkthrough#paired_comparison





    El Lunes 6 de febrero de 2017 3:10, Danielle Farrar <danielle.farrar at gmail.com> escribi?:


 Hello,
Just a quick question to follow up on this. I've gotten a bit further on this question, but now am stuck because ft_timelockstatistics requires a cfg.design field.? I was wondering how to construct this field?? I haven't been able to find an example in the documentation.
Thanks,Danielle
On Tue, Jan 31, 2017 at 11:40 AM, Danielle Farrar <danielle.farrar at gmail.com> wrote:

Hello,
My apologies if this has been covered before, I just joined the list and am having trouble searching the archives.
I have a set of EEG data that was recorded from a Biosemi apparatus using a 128-channel cap. The dataset is in text files, is post-processed and is the result of filtering, epoching, and averaging, and has been imported into matlab.? I created trial structs out of the datasets.? It is a dataset of 21 subjects with two conditions.? I'm trying to do some non-parametric clustering statistics on the dataset and I don't have access to the original bdf files.
I have the electrode names and coordinates saved in matlab matrices.? Now, I'd like to do clustering analysis using a monte carlo simulation to determine areas of significant differences between the two conditions, but am having trouble ensuring that my datasets are structured appropriately for input. It seems that the tutorials mostly assume that the data is in a raw output format from one of the systems. ?
I know that for ft_timelockstatistics, the data is supposed to be output from the ft_timelockanalysis. I was trying to use ft_timelockanalysis as an entry point ?However, I am having trouble constructing the data struct appropriate for the timelock function.? Can this be done?? Should I be starting further upstream? I'm attaching some of the code. I'm know the data struct needs additional information but am not sure how to go about using it. ?
The error I get when I run the following code is "Error using ft_checkdata (line 480). This function requires raw+comp or raw data as input."
Thanks!Danielle
****************************** **
for i=size(CD_condition.data,3),? ? ? CD_trial{i} = CD_condition.data(:,:,i);end
CD.trial = CD_trial;
cfg.channel = 'all';cfg.trials = 'all';cfg.covariance = 'yes';cfg.covariancewindow = 'prestim';cfg.removemean = 'yes';cfg.vartrllength = 0;
CD.type = 'raw+comp';ft_timelockanalysis(cfg,CD);




_______________________________________________
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https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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------------------------------

Message: 3
Date: Mon, 6 Feb 2017 08:40:04 +0000
From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen at donders.ru.nl>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] Symmetric Source Reconstruction
Message-ID: <3E18DBC0-CAA4-4C3D-8F6C-AFAC5AB5A21D at donders.ru.nl>
Content-Type: text/plain; charset="us-ascii"

Hi Behzad,

You could try to do the following, before calling ft_sourceinterpolate:

sourceC.pos = sourceC.pos(:,1:3);

Best,
Jan-Mathijs




J.M.Schoffelen, MD PhD
Senior Researcher, VIDI-fellow
Telephone: +31-24-3614793
Physical location: room 00.028
Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands





> On 26 Jan 2017, at 17:36, Behzad Iravani <behzadiravani at gmail.com> wrote:
>
>
> Dear FieldTrip experts ,
>
> I'm interested to perform symmetric source reconstruction on time lock data. However I encountered an error. here is my code:
>
> cfg                         = [];
> cfg.grid.unit            = 'mm';
> cfg.grid.resolution   = 5;
> cfg.grid.tight           = 'yes';
> cfg.inwardshift        = -2;
> cfg.headmodel        = vol;
> cfg.symmetric        ='y';  % symmetric sources
>
> grid                = ft_prepare_sourcemodel(cfg);
>
>
> % timelock data for two conditions
>
> load timelockA     %co-variance computed
> load timelockB     %co-variance computed
> load timeloackAB %co-variance computed
>
> load elecfile.mat   % sensor positions
> load vol.mat         % pre-compute head model
>
> cfg                     = [];
> cfg.method         = 'lcmv';
> cfg.grid               = grid;
> cfg.headmodel     = vol;
> cfg.elec               = elecfile;
> cfg.keepfilter        = 'yes';
> source                = ft_sourceanalysis(timeloackAB); % compute common filter
>
> cfg.keepfilter        = 'no';
> cfg.grid.filter         =source.avg.filter
> sourceA               = ft_sourceanalysis(timeloackA); % compute common filter
>
> sourceB               = ft_sourceanalysis(timeloackA); % compute common filter
>
>
> % Contrast Condition A versus B
> cfg           = [];
> cfg.parameter = 'pow';
> cfg.operation = '(x1./x2-1)';
> SourceC= ft_math(cfg,sourceA ,sourceB);
>
> load mri.mat       % load anatomical image
>
> cfg            = [];
> cfg.parameter  = 'pow';
> sourcePostInt  = ft_sourceinterpolate(cfg,  SourceC ,mri);
>
> here I get error in ft_warp_apply because the grid.pos is 6*n which it is supposed to be 3*n, since I chose the symmetric option it turned to 6*n.
>
> How can I solve this problem?
>
> Thanks in advance
> Best
>
> Behzad
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
fieldtrip Info Page - mailman.science.ru.nl<https://mailman.science.ru.nl/mailman/listinfo/fieldtrip>
mailman.science.ru.nl
FieldTrip is the MATLAB software toolbox for MEG and EEG analysis that is being developed by a team of researchers at the Donders Institute for Brain, Cognition and ...







------------------------------

Message: 4
Date: Mon, 6 Feb 2017 08:57:13 +0000
From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen at donders.ru.nl>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] Error reading fif file during
        ft_read_headshape
Message-ID: <AA46DD2B-E204-4283-ADAE-41610B9A2DAD at donders.ru.nl>
Content-Type: text/plain; charset="utf-8"

Hi Alba,

The first error that you report is a low-level reading error, that may have nothing to do with fieldtrip. You may want to check which version of the mne-matlab software you are using.

The workaround you tried out is not going to work, because ft_volumedownsample only works on data that is defined on a volumetric grid of dipole positions, not on a cortical sheet.

Best,
Jan-Mathijs


J.M.Schoffelen, MD PhD
Senior Researcher, VIDI-fellow
Telephone: +31-24-3614793
Physical location: room 00.028
Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands




On 30 Jan 2017, at 22:53, Alba Xifra Porxas, Ms <alba.xifraporxas at mail.mcgill.ca<mailto:alba.xifraporxas at mail.mcgill.ca>> wrote:


Dear FieldTrippers,

My name is Alba Xifra Porxas and I am working in the Biosignals and Systems Analysis Lab at McGill University. Currently I am analyzing MEG data from a motor-task paradigm from young and elderly subjects. I am following the tutorial: Source reconstruction of event-related fields using minimum-norm estimate (http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate).
[http://www.fieldtriptoolbox.org/_media/logo-share.png]<http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate>

tutorial:minimumnormestimate – FieldTrip<http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate>
fieldtrip.fcdonders.nl



I am having problems reading the downsampled mesh from MNE suite. When I call FT_READ_HEADSHAPE, I receive the following error message:

>> sourcespace = ft_read_headshape('s003-oct-6-src.fif', 'format', 'mne_source');

Error using fiff_read_tag (line 178)

Only two and three dimensional matrices are supported at this time

Error in mne_read_source_spaces/read_source_space/find_tag (line 288)

                    tag = fiff_read_tag(fid,node.dir(p).pos);

Error in mne_read_source_spaces/read_source_space (line 254)

        tag2 = find_tag(this,FIFF.FIFF_MNE_SOURCE_SPACE_NEAREST_DIST);

Error in mne_read_source_spaces (line 111)

    this = read_source_space(spaces(k));

Error in ft_read_headshape (line 391)

    src = mne_read_source_spaces(filename, 1);

However, I can visualize it correctly in MNE. The command I used to create the source space is:  mne_setup_source_space --ico -6.

Since I have the meshes from FreeSurfer, I tried a workaround. I call FT_READ_HEADSHAPE using lh.orig and rh.orig, which works. I successfully coregister the source space with the sensor-space and compute source reconstruction using minimum-norm estimation. However, when I try to downsample the output of FT_SOURCEANALYSIS calling FT_VOLUMEDOWNSAMPLE before parcellation, I receive the following error:

Reference to non-existent field 'dim'.

Error in ft_volumedownsample (line 100)

xsel = 1:cfg.downsample:source.dim(1);

Even if I manually introduce this missing field ?dim?, it seems the number of vertices is too big:

>> source.dim(1) = length(source.pos);source.dim(2) = length(source.pos);source.dim(3) = length(source.pos);

>> cfg = [];cfg.downsample = 4;source_down = ft_volumedownsample(cfg,source);

Error using repmat

Maximum variable size allowed by the program is exceeded.

Error in ndgrid (line 73)

        varargout{i} = repmat(x,s);

Error in pos2transform (line 25)

[X,Y,Z] = ndgrid(x, y, z);

Error in ft_checkdata>source2volume (line 1286)

  data.transform = pos2transform(data.pos, data.dim);

Error in ft_checkdata (line 350)

      data = source2volume(data);

Error in ft_volumedownsample (line 69)

source = ft_checkdata(source, 'datatype', 'volume', 'feedback', 'no');

The source I use is as follows:

>> display(source)

source =

      time: [1x3900 double]

    inside: [255462x1 logical]

       pos: [255462x3 double]

    method: 'average'

       avg: [1x1 struct]

       cfg: [1x1 struct]

       dim: [255462 255462 255462]

Therefore, I am back to where I started. I need to read the fif file from MNE suite.

I uploaded my fif file in Dropbox. Here is the link: https://www.dropbox.com/sh/uq181l76353hd8q/AACjTu8KI_rGaXlaDMyw-Diba?dl=0
[https://cfl.dropboxstatic.com/static/images/icons128/folder_dropbox.png]<https://www.dropbox.com/sh/uq181l76353hd8q/AACjTu8KI_rGaXlaDMyw-Diba?dl=0>

fieldtrip_data<https://www.dropbox.com/sh/uq181l76353hd8q/AACjTu8KI_rGaXlaDMyw-Diba?dl=0>
www.dropbox.com
Shared with Dropbox



Could someone tell me if there is something wrong with the file or with my workaround? Any help would be really appreciated. I am using Fieldtrip version 20170118.

Best,

Alba Xifra Porxas
PhD student, Biosignals and Systems Analysis Lab
McGill University, Montr?al, Canada
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------------------------------

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From michak at is.umk.pl  Tue Feb  7 12:38:33 2017
From: michak at is.umk.pl (=?UTF-8?Q?Micha=C5=82_Komorowski?=)
Date: Tue, 7 Feb 2017 12:38:33 +0100
Subject: [FieldTrip] ft_sourcestatistics / ft_statistics_montecarlo ref
	field meaning
Message-ID: <CAEJSOqi4uOaJNWMiSUf6bZoSk5e1XquCapor5-aM6GjOdWNT1g@mail.gmail.com>

Dear Community,

I am looking for an explanation of output field STAT.REF from
ft_sourcestatistics.
I guess it is a mean value of sample-level statistic for every voxel in
source data, because in function ft_statistics_montecarlo.m there is a line
484:

stat.ref = mean(statrand,2);

where statrand is a matrix of size: number of voxels times number of
resamplings (line 289).

Am I correct? Do you use field STAT.REF ? Why is it called ref?


With kind regards.

-- 
Michał Komorowski, MsC
Nicolaus Copernicus University in Toruń
Faculty of Physics, Astronomy and Informatics
Department of Informatics
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From stephen.whitmarsh at gmail.com  Tue Feb  7 15:15:17 2017
From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh)
Date: Tue, 7 Feb 2017 15:15:17 +0100
Subject: [FieldTrip] way to subset data in cfg structure?
In-Reply-To: <CAOpyOFWEGwwmcaW5-wdKZ5SChA6rFpnrM8QcNLSvtUyzQyE8jg@mail.gmail.com>
References: <CAOpyOFUMONNESb_g_oTXPcRHAmSeFB8QdDdJGfDfoze8vojrhQ@mail.gmail.com>
 <CAFrxm=wBUcj++=p_kJqG_uQFZiciJuwAUmT2WE6SrFJhr=WbAA@mail.gmail.com>
 <CAOpyOFWEGwwmcaW5-wdKZ5SChA6rFpnrM8QcNLSvtUyzQyE8jg@mail.gmail.com>
Message-ID: <CAFrxm=xU5aET9HFGXRFR+C=mkXcAPreS8_yRJNPqSpaYZ=QYrQ@mail.gmail.com>

Hi Tim,

In ft_selectdata, check cfg.latency. And maybe ft_redefinetrials, depending
on where you are in your pipeline, i.e. after or before
timelocking/epoching.

Cheers,
Stephen

On 6 February 2017 at 23:53, Tim Meehan <timeehan at gmail.com> wrote:

> Hi Stephen,
>
> Thanks, I checked out ft_selectdata, but what I really want is a way to
> subselect the time dimension, not the channel dimension. I don't see this
> as an option in ft_selectdata. I can do this subselection manually by going
> into the trials and time fields but it's a little bit clunky and was hoping
> there might be a more elegant way...
>
> Thanks,
> Tim
>
> On Sat, Feb 4, 2017 at 9:35 AM, Stephen Whitmarsh <
> stephen.whitmarsh at gmail.com> wrote:
>
>> Hi Tim,
>>
>> You might want to check out the cfg.channel setting in ft_preprocessing,
>> or use cfg.channel and cfg.trials in ft_selectdata. You can use
>> ft_appenddata to recombine data over trials or channels at a later point.
>>
>> Hope this helps,
>> Stephen
>>
>>
>> On 3 February 2017 at 23:23, Tim Meehan <timeehan at gmail.com> wrote:
>>
>>> Hello everyone,
>>>
>>> I'm trying to preprocess a block of continuous data, but the block is
>>> too long such that I can't hold all the channels in memory together, even
>>> after downsampling. Is there perhaps a setting in ft_preprocessing through
>>> which you can specify a subset of data from a larger block? This would
>>> solve my problem, I think.
>>>
>>> Thanks!
>>> Tim
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From timeehan at gmail.com  Tue Feb  7 16:52:41 2017
From: timeehan at gmail.com (Tim Meehan)
Date: Tue, 7 Feb 2017 10:52:41 -0500
Subject: [FieldTrip] way to subset data in cfg structure?
In-Reply-To: <CAFrxm=xU5aET9HFGXRFR+C=mkXcAPreS8_yRJNPqSpaYZ=QYrQ@mail.gmail.com>
References: <CAOpyOFUMONNESb_g_oTXPcRHAmSeFB8QdDdJGfDfoze8vojrhQ@mail.gmail.com>
 <CAFrxm=wBUcj++=p_kJqG_uQFZiciJuwAUmT2WE6SrFJhr=WbAA@mail.gmail.com>
 <CAOpyOFWEGwwmcaW5-wdKZ5SChA6rFpnrM8QcNLSvtUyzQyE8jg@mail.gmail.com>
 <CAFrxm=xU5aET9HFGXRFR+C=mkXcAPreS8_yRJNPqSpaYZ=QYrQ@mail.gmail.com>
Message-ID: <CAOpyOFVkvU39xC_Wz=mqnx27BKsnaQ5G9-X1_K7fBV==pt9YsA@mail.gmail.com>

Hi Stephen,

Aha, this looks like what I'm looking for. However, I've tried it and I'm
not sure what the effect is. For example, if I run:

nchan = 1;
blockbeg = 4197000;
blockend = 5782000;

for n = 1:nchan

  cfgp = [];
  cfgp.dataset = 'full_recording_session.edf';
  cfgp.channel = n;
  cfgp.latency = [blockbeg blockend];

  datp{n} = ft_preprocessing(cfgp);

end

>> datp{1}

ans =

           hdr: [1x1 struct]
         label: {'SEEG F11'}
          time: {[1x9002826 double]}
         trial: {[1x9002826 double]}
       fsample: 2000
    sampleinfo: [1 9002826]
           cfg: [1x1 struct]

>> datp{1}.cfg.latency

ans =

     4197000     5782000


So, the beginning and end points are being stored in the cfg.latency field,
but it seems they are not being used to subset the data since datp.time and
datp.trial contain the full session.

Is there a way to achieve the actual subsetting? Otherwise I will run out
of memory when looping through all the channels, even if I downsample each
channel at each iteration.

Thanks!
Tim

On Tue, Feb 7, 2017 at 9:15 AM, Stephen Whitmarsh <
stephen.whitmarsh at gmail.com> wrote:

> Hi Tim,
>
> In ft_selectdata, check cfg.latency. And maybe ft_redefinetrials,
> depending on where you are in your pipeline, i.e. after or before
> timelocking/epoching.
>
> Cheers,
> Stephen
>
> On 6 February 2017 at 23:53, Tim Meehan <timeehan at gmail.com> wrote:
>
>> Hi Stephen,
>>
>> Thanks, I checked out ft_selectdata, but what I really want is a way to
>> subselect the time dimension, not the channel dimension. I don't see this
>> as an option in ft_selectdata. I can do this subselection manually by going
>> into the trials and time fields but it's a little bit clunky and was hoping
>> there might be a more elegant way...
>>
>> Thanks,
>> Tim
>>
>> On Sat, Feb 4, 2017 at 9:35 AM, Stephen Whitmarsh <
>> stephen.whitmarsh at gmail.com> wrote:
>>
>>> Hi Tim,
>>>
>>> You might want to check out the cfg.channel setting in ft_preprocessing,
>>> or use cfg.channel and cfg.trials in ft_selectdata. You can use
>>> ft_appenddata to recombine data over trials or channels at a later point.
>>>
>>> Hope this helps,
>>> Stephen
>>>
>>>
>>> On 3 February 2017 at 23:23, Tim Meehan <timeehan at gmail.com> wrote:
>>>
>>>> Hello everyone,
>>>>
>>>> I'm trying to preprocess a block of continuous data, but the block is
>>>> too long such that I can't hold all the channels in memory together, even
>>>> after downsampling. Is there perhaps a setting in ft_preprocessing through
>>>> which you can specify a subset of data from a larger block? This would
>>>> solve my problem, I think.
>>>>
>>>> Thanks!
>>>> Tim
>>>>
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From timeehan at gmail.com  Tue Feb  7 19:34:52 2017
From: timeehan at gmail.com (Tim Meehan)
Date: Tue, 7 Feb 2017 13:34:52 -0500
Subject: [FieldTrip] way to subset data in cfg structure?
In-Reply-To: <CAOpyOFVkvU39xC_Wz=mqnx27BKsnaQ5G9-X1_K7fBV==pt9YsA@mail.gmail.com>
References: <CAOpyOFUMONNESb_g_oTXPcRHAmSeFB8QdDdJGfDfoze8vojrhQ@mail.gmail.com>
 <CAFrxm=wBUcj++=p_kJqG_uQFZiciJuwAUmT2WE6SrFJhr=WbAA@mail.gmail.com>
 <CAOpyOFWEGwwmcaW5-wdKZ5SChA6rFpnrM8QcNLSvtUyzQyE8jg@mail.gmail.com>
 <CAFrxm=xU5aET9HFGXRFR+C=mkXcAPreS8_yRJNPqSpaYZ=QYrQ@mail.gmail.com>
 <CAOpyOFVkvU39xC_Wz=mqnx27BKsnaQ5G9-X1_K7fBV==pt9YsA@mail.gmail.com>
Message-ID: <CAOpyOFXDWBrGSm_eQV52-POtaovWcN9XiHXM-kLQA=Kh5gStAw@mail.gmail.com>

Hi Stephen,

I was able to find the solution, which is to specify the trl field in the
ft_preprocessing cfg. I'll put it here for posterity.

cfg = [];
cfg.dataset = 'full_recording_session.edf';
cfg.trl = [blockbeg blockend 0]; % The 0 indicates there are no triggers
associated with the trial
cfg.continuous = 'yes';

datp = ft_preprocessing(cfg);

Found in this thread:
https://mailman.science.ru.nl/pipermail/fieldtrip/2016-January/009960.html

Cheers,
Tim

On Tue, Feb 7, 2017 at 10:52 AM, Tim Meehan <timeehan at gmail.com> wrote:

> Hi Stephen,
>
> Aha, this looks like what I'm looking for. However, I've tried it and I'm
> not sure what the effect is. For example, if I run:
>
> nchan = 1;
> blockbeg = 4197000;
> blockend = 5782000;
>
> for n = 1:nchan
>
>   cfgp = [];
>   cfgp.dataset = 'full_recording_session.edf';
>   cfgp.channel = n;
>   cfgp.latency = [blockbeg blockend];
>
>   datp{n} = ft_preprocessing(cfgp);
>
> end
>
> >> datp{1}
>
> ans =
>
>            hdr: [1x1 struct]
>          label: {'SEEG F11'}
>           time: {[1x9002826 double]}
>          trial: {[1x9002826 double]}
>        fsample: 2000
>     sampleinfo: [1 9002826]
>            cfg: [1x1 struct]
>
> >> datp{1}.cfg.latency
>
> ans =
>
>      4197000     5782000
>
>
> So, the beginning and end points are being stored in the cfg.latency
> field, but it seems they are not being used to subset the data since
> datp.time and datp.trial contain the full session.
>
> Is there a way to achieve the actual subsetting? Otherwise I will run out
> of memory when looping through all the channels, even if I downsample each
> channel at each iteration.
>
> Thanks!
> Tim
>
> On Tue, Feb 7, 2017 at 9:15 AM, Stephen Whitmarsh <
> stephen.whitmarsh at gmail.com> wrote:
>
>> Hi Tim,
>>
>> In ft_selectdata, check cfg.latency. And maybe ft_redefinetrials,
>> depending on where you are in your pipeline, i.e. after or before
>> timelocking/epoching.
>>
>> Cheers,
>> Stephen
>>
>> On 6 February 2017 at 23:53, Tim Meehan <timeehan at gmail.com> wrote:
>>
>>> Hi Stephen,
>>>
>>> Thanks, I checked out ft_selectdata, but what I really want is a way to
>>> subselect the time dimension, not the channel dimension. I don't see this
>>> as an option in ft_selectdata. I can do this subselection manually by going
>>> into the trials and time fields but it's a little bit clunky and was hoping
>>> there might be a more elegant way...
>>>
>>> Thanks,
>>> Tim
>>>
>>> On Sat, Feb 4, 2017 at 9:35 AM, Stephen Whitmarsh <
>>> stephen.whitmarsh at gmail.com> wrote:
>>>
>>>> Hi Tim,
>>>>
>>>> You might want to check out the cfg.channel setting in
>>>> ft_preprocessing, or use cfg.channel and cfg.trials in ft_selectdata. You
>>>> can use ft_appenddata to recombine data over trials or channels at a later
>>>> point.
>>>>
>>>> Hope this helps,
>>>> Stephen
>>>>
>>>>
>>>> On 3 February 2017 at 23:23, Tim Meehan <timeehan at gmail.com> wrote:
>>>>
>>>>> Hello everyone,
>>>>>
>>>>> I'm trying to preprocess a block of continuous data, but the block is
>>>>> too long such that I can't hold all the channels in memory together, even
>>>>> after downsampling. Is there perhaps a setting in ft_preprocessing through
>>>>> which you can specify a subset of data from a larger block? This would
>>>>> solve my problem, I think.
>>>>>
>>>>> Thanks!
>>>>> Tim
>>>>>
>>>>> _______________________________________________
>>>>> fieldtrip mailing list
>>>>> fieldtrip at donders.ru.nl
>>>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
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From Nicolas.Zink at uniklinikum-dresden.de  Wed Feb  8 10:24:43 2017
From: Nicolas.Zink at uniklinikum-dresden.de (Zink, Nicolas)
Date: Wed, 8 Feb 2017 09:24:43 +0000
Subject: [FieldTrip] Synchronization likelihood
Message-ID: <2DDD0A108FC1004DA65570D8BA0A267B04359809@G06EDBN1.med.tu-dresden.de>

Dear Fieltrip community,

I would also like to implement the synchronization likelihood algorithm in Matlab, in order to analyze data with Fieldtrip. It is based on a paper from Stam and van Dijk (2002) http://dl.acm.org/citation.cfm?id=604702. Has anyone done this since?

I am referring to a previous message by Sara Rombetto from 2013 in this mailing list.

Cheers to the Fieldtrip community and have a good day!
Nico
Nicolas Zink
wissenschaftlicher Mitarbeiter
Universitätsklinikum Carl Gustav Carus
Klinik für Kinder- und Jugendpsychiatrie und -psychotherapie
Schubertstraße 42
01307 Dresden
Tel. +49 (0)351 458-2303

Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://www.uniklinikum-dresden.de<http://www.uniklinikum-dresden.de/>
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

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From juan.garciaprieto at ctb.upm.es  Wed Feb  8 11:00:54 2017
From: juan.garciaprieto at ctb.upm.es (Juan)
Date: Wed, 8 Feb 2017 11:00:54 +0100
Subject: [FieldTrip] Synchronization likelihood
In-Reply-To: <2DDD0A108FC1004DA65570D8BA0A267B04359809@G06EDBN1.med.tu-dresden.de>
References: <2DDD0A108FC1004DA65570D8BA0A267B04359809@G06EDBN1.med.tu-dresden.de>
Message-ID: <CAPO7YL+2LvUWWGMOE9jLTECRDRRt66ekOcKXyLHZpZwvVdyPow@mail.gmail.com>

Hi,

If you are interested in Synchronization Likelihood I would read the work
you mention and also Montez et al, Neuroimage 2006. It would also be very
useful to read Pereda et al, Progress in Neurobiology, 2005 for a general
overview of different indices.

Implementations, there are a few, between them...

The authors have a Java based implementation, here: https://home.kpn.nl/
stam7883/brainwave.html

For a Matlab based implementation, I would start looking here,
http://hermes.ctb.upm.es/, In the toolbox there is a function called:
H_methods_SL.m with an implementation.

I think it is also implemented as part of the Neurophysiological Biomarker
Toolbox, here: http://www.nbtwiki.net/

A C based, although accessible from Matlab, here: http://link.springer.
com/article/10.1007%2Fs12021-014-9251-4

Best,

Juan

On Wed, Feb 8, 2017 at 10:24 AM, Zink, Nicolas <Nicolas.Zink at uniklinikum-
dresden.de> wrote:

> Dear Fieltrip community,
>
>
>
> I would also like to implement the *synchronization likelihood* algorithm
> in Matlab, in order to analyze data with Fieldtrip. It is based on a paper
> from Stam and van Dijk (2002) http://dl.acm.org/citation.cfm?id=604702.
> Has anyone done this since?
>
>
>
> I am referring to a previous message by Sara Rombetto from 2013 in this
> mailing list.
>
>
>
> Cheers to the Fieldtrip community and have a good day!
>
> Nico
>
> Nicolas Zink
> wissenschaftlicher Mitarbeiter
> Universitätsklinikum Carl Gustav Carus
> Klinik für Kinder- und Jugendpsychiatrie und -psychotherapie
> Schubertstraße 42
> 01307 Dresden
> Tel. +49 (0)351 458-2303 <+49%20351%204582303>
>
> Universitätsklinikum Carl Gustav Carus
> an der Technischen Universität Dresden
> Anstalt des öffentlichen Rechts des Freistaates Sachsen
> Fetscherstraße 74, 01307 Dresden
> http://www.uniklinikum-dresden.de
>
> Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
> Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba
> USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From Nicolas.Zink at uniklinikum-dresden.de  Wed Feb  8 12:06:43 2017
From: Nicolas.Zink at uniklinikum-dresden.de (Zink, Nicolas)
Date: Wed, 8 Feb 2017 11:06:43 +0000
Subject: [FieldTrip] Synchronization likelihood
In-Reply-To: <CAPO7YL+2LvUWWGMOE9jLTECRDRRt66ekOcKXyLHZpZwvVdyPow@mail.gmail.com>
References: <2DDD0A108FC1004DA65570D8BA0A267B04359809@G06EDBN1.med.tu-dresden.de>
 <CAPO7YL+2LvUWWGMOE9jLTECRDRRt66ekOcKXyLHZpZwvVdyPow@mail.gmail.com>
Message-ID: <2DDD0A108FC1004DA65570D8BA0A267B04359853@G06EDBN1.med.tu-dresden.de>

Hi Juan,

thank you very much for your quick respons ! I will go for the Matlab based implementation from the Hermes toolbox, because the function H_methods_SL.m is a “Synchronization Likelihood Stand-Alone Calculator”. I will keep you updated on how to successfully implement it in any Fieldtrip pipeline.

Cheers
Nico
Nicolas Zink
wissenschaftlicher Mitarbeiter
Universitätsklinikum Carl Gustav Carus
Klinik für Kinder- und Jugendpsychiatrie und -psychotherapie
Schubertstraße 42
01307 Dresden
Tel. +49 (0)351 458-2303

Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://www.uniklinikum-dresden.de<http://www.uniklinikum-dresden.de/>
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Juan
Sent: Wednesday, February 08, 2017 11:01 AM
To: FieldTrip discussion list
Cc: s.rombetto at cib.na.cnr.it
Subject: Re: [FieldTrip] Synchronization likelihood

Hi,

If you are interested in Synchronization Likelihood I would read the work you mention and also Montez et al, Neuroimage 2006. It would also be very useful to read Pereda et al, Progress in Neurobiology, 2005 for a general overview of different indices.

Implementations, there are a few, between them...

The authors have a Java based implementation, here: https://home.kpn.nl/stam7883/brainwave.html

For a Matlab based implementation, I would start looking here, http://hermes.ctb.upm.es/, In the toolbox there is a function called: H_methods_SL.m with an implementation.

I think it is also implemented as part of the Neurophysiological Biomarker Toolbox, here: http://www.nbtwiki.net/

A C based, although accessible from Matlab, here: http://link.springer.com/article/10.1007%2Fs12021-014-9251-4

Best,

Juan

On Wed, Feb 8, 2017 at 10:24 AM, Zink, Nicolas <Nicolas.Zink at uniklinikum-dresden.de<mailto:Nicolas.Zink at uniklinikum-dresden.de>> wrote:
Dear Fieltrip community,

I would also like to implement the synchronization likelihood algorithm in Matlab, in order to analyze data with Fieldtrip. It is based on a paper from Stam and van Dijk (2002) http://dl.acm.org/citation.cfm?id=604702. Has anyone done this since?

I am referring to a previous message by Sara Rombetto from 2013 in this mailing list.

Cheers to the Fieldtrip community and have a good day!
Nico
Nicolas Zink
wissenschaftlicher Mitarbeiter
Universitätsklinikum Carl Gustav Carus
Klinik für Kinder- und Jugendpsychiatrie und -psychotherapie
Schubertstraße 42
01307 Dresden
Tel. +49 (0)351 458-2303<tel:+49%20351%204582303>

Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://www.uniklinikum-dresden.de<http://www.uniklinikum-dresden.de/>
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113


_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From timeehan at gmail.com  Wed Feb  8 20:47:06 2017
From: timeehan at gmail.com (Tim Meehan)
Date: Wed, 8 Feb 2017 14:47:06 -0500
Subject: [FieldTrip] preprocessing procedures for ECoG/iEEG data
In-Reply-To: <c11f78d4-78a8-0ff5-3bd0-52bab1487bf2@gmail.com>
References: <CAOpyOFXvnSAKNNaS-OmkEoqg0wKhsEUQuXg-LZwNmnT6GbPNUQ@mail.gmail.com>
 <c11f78d4-78a8-0ff5-3bd0-52bab1487bf2@gmail.com>
Message-ID: <CAOpyOFXV3_v=hKZ_7+wfNjpf9_+byX-X6y8eALLA0AF3aU16vw@mail.gmail.com>

Hi Vitoria,

Thanks for your input.

Maybe you (or anyone else) could clarify one thing for me. When demeaning
and/or detrending, is it better to do on a long continuous block or within
individual trials?

Thanks,
Tim

On Thu, Feb 2, 2017 at 4:45 AM, Vitória Piai <v.piai.research at gmail.com>
wrote:

> Hi Tim,
>
> The answers to your questions will depend a lot on what you're planning on
> doing later.
>
> For 1), again it depends. If you're mainly interested in high gamma, it
> doesn't really matter that much since you'll do spectral decomposition
> later on. You could demean the data and not use any filters (or maybe a
> low-pass if you want to get some help with artifact rejection).
>
> For 2) here some more recent references that may help. The bottom line is,
> as David said, all methods have prons and cons. Choose wisely depending on
> what you want to be able to claim about your data!
> Mercier, M. R., Bickel, S., Megevand, P., Groppe, D. M., Schroeder, C. E.,
> Mehta, A. D., & Lado, F. A. (2017). Evaluation of cortical local field
> potential diffusion in stereotactic electro-encephalography recordings: a
> glimpse on white matter signal. NeuroImage, 147, 219–232.
> Arnulfo, G., Hirvonen, J., Nobili, L., Palva, S., & Palva, J. M. (2015).
> Phase and amplitude correlations in resting-state activity in human
> stereotactical EEG recordings. NeuroImage, 112, 114–127.
> Shirhatti, V., Borthakur, A., & Ray, S. (2016). Effect of reference scheme
> on power and phase of the local field potential. Neural Computation, 28,
> 882–913.
> Trongnetrpunya, A., Nandi, B., Kang, D., Kocsis, B., Schroeder, C. E., &
> Ding, M. (2016). Assessing granger causality in electrophysiological data:
> removing the adverse effects of Common Signals via Bipolar Derivations.
> Frontiers in Systems Neuroscience, 9: 189.
>
> Since you're mentioning high gamma, I'm assuming you have stimuli being
> presented and you want to look at changes in high gamma as a function of
> those. In that case, I guess you have a good idea what your time windows
> will be like. So for 3) your suggestion would be a good way to go. What I
> usually do is to segment longer chunks of data than my narrow time windows
> of interest, mark the artifacts but do not reject any trials yet. I then
> save the artifacts and once I finally settle on what my time windows will
> be, I exclude trials with artifacts within that time window.
> - ft_databrowser will allow you to mark and save artifacts,
> ft_rejectartifact will allow you to remove trials containing the artifacts.
>
>
> Good luck,
> Vitoria
>
>
>
>
> On 1/30/2017 11:10 PM, Tim Meehan wrote:
>
> Hello all,
>
> I am a new user of fieldtrip and new to analyzing electrophysiological
> data. I have familiarized myself with some basics of preprocessing of EEG
> data, but I would like to know if there are special considerations for
> dealing with ECoG/iEEG data -- our dataset has recordings from both
> subdural surface electrodes and depth electrodes, sampled at 2kHz. We are
> initially most interested in extracting the high-gamma band (70-150 Hz)
> envelope as a measure of local activity.
>
> First a general question: is there anyone who could point me to or provide
> me with a preprocessing procedure in fieldtrip that is tailored for
> ECoG/iEEG? I've perused the ECoG section in the wiki but there is no
> information on preprocessing there.
>
> If this is too vague, some specific questions I have are:
> 1) What cutoffs do people tend to use for low and high-pass filters?
>
> 2) What is your choice for re-referencing, if any? Our initial
> reference/ground are the left and right mastoids. I have seen papers that
> re-reference to the nearest neighbor. I think I need to use
> ft_apply_montage to do this, but beyond that I could use some guidance.
>
> 3) At what point do you epoch into trials? My guess is after high/low-pass
> filtering and re-referencing but before artifact detection and removal?
>
> Any feedback on these would be very much appreciated. If you need more
> details please let me know.
>
> Thanks!
> Tim
>
>
> _______________________________________________
> fieldtrip mailing listfieldtrip at donders.ru.nlhttps://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From alexander_nakhnikian at hms.harvard.edu  Thu Feb  9 20:18:08 2017
From: alexander_nakhnikian at hms.harvard.edu (Alexander Nakhnikian)
Date: Thu, 9 Feb 2017 14:18:08 -0500
Subject: [FieldTrip] Error in ft_sourcenalysis using Matlab 2016a
Message-ID: <99246059-60b4-fb16-0565-d94bf2aacc2e@hms.harvard.edu>

Dear All,

I have not been able to use ft_sourceanalysis since I updated to Matlab 
2016a and I've had to run by analyses using older versions of FT and 
Matlab 2015b. I'd like to resolve these issues. The flow of computation 
I'm using has always worked up until now. I'm trying to debug this 
myself but since I'm sure I'm not the only person who's had this issue I 
thought someone in the group could help out.

When I attempt to source localize frequency data using eLORETA I get the 
following error:

Error using cellfun
Input #2 expected to be a cell array, was double instead.

Error in ft_datatype_sens (line 221)
       if any(~cellfun(@isempty, regexp(sens.chanunit, '^T')))

Error in ft_checkconfig (line 242)
   cfg.elec = ft_datatype_sens(struct(cfg.elec));

Error in ft_preamble_trackconfig (line 37)
cfg = ft_checkconfig(cfg, 'trackconfig', 'on');

Error in ft_preamble (line 56)
     evalin('caller', ['ft_preamble_' cmd]);

Error in ft_sourceanalysis (line 157)
ft_preamble trackconfig
*
**To get the frequency data I use ft_freqanalysis with parameters:*

cfg.foi = 20;
cfg.method = 'mtmfft'
cfg.tapsmofreq = 3;
cfg.output = 'powandcsd';

This generates a structure with the following fields:


         label: {68x1 cell}
        dimord: 'chan_freq'
          freq: 20
     powspctrm: [68x1 double]
      labelcmb: {2278x2 cell}
     crsspctrm: [2278x1 double]
           cfg: [1x1 struct]

*For source analysis I'm using the built-in FT BEM*

cfg.headmodel = vol; %after loading standard_bem from FT templates
cfg.grid.resolution = 5; %Automatic 5 mm grid
cfg.elec = elec_aligned; %a home-grown file containing data for our 
custom electrode montage
cfg.method = 'eloreta';

Thanks!

Alexander

-- 
Alexander Nakhnikian, Ph.D.
Research Investigator
VA Boston Healthcare System
Instructor in Psychiatry, Harvard Medical School

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From mona at sdsc.edu  Fri Feb 10 03:10:35 2017
From: mona at sdsc.edu (Wong-Barnum, Mona)
Date: Fri, 10 Feb 2017 02:10:35 +0000
Subject: [FieldTrip] config documentation
Message-ID: <4338772B-D01A-4313-8D13-CF10F265A661@mail.ucsd.edu>


Hi:

Can someone kindly point me to the documentation for the config (cfg) object used by many of the functions?  Documentation for all the parameters and what each mean and how to use them?  I’m searching on the website but not finding it yet...

Thank you.

Mona

*********************************************
    Mona Wong
    Web & Mobile Application Developer
    San Diego Supercomputer Center

    "Forgive everyone everything."
-- Regina Brett
*********************************************





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From a.stolk8 at gmail.com  Fri Feb 10 04:03:16 2017
From: a.stolk8 at gmail.com (Arjen Stolk)
Date: Thu, 9 Feb 2017 19:03:16 -0800
Subject: [FieldTrip] config documentation
In-Reply-To: <4338772B-D01A-4313-8D13-CF10F265A661@mail.ucsd.edu>
References: <4338772B-D01A-4313-8D13-CF10F265A661@mail.ucsd.edu>
Message-ID: <CAAiwptRVP8p0Qd84VnUfOhv1F5F3aTRbMT=o=ckg0q9yPMAM2Q@mail.gmail.com>

Hi Mona,

Here you go: http://www.fieldtriptoolbox.org/reference/index
It was 'hidden' in the reference documentation section.

best
Arjen

2017-02-09 18:10 GMT-08:00 Wong-Barnum, Mona <mona at sdsc.edu>:

>
> Hi:
>
> Can someone kindly point me to the documentation for the config (cfg)
> object used by many of the functions?  Documentation for all the parameters
> and what each mean and how to use them?  I’m searching on the website but
> not finding it yet...
>
> Thank you.
>
> Mona
>
> *********************************************
>     Mona Wong
>     Web & Mobile Application Developer
>     San Diego Supercomputer Center
>
>     "Forgive everyone everything."
> -- Regina Brett
> *********************************************
>
>
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From ghumana at upmc.edu  Fri Feb 10 13:36:18 2017
From: ghumana at upmc.edu (Ghuman, Avniel)
Date: Fri, 10 Feb 2017 12:36:18 +0000
Subject: [FieldTrip] Postdoc in using MEG to understand deep brain
 stimulation - Pittsburgh PA, USA
Message-ID: <20385F716E75B746A7F52BBB3C46A130419EC279@MSXMBXNSPRD15.acct.upmchs.net>

Postdoctoral Associate in the Neural and Cognitive Correlates of Deep Brain Stimulation
University of Pittsburgh Neurological Surgery, Pennsylvania, USA

Applications are invited for a fully funded postdoctoral position using magenetoencephalography (MEG) in humans to study the cortical and cognitive effects of deep brain stimulation at the University of Pittsburgh, USA. This position will be jointly mentored by Mark Richardson, MD, PhD, Director of Adult Epilepsy and Movement Disorders Surgery and Avniel Ghuman, PhD, Director of MEG Research at the University of Pittsburgh. Both are faculty in the Neurological Surgery Department and members of the University of Pittsburgh Brain Institute and the Center for the Neural Basis of Cognition.

The research will focus on understanding the dynamic cortical consequences of deep brain stimulation and how these neural changes relate to cognitive effects of stimulation. Of particular interest is how this information is coded in interactive neural circuits at the level of large-scale brain networks. The neural data will primarily be MEG in humans. Advanced signal processing and statistical techniques will be applied to the data to both remove stimulation artifacts and decode the neural activity. Techniques to be applied include time-frequency analysis, ICA, PCA, signal-space separation, clustering, as a few examples.

The ideal applicant would hold a Ph.D. in Neuroscience, Psychology, Computer Science, Mathematics, Statistics, Engineering or a related field. Strong technical, computational, and signal processing skills are required. The ability to design and write scripts in MATLAB and/or Python is required. Superior organizational skills and attention to detail; ability to thrive independently, in addition to working with others; ability to handle fluctuating priorities, deadlines and changes in the clinical schedule is also required. Experience with developing and implementing artifact removal techniques in non-invasive electrophysiological data (EEG or MEG) is greatly desired, but not a requirement if the intellectual fit is otherwise good. Applicants should have a strong track record of publication.

Pittsburgh is consistently ranked the most livable city in America and the neuroscientific community here, particularly at the University of Pittsburgh and Carnegie Mellon University, is both very strong and collaborative.

Interested applicants should send a letter of interest, a CV, and the names and contact information for 3 researchers who can provide a recommendation. For further information or to submit an application, please contact Avniel Ghuman, Ph.D. at ghumana at upmc.edu or Mark Richardson, MD, PhD at richardsonrm at upmc.edu. More information about our research can be found at http://www.lcnd.pitt.edu/index.html and http://www.brainmodulationlab.org.



From mona at sdsc.edu  Fri Feb 10 21:00:30 2017
From: mona at sdsc.edu (Wong-Barnum, Mona)
Date: Fri, 10 Feb 2017 20:00:30 +0000
Subject: [FieldTrip] ft_selectdata
In-Reply-To: <60BAA83166F3DDF0.1216a9bc-f1de-4343-b94b-ca45fcef42f4@mail.outlook.com>
References: <47F41F00-2A78-48DA-8D7C-0CC66C6AF5FE@mail.ucsd.edu>
 <60BAA83166F3DDF0.1216a9bc-f1de-4343-b94b-ca45fcef42f4@mail.outlook.com>
Message-ID: <5F22884A-B56E-4C27-9914-C0095E0BCCE7@mail.ucsd.edu>

Hi Mike:

Thank you for your tip, I tried it but I am still the same eeg data as the filtered frequency data:

[cid:D3CC2A7D-9410-4738-B599-515649221DF4]

Do I still need to do the cfg.frequency setting in the ft_selectdata() call or just the cfg.bpfilter and cfg.bpfreq in the ft_preprocessing() call?

In case it wasn’t clear in my original email, the eeg.mat data has ALREADY been through the ft_preprocessing() in another script.

Mona



On Feb 2, 2017, at 12:17 PM, Hall, Michael (Research Student) <hallmbh at aston.ac.uk<mailto:hallmbh at aston.ac.uk>> wrote:


Hi Mona,

The cfg.frequency parameter in ft_selectdata only works on data with a frequency dimension.

Try using the cfg.bpfilter = 'yes'; cfg.bpfreq = [0.1 2]; in ft_preprocessing.

Best wishes,
Mike


Get Outlook for Android<https://aka.ms/ghei36>



From: Wong-Barnum, Mona
Sent: Thursday, 2 February, 18:22
Subject: [FieldTrip] ft_selectdata
To: FieldTrip discussion list


Hi:

I’m trying to do some frequency band filtering on my data using ft_selectdata but it doesn’t seem to be working…the new “filtered” data is the same as the original data.

Here is my code (note the eeg.mat file has been through the ft_preprocessing function):

addpath /path/to/fieldtrip

ft_defaults

disp ( 'Reading eeg.mat...' )

data = importdata ( 'eeg.mat' );

disp ( 'Getting low delta band...' )

cfg = [];

cfg.frequency = [0.1 2];

eeg_low_delta = ft_selectdata ( cfg, data );

disp ( 'Saving eeg_low_delta.mat...' );

save eeg_low_delta.mat eeg_low_delta -v7.3;

What am I doing wrong?  All help is appreciated.

thanks,

Mona

*********************************************
    Mona Wong
    Web & Mobile Application Developer
    San Diego Supercomputer Center

    "To handle yourself, use your head;
    to handle others, use your heart."

-- Eleanor Roosevelt
*********************************************

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From mona at sdsc.edu  Fri Feb 10 21:23:16 2017
From: mona at sdsc.edu (Wong-Barnum, Mona)
Date: Fri, 10 Feb 2017 20:23:16 +0000
Subject: [FieldTrip] config documentation
In-Reply-To: <CAAiwptRVP8p0Qd84VnUfOhv1F5F3aTRbMT=o=ckg0q9yPMAM2Q@mail.gmail.com>
References: <4338772B-D01A-4313-8D13-CF10F265A661@mail.ucsd.edu>
 <CAAiwptRVP8p0Qd84VnUfOhv1F5F3aTRbMT=o=ckg0q9yPMAM2Q@mail.gmail.com>
Message-ID: <314F81CE-B936-4910-8572-40B036800D8C@mail.ucsd.edu>


Thank you so much!

On Feb 9, 2017, at 7:03 PM, Arjen Stolk <a.stolk8 at gmail.com<mailto:a.stolk8 at gmail.com>> wrote:

Hi Mona,

Here you go: http://www.fieldtriptoolbox.org/reference/index
It was 'hidden' in the reference documentation section.

best
Arjen

*********************************************
    Mona Wong
    Web & Mobile Application Developer
    San Diego Supercomputer Center

    "The two most important days in
     your life are the day you are born
     and the day you find out why."
                                      -- Mark Twain
*********************************************




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From mona at sdsc.edu  Sat Feb 11 04:08:17 2017
From: mona at sdsc.edu (Wong-Barnum, Mona)
Date: Sat, 11 Feb 2017 03:08:17 +0000
Subject: [FieldTrip] problem getting frequency bands
Message-ID: <380251EF-CC46-44D1-8D5B-FBA1DB12A962@mail.ucsd.edu>


Hi:

I am having trouble getting the frequency bands for my EEG data.  All my different EEG frequency plots (for channel 1) come out the same as the original unfiltered EEG :

[cid:E9FC888B-B6C1-4CA4-9966-5F9DB37D24E7]

I’d appreciate all tips on what I am doing wrong.  Here is my partial script for the first 3 plots:

addpath /path/to/fieldtrip
ft_defaults

% 1. EEG
disp ( 'EEG...' )
cfg = [];
cfg.dataset = '1.fif';
data = ft_preprocessing ( cfg );

disp ( 'Getting eeg channels...' )
eeg_channels = ft_channelselection ( 'EEG*', data.label );
cfg = [];
cfg.channel = eeg_channels;
eeg = ft_selectdata ( cfg, data );
disp ( 'Saving eeg...' )
save eeg.mat eeg -v7.3;
clearvars cfg eeg;

% 2. Low delta EEG
disp ( 'Low delta EEG...' )
cfg = [];
cfg.bgfilter = 'yes';
cfg.bpfreq = [0.1 2];
cfg.dataset = '1.fif';
data = ft_preprocessing ( cfg );

cfg = [];
cfg.channel = eeg_channels;
cfg.frequency = [0.1 2];
eeg = ft_selectdata ( cfg, data );
disp ( 'Saving low delta eeg...' )
save low_delta_eeg.mat eeg -v7.3;
clearvars cfg eeg;

% 3. Delta EEG
disp ( 'Delta EEG...' )
cfg = [];
cfg.bgfilter = 'yes';
cfg.bpfreq = [2 4];
cfg.dataset = '1.fif';
data = ft_preprocessing ( cfg );

cfg = [];
cfg.channel = eeg_channels;
cfg.frequency = [2 4];
eeg = ft_selectdata ( cfg, data );
disp ( 'Saving delta eeg...' )
save delta_eeg.mat eeg -v7.3;
clearvars cfg eeg;



Thanks!

Mona


*********************************************
    Mona Wong
    Web & Mobile Application Developer
    San Diego Supercomputer Center

    "I've learned that people will forget
    what you said, people will forget
    what you did, but people will never
    forget how you made them feel."
                                --- Maya Angelou
*********************************************


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From julian.keil at gmail.com  Sat Feb 11 08:10:24 2017
From: julian.keil at gmail.com (Julian Keil)
Date: Sat, 11 Feb 2017 07:10:24 +0000
Subject: [FieldTrip] problem getting frequency bands
In-Reply-To: <380251EF-CC46-44D1-8D5B-FBA1DB12A962@mail.ucsd.edu>
References: <380251EF-CC46-44D1-8D5B-FBA1DB12A962@mail.ucsd.edu>
Message-ID: <CACXO-RPX388dNSPnfmsbG31a2Og5cbrMyEuWxbnDWKCg41OEpw@mail.gmail.com>

Hi Mona,
You have a typo in you cfg call.
Check thr cfg.bpfilter='yes' setting.

Hope that hepls,

Julian


Wong-Barnum, Mona <mona at sdsc.edu> schrieb am Sa. 11. Feb. 2017 um 04:09:

>
> Hi:
>
> I am having trouble getting the frequency bands for my EEG data.  All my
> different EEG frequency plots (for channel 1) come out the same as the
> original unfiltered EEG :
>
>
> I’d appreciate all tips on what I am doing wrong.  Here is my partial
> script for the first 3 plots:
>
> addpath /path/to/fieldtrip
> ft_defaults
>
> % 1. EEG
> disp ( 'EEG...' )
> cfg = [];
> cfg.dataset = '1.fif';
> data = ft_preprocessing ( cfg );
>
> disp ( 'Getting eeg channels...' )
> eeg_channels = ft_channelselection ( 'EEG*', data.label );
> cfg = [];
> cfg.channel = eeg_channels;
> eeg = ft_selectdata ( cfg, data );
> disp ( 'Saving eeg...' )
> save eeg.mat eeg -v7.3;
> clearvars cfg eeg;
>
> % 2. Low delta EEG
> disp ( 'Low delta EEG...' )
> cfg = [];
> cfg.bgfilter = 'yes';
> cfg.bpfreq = [0.1 2];
> cfg.dataset = '1.fif';
> data = ft_preprocessing ( cfg );
>
> cfg = [];
> cfg.channel = eeg_channels;
> cfg.frequency = [0.1 2];
> eeg = ft_selectdata ( cfg, data );
> disp ( 'Saving low delta eeg...' )
> save low_delta_eeg.mat eeg -v7.3;
> clearvars cfg eeg;
>
> % 3. Delta EEG
> disp ( 'Delta EEG...' )
> cfg = [];
> cfg.bgfilter = 'yes';
> cfg.bpfreq = [2 4];
> cfg.dataset = '1.fif';
> data = ft_preprocessing ( cfg );
>
> cfg = [];
> cfg.channel = eeg_channels;
> cfg.frequency = [2 4];
> eeg = ft_selectdata ( cfg, data );
> disp ( 'Saving delta eeg...' )
> save delta_eeg.mat eeg -v7.3;
> clearvars cfg eeg;
>
>
>
> Thanks!
>
> Mona
>
>
> *********************************************
>     Mona Wong
>     Web & Mobile Application Developer
>     San Diego Supercomputer Center
>
>     "I've learned that people will forget
>     what you said, people will forget
>     what you did, but people will never
>     forget how you made them feel."
>                                 --- Maya Angelou
> *********************************************
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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From malgorzata.wislowska at gmail.com  Mon Feb 13 17:42:25 2017
From: malgorzata.wislowska at gmail.com (Malgorzata Wislowska)
Date: Mon, 13 Feb 2017 17:42:25 +0100
Subject: [FieldTrip] incorrect channel identification with ft_databrowser
 after the latest fieldtrip version release
Message-ID: <CAOt24TUUcr5E=ky_WvHP3vHdUMVA_R3UG9N+gF1BXGfNvA=MJQ@mail.gmail.com>

Dear community,


My name is Malgorzata Wislowska and I am working in Lab for Sleep and
Consciousness Research at the University of Salzburg in Austria. Currently
I am analyzing data recorded with high-density EEG (EGI, 128-channel net).

In my pre-processing pipeline I use ft_databrowser to visually and
interactively identify noisy channels (in GUI with 'identify' option).

The cfg I use is as follows:

cfg = [];
cfg.viewmode = 'vertical';
cfg.continuous = 'yes';
cfg.blocksize = 20;
cfg.preproc.lpfilter = 'yes';
cfg.preproc.lpfreq = 35;
cfg.ylim = [0 30];


After updating my fieldtrip to the lastest version, the 'identify' option
began to work incorrectly. When indicating a channel with a cursor, one
another channel is being highlighted (e.g. #86 instead of #24).

Probably it has something to do with one of the two recently introduced
changes:
https://github.com/fieldtrip/fieldtrip/commit/81fe75d296d2623f6330797def8b91ec415a9af4
or
https://github.com/fieldtrip/fieldtrip/commit/1d7170b782f70d2614fe676aae9e6417fd7fb47a

I would appreciate if somebody could have a look at that.


Best regards,
Malgorzata
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From juan.garciaprieto at ctb.upm.es  Mon Feb 13 19:14:10 2017
From: juan.garciaprieto at ctb.upm.es (Juan)
Date: Mon, 13 Feb 2017 19:14:10 +0100
Subject: [FieldTrip] Glasser et al. 2016 related atlas
Message-ID: <CAPO7YLL8VLo=CAUU2nDq5o0rVU3TB4O-KO=6dkUWRp8mAnUR2Q@mail.gmail.com>

Hi,

I would like to use the Glasser et al. Nature 2016 multimodal parcellation
as a fieldtrip compatible atlas. Has anyone had luck with this?

​​Could anyone suggest an actual file among all supplied with the
publication where the association between mri coordinates and parcellation
labelling might be?

So far, I've been able to read several nifti and nifti2 files but I don't
seem to find the correct file.

Many thanks,

Juan
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From roberto.bottini at unitn.it  Mon Feb 13 19:47:09 2017
From: roberto.bottini at unitn.it (Roberto Bottini)
Date: Mon, 13 Feb 2017 19:47:09 +0100
Subject: [FieldTrip] Postdoc position in MEG
Message-ID: <CAGEJZar2bq2mW8tEmF7PsMxKXCpOarP9CrscvArTeERy+McD2w@mail.gmail.com>

*Postdoctoral Position: *Language processing in blind individuals.

Applications for a post-doctoral position are invited in the context of a
joint research project between the International School of Advanced Studies
(SISSA) in Trieste and the Center for Mind/Brain Sciences (CIMeC) in Trento
(Italy). The project is funded by a PRIN grant from the Italian Ministry of
Education and Research (MIUR). The project is dedicated to investigate the
neural circuits involved in semantic processes and their plasticity,
comparing sighted and blind individuals using *combined MEG/fMRI
methodologies*.

The project is coordinated by Prof. Davide Crepaldi [
http://www.davidecrepaldi.net] and Prof. Olivier Collignon [
https://sites.google.com/site/collignonlab/home].

SISSA and the CIMeC are ranked among the top research universities in
Italy, and they both offer a friendly international environment with
state-of-the-art research tools, including MRI, EEG, MEG, TMS, eye
tracking, motion tracking, and access to neuropsychological patients.
English is the official language at both institutions, where a large
portion of the faculty, post-docs and students come from a wide range of
countries. Moreover, both Trieste e the Trentino region are consistently at
the top levels for quality of life, with fantastic nature (the Dolomite,
lake Garda, the Triestinian Karst) and a vibrant cultural environment
(Trento film festival, Christmas markets, la Barcolana, Trieste jazz
festival).

The ideal candidate has experience with electrophysiological neuroimaging
(EEG/MEG) and/or fMRI research. Programming skills, as well as interest in
methodological development (brain connectivity, pattern recognition,
machine learning) will be highly evaluated. Experience in language research
and/or research with special populations is a plus but not a necessity. We
are seeking for candidates with clear potential for publication in high–impact
neuroscience/experimental psychology journals, attention to details, and
good attitude towards teamwork.  Knowledge of Italian language is a bonus
but not required. Since the work will mostly involve testing blind people
with neuroimaging techniques, the post holder will spend most of her/his
time at CIMeC (University of Trento).

The commitment is for up to three years (1+2), with a competitive
European-level salary, depending upon qualifications and experience.

Ideal starting date would be around April-May 2017, but is negotiable, and
applications will be considered until mid March.

Applications including a CV and the names and contact details of two
referees should be sent to: davide.crepaldi at sissa.it, and/or
olivier.collignon at unitn.it. Informal inquiries are most welcome.

-- 
******************************************
Roberto Bottini
Post-Doctoral Fellow
CIMeC - Center for Mind/Brain Sciences
University of Trento
Via delle Regole 101
38123, Mattarello (TN)
Phone: +390461283010
Italy
******************************************
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From jan.schoffelen at donders.ru.nl  Tue Feb 14 09:04:14 2017
From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Tue, 14 Feb 2017 08:04:14 +0000
Subject: [FieldTrip] Glasser et al. 2016 related atlas
In-Reply-To: <CAPO7YLL8VLo=CAUU2nDq5o0rVU3TB4O-KO=6dkUWRp8mAnUR2Q@mail.gmail.com>
References: <CAPO7YLL8VLo=CAUU2nDq5o0rVU3TB4O-KO=6dkUWRp8mAnUR2Q@mail.gmail.com>
Message-ID: <7BE30C20-EBE1-4701-A0B9-B17D6CE5C79A@donders.ru.nl>

Hi Juan,

The network tutorial on the fieldtrip wiki uses this parcellation. There’s a mat-file version on the ftp-server.

Best,
Jan-Mathijs


J.M.Schoffelen, MD PhD
Senior Researcher, VIDI-fellow
Telephone: +31-24-3614793
Physical location: room 00.028
Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands


On 13 Feb 2017, at 19:14, Juan <juan.garciaprieto at ctb.upm.es<mailto:juan.garciaprieto at ctb.upm.es>> wrote:

Hi,

I would like to use the Glasser et al. Nature 2016 multimodal parcellation as a fieldtrip compatible atlas. Has anyone had luck with this?

​​Could anyone suggest an actual file among all supplied with the publication where the association between mri coordinates and parcellation labelling might be?

So far, I've been able to read several nifti and nifti2 files but I don't seem to find the correct file.

Many thanks,

Juan
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip




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From juangpc at gmail.com  Tue Feb 14 11:18:56 2017
From: juangpc at gmail.com (Juan)
Date: Tue, 14 Feb 2017 11:18:56 +0100
Subject: [FieldTrip] Glasser et al. 2016 related atlas
In-Reply-To: <7BE30C20-EBE1-4701-A0B9-B17D6CE5C79A@donders.ru.nl>
References: <CAPO7YLL8VLo=CAUU2nDq5o0rVU3TB4O-KO=6dkUWRp8mAnUR2Q@mail.gmail.com>
 <7BE30C20-EBE1-4701-A0B9-B17D6CE5C79A@donders.ru.nl>
Message-ID: <CAPO7YLK=A-JntrSXeS6AFbhBuURtWsCNGbF0rb2yVveVPPyFYw@mail.gmail.com>

Thanks a lot.

By the way, there is another atlas I've been interested on, the Brainnetome
atlas (Fan et al 2016. Cerebral Cortex). It was mentioned before in this
forum. Maybe it has been already imported, but just in case, this one, I
could successfully import it. It's here
<https://www.dropbox.com/s/xdox87ka36e42xv/atlas_brainnetome.mat?dl=0>.

Juan

On Tue, Feb 14, 2017 at 9:04 AM, Schoffelen, J.M. (Jan Mathijs) <
jan.schoffelen at donders.ru.nl> wrote:

> Hi Juan,
>
> The network tutorial on the fieldtrip wiki uses this parcellation. There’s
> a mat-file version on the ftp-server.
>
> Best,
> Jan-Mathijs
>
>
> J.M.Schoffelen, MD PhD
> Senior Researcher, VIDI-fellow
> Telephone: +31-24-3614793 <+31%2024%20361%204793>
> Physical location: room 00.028
> Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands
>
>
> On 13 Feb 2017, at 19:14, Juan <juan.garciaprieto at ctb.upm.es> wrote:
>
> Hi,
>
> I would like to use the Glasser et al. Nature 2016 multimodal parcellation
> as a fieldtrip compatible atlas. Has anyone had luck with this?
>
> ​​Could anyone suggest an actual file among all supplied with the
> publication where the association between mri coordinates and parcellation
> labelling might be?
>
> So far, I've been able to read several nifti and nifti2 files but I don't
> seem to find the correct file.
>
> Many thanks,
>
> Juan
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From aarjona at us.es  Tue Feb 14 12:37:27 2017
From: aarjona at us.es (Antonio Arjona Valladares)
Date: Tue, 14 Feb 2017 12:37:27 +0100
Subject: [FieldTrip] Cluster-based permutation tests on event related
	potentials
Message-ID: <47672490e00babb1106026384bbbe1a9@us.es>

Hello everyone! 

This is my query:

> We have two groups of EEG data (recorded in a 'Delayed Match to Sample task') pre-processed with Matlab and EEGlab. Each group is a matrix (.mat) which has 3 dimensions (channels x time x subjects). At this point, we are interested in apply the Cluster-based permutation test for nonparametric tests (Maris and Oostenveld, 2007) in order to find out the possible significant differences between these two groups on the different event related potentials.  
> 
> The question is wether we have the possibility to apply this non parametric test, using field trip, EEGLAB or any other software, on this EEGLAB pre-processed matrix data (.mat); or, on the other hand, we have to start from the raw data (recorded with ASA (.cnt)) and go through all the necessary steps indicated on the methodology of the Cluster-based permutation test. 
> 
> Thank you very much. 
> 
> Best,

-- 
Antonio Arjona Valladares

Research Technician (BS)
Human Psychobiology Lab, 
Experimental Psychology Department, University of Seville, 
C/Camilo José Cela s/n, 41018-Sevilla, 
Spain
Tel: +34 954 55 78 00 - 954 55 69 41
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From zk578 at york.ac.uk  Tue Feb 14 13:08:06 2017
From: zk578 at york.ac.uk (=?UTF-8?Q?Zdenko_Koh=C3=BAt?=)
Date: Tue, 14 Feb 2017 12:08:06 +0000
Subject: [FieldTrip] Cluster-based permutation tests on event related
	potentials
In-Reply-To: <47672490e00babb1106026384bbbe1a9@us.es>
References: <47672490e00babb1106026384bbbe1a9@us.es>
Message-ID: <CABDkvO1qubd+LpZ8RJ53_0J+AOS1iXTzzfW9U0G9mPE_vavQDw@mail.gmail.com>

Hi Antonio,

There is a toolbox for Matlab designed specifically for permutation testing
of ERPs, including the cluster corrected version - 'Mass Univariate ERP
Toolbox' and you it works with data in EEGlab format (.set); url:
http://www.openwetware.org/wiki/Mass_Univariate_ERP_Toolbox

Best regards,
Zdenko


On 14 February 2017 at 11:37, Antonio Arjona Valladares <aarjona at us.es>
wrote:

> Hello everyone!
>
> This is my query:
>
> We have two groups of EEG data (recorded in a 'Delayed Match to Sample
> task') pre-processed with Matlab and EEGlab. Each group is a matrix (.mat)
> which has 3 dimensions (channels x time x subjects). At this point, we are
> interested in apply the Cluster-based permutation test for nonparametric
> tests (Maris and Oostenveld, 2007) in order to find out the possible
> significant differences between these two groups on the different event
> related potentials.
>
> The question is wether we have the possibility to apply this non
> parametric test, using field trip, EEGLAB or any other software, on this
> EEGLAB pre-processed matrix data (.mat); or, on the other hand, we have to
> start from the raw data (recorded with ASA (.cnt)) and go through all the
> necessary steps indicated on the methodology of the Cluster-based
> permutation test.
>
> Thank you very much.
>
> Best,
>
> --
> Antonio Arjona Valladares
>
> Research Technician (BS)
> Human Psychobiology Lab,
> Experimental Psychology Department, University of Seville,
> C/Camilo José Cela s/n, 41018-Sevilla,
> Spain
> Tel: +34 954 55 78 00 <+34%20954%2055%2078%2000> - 954 55 69 41
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From CLSG at lundbeck.com  Tue Feb 14 16:07:59 2017
From: CLSG at lundbeck.com (Claus Agerskov)
Date: Tue, 14 Feb 2017 16:07:59 +0100
Subject: [FieldTrip] Error: some of the requested samples occur twice in the
 data and have conflicting values
Message-ID: <6E86AEA655DAF64AA9387E5F72EA6CE1177D003AC0@EMEAEXMBX05.hlu.corp.lundbeck.com>

Hi
I am processing eeg data that consists of many trials that are cut out of a continuous recording, centered around an auditory stimulus.
These trials are two seconds apart and each trial is extracted from -1 to 3.5 seconds with respect to each stimulus.
This means that I have an overlap (of 0.5 seconds) of each trial with the preceding and succeeding trials. Is this supported by fieldtrip?
I am in general able to run my code when the overlap is 0.5 seconds or shorter, but when it exceeds 0.5 seconds, I get the error: "some of the requested samples occur twice in the data and have conflicting values", when running the ft_rejectartifact function.
It seems strange that this runs at certain overlap sizes but not others.

Med venlig hilsen,
Claus Agerskov, tlf: +4561787996

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From eriksenj at ohsu.edu  Wed Feb 15 01:14:38 2017
From: eriksenj at ohsu.edu (K Jeffrey Eriksen)
Date: Wed, 15 Feb 2017 00:14:38 +0000
Subject: [FieldTrip] mex file cannot be found
Message-ID: <FC8F960C75FCA14493D57C730DD538EFC88CD755@EXMB14.ohsu.edu>

Hi,

I just installed FieldTrip r10442 on Win7-64bit, Matlab 2016b. I picked this version because it matches the megconnectome 3.0. I am using EEG, not MEG data, and simply want to use some of the FieldTrip functions.

I installed per the FT recommendations regarding addpath and ft_defaults.

When I try to use ft_read_mri, it tries to call ft_getopt, and fails as follows:

**********************************************************************************
path_data = 'J:\Projects\HCP\HCP_A01';
cd (path_data)
filename = 'T1w_acpc_dc_restore.nii'
[mri]=ft_read_mri(filename);
Invalid MEX-file
'J:\Projects\HCP_MEG\fieldtrip-r10442\fileio\private\ft_getopt.mexw64':
The specified procedure could not be found..

Error in ft_read_mri (line 79)
mriformat = ft_getopt(varargin, 'dataformat');

Error in try_ft_read_mri (line 7)
[mri]=ft_read_mri(filename);
*********************************************************************************

I searched for this error but did not come up with anything specific on general Matlab help. I can see that the ft_getopt.mexw64 file is in the correct folder, so do not understand why Matlab cannot find it.

-Jeff

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From eriksenj at ohsu.edu  Wed Feb 15 01:34:13 2017
From: eriksenj at ohsu.edu (K Jeffrey Eriksen)
Date: Wed, 15 Feb 2017 00:34:13 +0000
Subject: [FieldTrip] FW: mex file cannot be found
Message-ID: <FC8F960C75FCA14493D57C730DD538EFC88CD76F@EXMB14.ohsu.edu>

Hi again,

I followed some general advice from the Matlab site and downloaded "dependency walker" and ran it on (ft_getopt.mexw64). I was informed that I am missing libmx.dll and libmex.dll, per the screenshot below.

[cid:image001.png at 01D286E0.2CDEA230]

I am unable to proceed, please advise.
-Jeff

From: K Jeffrey Eriksen
Sent: Tuesday, February 14, 2017 4:15 PM
To: 'fieldtrip at science.ru.nl'
Subject: mex file cannot be found

Hi,

I just installed FieldTrip r10442 on Win7-64bit, Matlab 2016b. I picked this version because it matches the megconnectome 3.0. I am using EEG, not MEG data, and simply want to use some of the FieldTrip functions.

I installed per the FT recommendations regarding addpath and ft_defaults.

When I try to use ft_read_mri, it tries to call ft_getopt, and fails as follows:

**********************************************************************************
path_data = 'J:\Projects\HCP\HCP_A01';
cd (path_data)
filename = 'T1w_acpc_dc_restore.nii'
[mri]=ft_read_mri(filename);

Invalid MEX-file
'J:\Projects\HCP_MEG\fieldtrip-r10442\fileio\private\ft_getopt.mexw64':
The specified procedure could not be found..

Error in ft_read_mri (line 79)
mriformat = ft_getopt(varargin, 'dataformat');

Error in try_ft_read_mri (line 7)
[mri]=ft_read_mri(filename);
*********************************************************************************

I searched for this error but did not come up with anything specific on general Matlab help. I can see that the ft_getopt.mexw64 file is in the correct folder, so do not understand why Matlab cannot find it.

-Jeff

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From politzerahless at gmail.com  Wed Feb 15 01:43:54 2017
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Wed, 15 Feb 2017 08:43:54 +0800
Subject: [FieldTrip] Cluster-based permutation tests on event related
	potentials
Message-ID: <CAJT2k__bKh=hOYYNvx=ea0mD6W9H0eqiyXdLjGO19xDZCEex0A@mail.gmail.com>

Hi Antonio,

It is possible to run cluster tests on the data you have already
pre-processed, you just need to get the data into a fieldtrip structure. I
usually find the easiest way to do this is to process two original files by
hand in fieldtrip up to the point of creating a grand average structure
using ft_timelockgrandaverage, to see what the appropriate structure looks
like, and then sticking the actual data into that structure (in the
.individual or .avg field) and updating the appropriate fields.

As Zdenko mentioned, there are also other tools available that can do this,
including EEGLAB itself and the mass univariate toolbox.

Steve


---
Stephen Politzer-Ahles
The Hong Kong Polytechnic University
Department of Chinese and Bilingual Studies
http://www.mypolyuweb.hk/~sjpolit/
<http://www.nyu.edu/projects/politzer-ahles/>

On Wed, Feb 15, 2017 at 8:34 AM, <fieldtrip-request at science.ru.nl> wrote:

> Send fieldtrip mailing list submissions to
>         fieldtrip at science.ru.nl
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
>         fieldtrip-request at science.ru.nl
>
> You can reach the person managing the list at
>         fieldtrip-owner at science.ru.nl
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."
>
>
>

> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 14 Feb 2017 12:37:27 +0100
> From: Antonio Arjona Valladares <aarjona at us.es>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] Cluster-based permutation tests on event related
>         potentials
> Message-ID: <47672490e00babb1106026384bbbe1a9 at us.es>
> Content-Type: text/plain; charset="utf-8"
>
> Hello everyone!
>
> This is my query:
>
> > We have two groups of EEG data (recorded in a 'Delayed Match to Sample
> task') pre-processed with Matlab and EEGlab. Each group is a matrix (.mat)
> which has 3 dimensions (channels x time x subjects). At this point, we are
> interested in apply the Cluster-based permutation test for nonparametric
> tests (Maris and Oostenveld, 2007) in order to find out the possible
> significant differences between these two groups on the different event
> related potentials.
> >
> > The question is wether we have the possibility to apply this non
> parametric test, using field trip, EEGLAB or any other software, on this
> EEGLAB pre-processed matrix data (.mat); or, on the other hand, we have to
> start from the raw data (recorded with ASA (.cnt)) and go through all the
> necessary steps indicated on the methodology of the Cluster-based
> permutation test.
> >
> > Thank you very much.
> >
> > Best,
>
> --
> Antonio Arjona Valladares
>
> Research Technician (BS)
> Human Psychobiology Lab,
> Experimental Psychology Department, University of Seville,
> C/Camilo Jos? Cela s/n, 41018-Sevilla,
> Spain
> Tel: +34 954 55 78 00 - 954 55 69 41
> -------------- next part --------------
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>
>
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From nick.ketz at gmail.com  Wed Feb 15 02:40:45 2017
From: nick.ketz at gmail.com (Nick Ketz)
Date: Tue, 14 Feb 2017 17:40:45 -0800
Subject: [FieldTrip] Clustering a conjunctive stat map
Message-ID: <CADsGUk+szM+tNe2Gqxf8ey6EeCbjQx5DzqwM7iVLG38nKa7MzQ@mail.gmail.com>

Hi trippers,

I'm considering implementing some code to cluster a stat matrix that was
calculated using the ft_conjunctiveanalysis function.

Looking through the code and reading up on this form of conjunctive
statistics, my impression is that I could do a similar clustering of this
stat output if I hold on to the original statrand matrixes calculated in
ft_statistics_montecarlo.m for each of the stat structs that are being
input into ft_conjunctiveanalysis.  If I have those statrand mats present,
I can do a similar minimum statistic conjunction across the various stat
objects to create an analogous statrand matrix that can then be used with
the conjunction of the true data as input into clusterstat.m

I'd like to make this workable as a possible submission to the fieldtrip
code base, but didn't want to dig into it unless it was statistically
sound/made any sense to begin with.  So, please chime in if I'm missing
something and the cluster of on this conjunction of statrands is nonsense,
but also please chime in if this does make sense and I can proceed as
described.


Nick
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From mervekaptan5 at gmail.com  Wed Feb 15 05:03:40 2017
From: mervekaptan5 at gmail.com (Merve Kaptan)
Date: Wed, 15 Feb 2017 05:03:40 +0100
Subject: [FieldTrip] FW: mex file cannot be found
In-Reply-To: <FC8F960C75FCA14493D57C730DD538EFC88CD76F@EXMB14.ohsu.edu>
References: <FC8F960C75FCA14493D57C730DD538EFC88CD76F@EXMB14.ohsu.edu>
Message-ID: <CABvEqfHwwwejs-GTL97uFA--tgiVVz8d5D25niZhQ51DWVW8Tw@mail.gmail.com>

Hi,

We also had the same error, with Suma files. And with diffent FieldTrip
version  it worked.

Best
Merve

15 Şub 2017 01:34 tarihinde "K Jeffrey Eriksen" <eriksenj at ohsu.edu> yazdı:

> Hi again,
>
>
>
> I followed some general advice from the Matlab site and downloaded
> “dependency walker” and ran it on (ft_getopt.mexw64). I was informed that I
> am missing libmx.dll and libmex.dll, per the screenshot below.
>
>
>
>
>
> I am unable to proceed, please advise.
>
> -Jeff
>
>
>
> *From:* K Jeffrey Eriksen
> *Sent:* Tuesday, February 14, 2017 4:15 PM
> *To:* 'fieldtrip at science.ru.nl'
> *Subject:* mex file cannot be found
>
>
>
> Hi,
>
>
>
> I just installed FieldTrip r10442 on Win7-64bit, Matlab 2016b. I picked
> this version because it matches the megconnectome 3.0. I am using EEG, not
> MEG data, and simply want to use some of the FieldTrip functions.
>
>
>
> I installed per the FT recommendations regarding addpath and ft_defaults.
>
>
>
> When I try to use ft_read_mri, it tries to call ft_getopt, and fails as
> follows:
>
>
>
> ************************************************************
> **********************
>
> path_data = 'J:\Projects\HCP\HCP_A01';
>
> cd (path_data)
>
> filename = 'T1w_acpc_dc_restore.nii'
>
> [mri]=ft_read_mri(filename);
>
>
>
> Invalid MEX-file
>
> 'J:\Projects\HCP_MEG\fieldtrip-r10442\fileio\private\ft_getopt.mexw64':
>
> The specified procedure could not be found..
>
>
>
> Error in ft_read_mri (line 79)
>
> mriformat = ft_getopt(varargin, 'dataformat');
>
>
>
> Error in try_ft_read_mri (line 7)
>
> [mri]=ft_read_mri(filename);
>
> ************************************************************
> *********************
>
>
>
> I searched for this error but did not come up with anything specific on
> general Matlab help. I can see that the ft_getopt.mexw64 file is in the
> correct folder, so do not understand why Matlab cannot find it.
>
>
>
> -Jeff
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From juangpc at gmail.com  Wed Feb 15 09:35:55 2017
From: juangpc at gmail.com (Juan)
Date: Wed, 15 Feb 2017 09:35:55 +0100
Subject: [FieldTrip] FW: mex file cannot be found
In-Reply-To: <CABvEqfHwwwejs-GTL97uFA--tgiVVz8d5D25niZhQ51DWVW8Tw@mail.gmail.com>
References: <FC8F960C75FCA14493D57C730DD538EFC88CD76F@EXMB14.ohsu.edu>
 <CABvEqfHwwwejs-GTL97uFA--tgiVVz8d5D25niZhQ51DWVW8Tw@mail.gmail.com>
Message-ID: <CAPO7YL+CLBC70aYjkDB--hy9UwHXhmVGzjXYq67BiogktwRxQg@mail.gmail.com>

Hi,

Usually libmx.dll and libmex.dll are in the Matlab installation folder.
This is in C:/Program Files/Matlab/(version)/bin/win32 or win64 (depending
on version). I would try either:

- fast and dirty solution: copy both libraries to the folder where you are
running your Matlab code.

- update the windows' path (not matlab's path) to include this folder.

I hope it works.



Juan

On Wed, Feb 15, 2017 at 5:03 AM, Merve Kaptan <mervekaptan5 at gmail.com>
wrote:

> Hi,
>
> We also had the same error, with Suma files. And with diffent FieldTrip
> version  it worked.
>
> Best
> Merve
>
> 15 Şub 2017 01:34 tarihinde "K Jeffrey Eriksen" <eriksenj at ohsu.edu> yazdı:
>
>> Hi again,
>>
>>
>>
>> I followed some general advice from the Matlab site and downloaded
>> “dependency walker” and ran it on (ft_getopt.mexw64). I was informed that I
>> am missing libmx.dll and libmex.dll, per the screenshot below.
>>
>>
>>
>>
>>
>> I am unable to proceed, please advise.
>>
>> -Jeff
>>
>>
>>
>> *From:* K Jeffrey Eriksen
>> *Sent:* Tuesday, February 14, 2017 4:15 PM
>> *To:* 'fieldtrip at science.ru.nl'
>> *Subject:* mex file cannot be found
>>
>>
>>
>> Hi,
>>
>>
>>
>> I just installed FieldTrip r10442 on Win7-64bit, Matlab 2016b. I picked
>> this version because it matches the megconnectome 3.0. I am using EEG, not
>> MEG data, and simply want to use some of the FieldTrip functions.
>>
>>
>>
>> I installed per the FT recommendations regarding addpath and ft_defaults.
>>
>>
>>
>> When I try to use ft_read_mri, it tries to call ft_getopt, and fails as
>> follows:
>>
>>
>>
>> ************************************************************
>> **********************
>>
>> path_data = 'J:\Projects\HCP\HCP_A01';
>>
>> cd (path_data)
>>
>> filename = 'T1w_acpc_dc_restore.nii'
>>
>> [mri]=ft_read_mri(filename);
>>
>>
>>
>> Invalid MEX-file
>>
>> 'J:\Projects\HCP_MEG\fieldtrip-r10442\fileio\private\ft_getopt.mexw64':
>>
>> The specified procedure could not be found..
>>
>>
>>
>> Error in ft_read_mri (line 79)
>>
>> mriformat = ft_getopt(varargin, 'dataformat');
>>
>>
>>
>> Error in try_ft_read_mri (line 7)
>>
>> [mri]=ft_read_mri(filename);
>>
>> ************************************************************
>> *********************
>>
>>
>>
>> I searched for this error but did not come up with anything specific on
>> general Matlab help. I can see that the ft_getopt.mexw64 file is in the
>> correct folder, so do not understand why Matlab cannot find it.
>>
>>
>>
>> -Jeff
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From k.kessler at aston.ac.uk  Wed Feb 15 12:56:39 2017
From: k.kessler at aston.ac.uk (Kessler, Klaus)
Date: Wed, 15 Feb 2017 11:56:39 +0000
Subject: [FieldTrip] PhD opportunity at Aston University, UK
Message-ID: <CBD4F94BEFCA464A93D9419C8404E1B701A16725B9@exch-mb-g50-01.campus.aston.ac.uk>

Dear Fieldtrippers

We are seeking a suitable PhD candidate to work on age-related changes in Social Cognitive Function across healthy, older adults using multi-modal neuroimaging (fMRi, MEG). It will strictly follow principles of Open Science (fully pre-registered study design, open data, etc.) and will be supervised by Dr Charlotte (1st) and Prof Klaus Kessler (2nd). Eligible candidates will be from the UK or EU and please note that Brexit will not affect the progression of the scholarship.
More information can be found here: https://www.findaphd.com/search/ProjectDetails.aspx?PJID=83697

Thanks
Klaus




Klaus Kessler (Professor of Cognitive Neuroscience)
Aston Brain Centre
School of Life and Health Sciences
Aston University
Aston Triangle
Birmingham, B4 7ET
Phone: +44 (0)121 204 3187

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From jan.freyberg at gmail.com  Wed Feb 15 16:20:08 2017
From: jan.freyberg at gmail.com (Jan Freyberg)
Date: Wed, 15 Feb 2017 15:20:08 +0000
Subject: [FieldTrip] Erros using peer and peercompile
Message-ID: <CAHHLuSCRRTQU9DqzXqbJAk_d1QO+ji1TYMRzEm-RpXoTEXbZpg@mail.gmail.com>

Hi fieldtrippers,

I was trying to get peer working on a 64-bit linux installation.

I downloaded the peer zip file from the modules folder on the FTP server,
added it to my path, and tried running peerinfo.

I was expecting that the pre-compiled mex files would work, but this
yielded an error:

>>peerinfo
Invalid MEX-file
'/home/k1513504/Documents/MATLAB/toolbox/peer-20170213/private/peer.mexa64':
/home/k1513504/Documents/MATLAB/toolbox/peer-20170213/private/peer.mexa64:
undefined symbol: mxSerialize.

Error in peerinfo (line 31)
info = peer('peerinfo');

I then thought I would run peercompile to see if this would generate the
necessary file, but received this error:

Compiling and linking MEX file:
mex -outdir ../private -I. -g -DSYSLOG=3 -g peer.c  announce.o discover.o
expire.o extern.o peerinit.o util.o udsserver.o tcpserver.o tcpsocket.o
security.o localhost.o smartshare.o smartmem.o smartcpu.o connect.o
Building with 'gcc'.
Error using mex
/tmp/mex_6036383241028850_9086/peer.o: In function
`mexFunction':
/home/k1513504/Documents/MATLAB/toolbox/peer-20170213/src/peer.c:1094:
undefined reference to `mxSerialize'
/home/k1513504/Documents/MATLAB/toolbox/peer-20170213/src/peer.c:1099:
undefined reference to `mxSerialize'
/home/k1513504/Documents/MATLAB/toolbox/peer-20170213/src/peer.c:1266:
undefined reference to `mxDeserialize'
/home/k1513504/Documents/MATLAB/toolbox/peer-20170213/src/peer.c:1267:
undefined reference to `mxDeserialize'
collect2: ld returned 1 exit status

Error in peercompile (line 147)
eval(cmd);

I should note that other mex files (before the above) were compiled OK. The
full output of peercompile is here
<https://dl.dropboxusercontent.com/u/42897873/peer-error.txt>.

Is there anything else I need to do to get set up? I couldn't quite figure
out which steps to take for peer to work.

Thanks for any help,
Jan
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From braingirl at gmail.com  Wed Feb 15 17:27:42 2017
From: braingirl at gmail.com (Teresa Madsen)
Date: Wed, 15 Feb 2017 11:27:42 -0500
Subject: [FieldTrip] preprocessing procedures for ECoG/iEEG data
In-Reply-To: <CAOpyOFXV3_v=hKZ_7+wfNjpf9_+byX-X6y8eALLA0AF3aU16vw@mail.gmail.com>
References: <CAOpyOFXvnSAKNNaS-OmkEoqg0wKhsEUQuXg-LZwNmnT6GbPNUQ@mail.gmail.com>
 <c11f78d4-78a8-0ff5-3bd0-52bab1487bf2@gmail.com>
 <CAOpyOFXV3_v=hKZ_7+wfNjpf9_+byX-X6y8eALLA0AF3aU16vw@mail.gmail.com>
Message-ID: <CAM2YbcYjestG=YAm3_154AnVLCTR0r-mjisQRLnri7iCWjtQmg@mail.gmail.com>

I would say it depends on your data:  is your DC offset fairly consistent
(in which case demeaning once would probably be fine), or do your signals
have slow drift over time (in which case detrending trials might be
better)?  You might also want to consider removing large artifacts first,
as extreme values can skew your mean or trends.  Have a look at your raw
data using ft_databrowser to decide.

~Teresa


On Wed, Feb 8, 2017 at 2:47 PM, Tim Meehan <timeehan at gmail.com> wrote:

> Hi Vitoria,
>
> Thanks for your input.
>
> Maybe you (or anyone else) could clarify one thing for me. When demeaning
> and/or detrending, is it better to do on a long continuous block or within
> individual trials?
>
> Thanks,
> Tim
>
> On Thu, Feb 2, 2017 at 4:45 AM, Vitória Piai <v.piai.research at gmail.com>
> wrote:
>
>> Hi Tim,
>>
>> The answers to your questions will depend a lot on what you're planning
>> on doing later.
>>
>> For 1), again it depends. If you're mainly interested in high gamma, it
>> doesn't really matter that much since you'll do spectral decomposition
>> later on. You could demean the data and not use any filters (or maybe a
>> low-pass if you want to get some help with artifact rejection).
>>
>> For 2) here some more recent references that may help. The bottom line
>> is, as David said, all methods have prons and cons. Choose wisely depending
>> on what you want to be able to claim about your data!
>> Mercier, M. R., Bickel, S., Megevand, P., Groppe, D. M., Schroeder, C.
>> E., Mehta, A. D., & Lado, F. A. (2017). Evaluation of cortical local field
>> potential diffusion in stereotactic electro-encephalography recordings: a
>> glimpse on white matter signal. NeuroImage, 147, 219–232.
>> Arnulfo, G., Hirvonen, J., Nobili, L., Palva, S., & Palva, J. M. (2015).
>> Phase and amplitude correlations in resting-state activity in human
>> stereotactical EEG recordings. NeuroImage, 112, 114–127.
>> Shirhatti, V., Borthakur, A., & Ray, S. (2016). Effect of reference
>> scheme on power and phase of the local field potential. Neural Computation,
>> 28, 882–913.
>> Trongnetrpunya, A., Nandi, B., Kang, D., Kocsis, B., Schroeder, C. E., &
>> Ding, M. (2016). Assessing granger causality in electrophysiological data:
>> removing the adverse effects of Common Signals via Bipolar Derivations.
>> Frontiers in Systems Neuroscience, 9: 189.
>>
>> Since you're mentioning high gamma, I'm assuming you have stimuli being
>> presented and you want to look at changes in high gamma as a function of
>> those. In that case, I guess you have a good idea what your time windows
>> will be like. So for 3) your suggestion would be a good way to go. What I
>> usually do is to segment longer chunks of data than my narrow time windows
>> of interest, mark the artifacts but do not reject any trials yet. I then
>> save the artifacts and once I finally settle on what my time windows will
>> be, I exclude trials with artifacts within that time window.
>> - ft_databrowser will allow you to mark and save artifacts,
>> ft_rejectartifact will allow you to remove trials containing the artifacts.
>>
>>
>> Good luck,
>> Vitoria
>>
>>
>>
>>
>> On 1/30/2017 11:10 PM, Tim Meehan wrote:
>>
>> Hello all,
>>
>> I am a new user of fieldtrip and new to analyzing electrophysiological
>> data. I have familiarized myself with some basics of preprocessing of EEG
>> data, but I would like to know if there are special considerations for
>> dealing with ECoG/iEEG data -- our dataset has recordings from both
>> subdural surface electrodes and depth electrodes, sampled at 2kHz. We are
>> initially most interested in extracting the high-gamma band (70-150 Hz)
>> envelope as a measure of local activity.
>>
>> First a general question: is there anyone who could point me to or
>> provide me with a preprocessing procedure in fieldtrip that is tailored for
>> ECoG/iEEG? I've perused the ECoG section in the wiki but there is no
>> information on preprocessing there.
>>
>> If this is too vague, some specific questions I have are:
>> 1) What cutoffs do people tend to use for low and high-pass filters?
>>
>> 2) What is your choice for re-referencing, if any? Our initial
>> reference/ground are the left and right mastoids. I have seen papers that
>> re-reference to the nearest neighbor. I think I need to use
>> ft_apply_montage to do this, but beyond that I could use some guidance.
>>
>> 3) At what point do you epoch into trials? My guess is after
>> high/low-pass filtering and re-referencing but before artifact detection
>> and removal?
>>
>> Any feedback on these would be very much appreciated. If you need more
>> details please let me know.
>>
>> Thanks!
>> Tim
>>
>>
>> _______________________________________________
>> fieldtrip mailing listfieldtrip at donders.ru.nlhttps://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
Teresa E. Madsen, PhD
Research Technical Specialist:  *in vivo *electrophysiology & data analysis
Division of Behavioral Neuroscience and Psychiatric Disorders
Yerkes National Primate Research Center
Emory University
Rainnie Lab, NSB 5233
954 Gatewood Rd. NE
Atlanta, GA 30329
(770) 296-9119
braingirl at gmail.com
https://www.linkedin.com/in/temadsen
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From justyna_marie at yahoo.com  Wed Feb 15 22:13:52 2017
From: justyna_marie at yahoo.com (justyna marie)
Date: Wed, 15 Feb 2017 21:13:52 +0000 (UTC)
Subject: [FieldTrip] Question about ft_definetrials
References: <44161332.74112.1487193232330.ref@mail.yahoo.com>
Message-ID: <44161332.74112.1487193232330@mail.yahoo.com>

Dear community members,
I am new to Fieldtrip therefore would very much appreciate your advice on the following:I have been trying to convert my pre-processed and segmented EEG data from eeglab .set format to Fieldtrip to perform some analyses. My data contains epochs marked by 5 types of trigger values ('3','4','5','6','7'). 
I used:
mydata = eeglab2fieldtrip (EEG, 'preprocessing');

to convert between data formats and then build condition corresponding to my markers  with cfg.trialdef structure but unfortunately I keep getting the following message:
Error using ft_definetrial (line 188)no trials were defined, see FT_DEFINETRIAL for help
I then tried to define the trial structure with the following script:
eventValues = {'3','4','5','6','7'};prepost = [0.2 1.7];ftype = 'eeglab_set';data = struct;for evVal = 1:length(eventValues)    infile = fullfile(strcat('D:\Exp_8\EEG_analyses\filename', [eventValues{evVal}],'.set'));    cfg = [];    cfg.dataset = infile;    cfg.headerfile = infile;    cfg.dataformat = ftype;    cfg.headerformat = ftype;       cfg.continuous = 'no';    cfg.trialdef.prestim = prepost(1);    cfg.trialdef.poststim = prepost(2);    cfg.trialfun = 'ft_trialfun_general';    cfg.trialdef.eventtype = 'Trigger';    cfg.trialdef.eventvalue = eventValues{evVal};    cfg = ft_definetrial(cfg);    data.(eventValues{evVal}) = ft_preprocessing(cfg);end

but I am getting exactly the same error...
Any suggestions of likely mistakes of my part/ problem with script would be most helpful.
Many thanks,
Justyna 
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From anne.hauswald at me.com  Thu Feb 16 09:05:28 2017
From: anne.hauswald at me.com (anne Hauswald)
Date: Thu, 16 Feb 2017 09:05:28 +0100
Subject: [FieldTrip] Question about ft_definetrials
In-Reply-To: <44161332.74112.1487193232330@mail.yahoo.com>
References: <44161332.74112.1487193232330.ref@mail.yahoo.com>
 <44161332.74112.1487193232330@mail.yahoo.com>
Message-ID: <B60F24D2-BEE8-4553-B019-7A56527FE86F@me.com>

Hi Justyna, 

I just scanned your code, but just to be sure: did you check your event type with fieldtrip?

For my EEG data e.g. the event type is ‚Stimulus‘.
You can check it with the following code
cfg = [];
cfg.dataset            = 'yourfile.ext';
cfg.trialdef.eventtype = '?';
ft_definetrial(cfg);
(http://www.fieldtriptoolbox.org/faq/how_can_i_find_out_what_eventvalues_and_eventtypes_there_are_in_my_data)

Best Anne




> Am 15.02.2017 um 22:13 schrieb justyna marie <justyna_marie at yahoo.com>:
> 
> Dear community members,
> 
> I am new to Fieldtrip therefore would very much appreciate your advice on the following:
> I have been trying to convert my pre-processed and segmented EEG data from eeglab .set format to Fieldtrip to perform some analyses. My data contains epochs marked by 5 types of trigger values ('3','4','5','6','7'). 
> 
> I used:
> 
> mydata = eeglab2fieldtrip (EEG, 'preprocessing');
> 
> to convert between data formats and then build condition corresponding to my markers  with cfg.trialdef structure but unfortunately I keep getting the following message:
> 
> Error using ft_definetrial (line 188)
> no trials were defined, see FT_DEFINETRIAL for help
> 
> I then tried to define the trial structure with the following script:
> 
> eventValues = {'3','4','5','6','7'};
> prepost = [0.2 1.7];
> ftype = 'eeglab_set';
> data = struct;
> for evVal = 1:length(eventValues)
>     infile = fullfile(strcat('D:\Exp_8\EEG_analyses\filename', [eventValues{evVal}],'.set'));
>     cfg = [];
>     cfg.dataset = infile;
>     cfg.headerfile = infile;
>     cfg.dataformat = ftype;
>     cfg.headerformat = ftype;
>    
>     cfg.continuous = 'no';
>     cfg.trialdef.prestim = prepost(1);
>     cfg.trialdef.poststim = prepost(2);
>     cfg.trialfun = 'ft_trialfun_general';
>     cfg.trialdef.eventtype = 'Trigger';
>     cfg.trialdef.eventvalue = eventValues{evVal};
>     cfg = ft_definetrial(cfg);
>     data.(eventValues{evVal}) = ft_preprocessing(cfg);
> end
> 
> 
> but I am getting exactly the same error...
> 
> Any suggestions of likely mistakes of my part/ problem with script would be most helpful.
> 
> Many thanks,
> 
> Justyna
>  
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From johan.wessberg at gu.se  Thu Feb 16 13:25:37 2017
From: johan.wessberg at gu.se (Johan Wessberg)
Date: Thu, 16 Feb 2017 12:25:37 +0000
Subject: [FieldTrip] Problem with ft_volumewrite and axis labels
Message-ID: <EA784669-DC3E-46E1-ADBD-42E489D640C8@gu.se>

Hi!

I have checked the archives without finding an answer or seeing a discussion of this problem.

We are trying to use ft_volumewrite() to export functional and anatomical data for visualization outside FieldTrip, for example with Freeview. The problem is that the orientation of the axes is wrong, AP and RL have been swapped. But when checking the axes with ft_determine_coordsys() they are fine.

Using either MGZ or NIFTI file formats does not matter. I get the same problem when opening the files in either Freeview or MRIcron.
ft_volumewrite() has a cfg.coordsys option that includes a ‘ctf’, but it does not help (and the documentation says that this will only matter for Analyze, vmp, and vmr file formats anyway).


Here is a screen copy from FreeView:

[cid:image001.png at 01D28858.28D2D110]


And here is the figure from ft_determine_coordys()  (the yellow labels are hard to read, but they are correct)

[cid:image002.png at 01D28858.28D2D110]


The functional data have been acquired with the CTF MEG in Nottingham, and the MRI data have been co-registered in CTF coordinates for functional analysis. All source analyses and plots are fine inside FT, my problem is only to export the data correctly using ft_volumewrite().

Has anyone had the same problem?


Johan Wessberg

Inst. of Neuroscience and Physiology
University of Gothenburg, Sweden



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From justyna_marie at yahoo.com  Thu Feb 16 13:51:59 2017
From: justyna_marie at yahoo.com (justyna marie)
Date: Thu, 16 Feb 2017 12:51:59 +0000 (UTC)
Subject: [FieldTrip] Question about ft_definetrials
In-Reply-To: <B60F24D2-BEE8-4553-B019-7A56527FE86F@me.com>
References: <44161332.74112.1487193232330.ref@mail.yahoo.com>
 <44161332.74112.1487193232330@mail.yahoo.com>
 <B60F24D2-BEE8-4553-B019-7A56527FE86F@me.com>
Message-ID: <1242059752.725857.1487249519167@mail.yahoo.com>

Hi Anne,
Many thanks for your advice. I have finally got this fixed!
I tried to  check the event type but at first I couldn't use the line (cfg.trialdef.eventtype='?') -- it turned out there was no events list imported which I managed to overlook. To fix it I first used:event = ft_read_event(''filename.set') and then check the event type in fieldtrip with the line you sent. Once I'd done this I could then use the event type in my old code. Thanks again as I wouldn't think about it if not for your suggestion.
Best,Justyna  


      From: anne Hauswald <anne.hauswald at me.com>
 To: justyna marie <justyna_marie at yahoo.com>; FieldTrip discussion list <fieldtrip at science.ru.nl> 
 Sent: Thursday, 16 February 2017, 8:05
 Subject: Re: [FieldTrip] Question about ft_definetrials
   
Hi Justyna, 
I just scanned your code, but just to be sure: did you check your event type with fieldtrip?
For my EEG data e.g. the event type is ‚Stimulus‘.You can check it with the following codecfg = [];
cfg.dataset            = 'yourfile.ext';
cfg.trialdef.eventtype = '?';
ft_definetrial(cfg);(http://www.fieldtriptoolbox.org/faq/how_can_i_find_out_what_eventvalues_and_eventtypes_there_are_in_my_data)
Best Anne




Am 15.02.2017 um 22:13 schrieb justyna marie <justyna_marie at yahoo.com>:
Dear community members,
I am new to Fieldtrip therefore would very much appreciate your advice on the following:I have been trying to convert my pre-processed and segmented EEG data from eeglab .set format to Fieldtrip to perform some analyses. My data contains epochs marked by 5 types of trigger values ('3','4','5','6','7'). 
I used:
mydata = eeglab2fieldtrip (EEG, 'preprocessing');

to convert between data formats and then build condition corresponding to my markers  with cfg.trialdef structure but unfortunately I keep getting the following message:
Error using ft_definetrial (line 188)no trials were defined, see FT_DEFINETRIAL for help
I then tried to define the trial structure with the following script:
eventValues = {'3','4','5','6','7'};prepost = [0.2 1.7];ftype = 'eeglab_set';data = struct;for evVal = 1:length(eventValues)    infile = fullfile(strcat('D:\Exp_8\EEG_ analyses\filename', [eventValues{evVal}],'.set'));    cfg = [];    cfg.dataset = infile;    cfg.headerfile = infile;    cfg.dataformat = ftype;    cfg.headerformat = ftype;       cfg.continuous = 'no';    cfg.trialdef.prestim = prepost(1);    cfg.trialdef.poststim = prepost(2);    cfg.trialfun = 'ft_trialfun_general';    cfg.trialdef.eventtype = 'Trigger';    cfg.trialdef.eventvalue = eventValues{evVal};    cfg = ft_definetrial(cfg);    data.(eventValues{evVal}) = ft_preprocessing(cfg);end

but I am getting exactly the same error...
Any suggestions of likely mistakes of my part/ problem with script would be most helpful.
Many thanks,
Justyna 
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip



   
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From jan.schoffelen at donders.ru.nl  Thu Feb 16 15:09:34 2017
From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Thu, 16 Feb 2017 14:09:34 +0000
Subject: [FieldTrip] Problem with ft_volumewrite and axis labels
In-Reply-To: <EA784669-DC3E-46E1-ADBD-42E489D640C8@gu.se>
References: <EA784669-DC3E-46E1-ADBD-42E489D640C8@gu.se>
Message-ID: <30FDC868-D270-41E0-8EBF-8E965A566529@donders.ru.nl>

Hi Johan,

ft_volumewrite does not write any information with respect to how the axes in the coordinate system need to be interpreted to the output file. In other words, it only writes the anatomical image, along with some transformation matrix that typically maps voxels to head coordinates. If the external software ‘expects’ some specific coordinate system, or if it defaults to interpreting the coordinate system along to some convention, if it cannot find the required information in the file, the mapping may or may not be correct.

In your case it seems that freeview interprets the x/y/z axes in the coordinate system (attached with the MRI-file) as RAS, whereas you expected it to be correctly interpreted as ALS (CTF-convention). You could write the volume with a RAS transformation matrix.

Best,

Jan-Mathijs


J.M.Schoffelen, MD PhD
Senior Researcher, VIDI-fellow
Telephone: +31-24-3614793
Physical location: room 00.028
Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands



On 16 Feb 2017, at 13:25, Johan Wessberg <johan.wessberg at gu.se<mailto:johan.wessberg at gu.se>> wrote:

Hi!

I have checked the archives without finding an answer or seeing a discussion of this problem.

We are trying to use ft_volumewrite() to export functional and anatomical data for visualization outside FieldTrip, for example with Freeview. The problem is that the orientation of the axes is wrong, AP and RL have been swapped. But when checking the axes with ft_determine_coordsys() they are fine.

Using either MGZ or NIFTI file formats does not matter. I get the same problem when opening the files in either Freeview or MRIcron.
ft_volumewrite() has a cfg.coordsys option that includes a ‘ctf’, but it does not help (and the documentation says that this will only matter for Analyze, vmp, and vmr file formats anyway).


Here is a screen copy from FreeView:

<image001.png>


And here is the figure from ft_determine_coordys()  (the yellow labels are hard to read, but they are correct)

<image002.png>


The functional data have been acquired with the CTF MEG in Nottingham, and the MRI data have been co-registered in CTF coordinates for functional analysis. All source analyses and plots are fine inside FT, my problem is only to export the data correctly using ft_volumewrite().

Has anyone had the same problem?


Johan Wessberg

Inst. of Neuroscience and Physiology
University of Gothenburg, Sweden



_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip




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From johan.wessberg at gu.se  Thu Feb 16 16:27:47 2017
From: johan.wessberg at gu.se (Johan Wessberg)
Date: Thu, 16 Feb 2017 15:27:47 +0000
Subject: [FieldTrip] Problem with ft_volumewrite and axis labels
In-Reply-To: <30FDC868-D270-41E0-8EBF-8E965A566529@donders.ru.nl>
References: <EA784669-DC3E-46E1-ADBD-42E489D640C8@gu.se>
 <30FDC868-D270-41E0-8EBF-8E965A566529@donders.ru.nl>
Message-ID: <97DB0591-1FCA-45FC-B37C-56A79A1B09D0@gu.se>

Thanks! I erroneously assumed that the axes coordinate system was exported along with the volume data.

Regards,
Johan Wessberg





From: <fieldtrip-bounces at science.ru.nl> on behalf of "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen at donders.ru.nl>
Reply-To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Date: Thursday, 16 February 2017 at 15:09
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] Problem with ft_volumewrite and axis labels

Hi Johan,

ft_volumewrite does not write any information with respect to how the axes in the coordinate system need to be interpreted to the output file. In other words, it only writes the anatomical image, along with some transformation matrix that typically maps voxels to head coordinates. If the external software ‘expects’ some specific coordinate system, or if it defaults to interpreting the coordinate system along to some convention, if it cannot find the required information in the file, the mapping may or may not be correct.

In your case it seems that freeview interprets the x/y/z axes in the coordinate system (attached with the MRI-file) as RAS, whereas you expected it to be correctly interpreted as ALS (CTF-convention). You could write the volume with a RAS transformation matrix.

Best,

Jan-Mathijs


J.M.Schoffelen, MD PhD
Senior Researcher, VIDI-fellow
Telephone: +31-24-3614793
Physical location: room 00.028
Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands


On 16 Feb 2017, at 13:25, Johan Wessberg <johan.wessberg at gu.se<mailto:johan.wessberg at gu.se>> wrote:

Hi!

I have checked the archives without finding an answer or seeing a discussion of this problem.

We are trying to use ft_volumewrite() to export functional and anatomical data for visualization outside FieldTrip, for example with Freeview. The problem is that the orientation of the axes is wrong, AP and RL have been swapped. But when checking the axes with ft_determine_coordsys() they are fine.

Using either MGZ or NIFTI file formats does not matter. I get the same problem when opening the files in either Freeview or MRIcron.
ft_volumewrite() has a cfg.coordsys option that includes a ‘ctf’, but it does not help (and the documentation says that this will only matter for Analyze, vmp, and vmr file formats anyway).


Here is a screen copy from FreeView:

<image001.png>


And here is the figure from ft_determine_coordys()  (the yellow labels are hard to read, but they are correct)

<image002.png>


The functional data have been acquired with the CTF MEG in Nottingham, and the MRI data have been co-registered in CTF coordinates for functional analysis. All source analyses and plots are fine inside FT, my problem is only to export the data correctly using ft_volumewrite().

Has anyone had the same problem?


Johan Wessberg

Inst. of Neuroscience and Physiology
University of Gothenburg, Sweden



_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip



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From michele.scaltritti at gmail.com  Fri Feb 17 10:33:52 2017
From: michele.scaltritti at gmail.com (Michele Scaltritti)
Date: Fri, 17 Feb 2017 10:33:52 +0100
Subject: [FieldTrip] time windows and number of channels in cluster based
	permutation tests
Message-ID: <CABGEo=TM-TGqh3bQubOD_29z-cxQ93grvXQHNMo70zqLcpjjEg@mail.gmail.com>

Dear FieldTrip users,

I have a rather general question regarding cluster-based permutation test.

In the tutorial for Cluster-based permutation tests on event related
fields, I read that sensitivity of the analysis depends on the length of
the time interval that is analyzed. Elsewhere, I found a similar reasoning
regarding channels, in the sense that it the exclusion of the sensors where
no effect is likely to be present should yield a more sensitive analysis.

In my experiment, I analyzed a limited set of central electrodes (where
previous evidence suggests that the difference should be located) and found
a significant positive cluster, and a (smaller) significant negative one.
When doing the same analysis considering all the electrodes, no significant
negative cluster is found, just a positive one. Among other things, this
may reflect a different sensitivity as a function of the number of channels
considered in the analysis. I explored a bit the different parameters (such
as neighbors channels definition), but I did not identify the source of the
difference between the analyses.

Leaving aside my specific case, in more general terms I cannot understand
how sensitivity is increased by focusing on a smaller time-windows, or on a
specific set of electrodes. After all, the number of comparisons we make
should not affect the number of samples surpassing the threshold, nor the
clustering as a function of the spatial and temporal adjacency of these
supra-theshold samples. I understand that the same cluster may vary when
other samples are considered in the analyses (for example, samples from
other electrodes may get included), but again, I am failing to see how this
may be related to the sensitivity of the analysis. The cluster-level
statistics, for example, should not be weakened by this.

I apologize if this message underlies any gross misunderstanding.

Michele Scaltritti
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From elizabeth.1.shephard at kcl.ac.uk  Fri Feb 17 12:05:54 2017
From: elizabeth.1.shephard at kcl.ac.uk (Shephard, Elizabeth)
Date: Fri, 17 Feb 2017 11:05:54 +0000
Subject: [FieldTrip] Negative values with debiased weighted phase lag index
Message-ID: <HE1PR03MB1641555DB4A0BFBB22D8051FC25D0@HE1PR03MB1641.eurprd03.prod.outlook.com>

Dear all


I am using FieldTrip to explore connectivity in resting-state EEG data and aimed to use the debiased weighted phase lag index (dwPLI) to index this. However, I am finding a lot of negative values in my connectivity matrices when I compute the dwPLI, and I am unsure why this might be - has anyone found this previously, or have an idea of why this might be happening? I do not get this if I compute other connectivity measures (e.g. coherence) and I have a decent amount of clean trials (around 80 per subject) on which to run the connectivity. I am computing the dwPLI from fourier coefficients exported from a straightforward FFT.


Many thanks in advance for any advice

Best wishes

Lizzie

---------------------------------------------------------------------------
Lizzie Shephard, PhD
Postdoctoral researcher
2.21 MRC SGDP Centre
Institute of Psychiatry, Psychology, & Neuroscience
King’s College London
De Crespigny Park
London, SE5 8AF
0207 848 5272
elizabeth.1.shephard at kcl.ac.uk

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From julian.keil at gmail.com  Fri Feb 17 12:10:17 2017
From: julian.keil at gmail.com (Julian Keil)
Date: Fri, 17 Feb 2017 12:10:17 +0100
Subject: [FieldTrip] Negative values with debiased weighted phase lag
	index
In-Reply-To: <HE1PR03MB1641555DB4A0BFBB22D8051FC25D0@HE1PR03MB1641.eurprd03.prod.outlook.com>
References: <HE1PR03MB1641555DB4A0BFBB22D8051FC25D0@HE1PR03MB1641.eurprd03.prod.outlook.com>
Message-ID: <69EC263C-5A16-4CC3-8498-3C2AB7E75781@gmail.com>

Dear Lizzie,

this comes up from time to time on the Mailinglist.
Check for example this response by Martin Vinck:
https://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003892.html

Quote: The debiased WPLI estimator gets negative however as a consequence of the debiasing method - different issue.

Cheers,

Julian

Am 17.02.2017 um 12:05 schrieb Shephard, Elizabeth:

> Dear all
> 
> I am using FieldTrip to explore connectivity in resting-state EEG data and aimed to use the debiased weighted phase lag index (dwPLI) to index this. However, I am finding a lot of negative values in my connectivity matrices when I compute the dwPLI, and I am unsure why this might be - has anyone found this previously, or have an idea of why this might be happening? I do not get this if I compute other connectivity measures (e.g. coherence) and I have a decent amount of clean trials (around 80 per subject) on which to run the connectivity. I am computing the dwPLI from fourier coefficients exported from a straightforward FFT.
> 
> Many thanks in advance for any advice
> Best wishes
> Lizzie
> 
> ---------------------------------------------------------------------------
> Lizzie Shephard, PhD
> Postdoctoral researcher
> 2.21 MRC SGDP Centre
> Institute of Psychiatry, Psychology, & Neuroscience
> King’s College London
> De Crespigny Park
> London, SE5 8AF
> 0207 848 5272
> elizabeth.1.shephard at kcl.ac.uk
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From elizabeth.1.shephard at kcl.ac.uk  Fri Feb 17 12:41:09 2017
From: elizabeth.1.shephard at kcl.ac.uk (Shephard, Elizabeth)
Date: Fri, 17 Feb 2017 11:41:09 +0000
Subject: [FieldTrip] Negative values with debiased weighted phase
	lag	index
In-Reply-To: <69EC263C-5A16-4CC3-8498-3C2AB7E75781@gmail.com>
References: <HE1PR03MB1641555DB4A0BFBB22D8051FC25D0@HE1PR03MB1641.eurprd03.prod.outlook.com>,
 <69EC263C-5A16-4CC3-8498-3C2AB7E75781@gmail.com>
Message-ID: <HE1PR03MB16413FA5F596A4D54F9C2FE8C25D0@HE1PR03MB1641.eurprd03.prod.outlook.com>

Thanks Julian - I found the info I was looking for. Apologies - I should have checked the previous discussions first.


Best wishes

Lizzie

---------------------------------------------------------------------------
Lizzie Shephard, PhD
Postdoctoral researcher
2.21 MRC SGDP Centre
Institute of Psychiatry, Psychology, & Neuroscience
King’s College London
De Crespigny Park
London, SE5 8AF
0207 848 5272
elizabeth.1.shephard at kcl.ac.uk



________________________________
From: fieldtrip-bounces at science.ru.nl <fieldtrip-bounces at science.ru.nl> on behalf of Julian Keil <julian.keil at gmail.com>
Sent: 17 February 2017 11:10
To: FieldTrip discussion list
Subject: Re: [FieldTrip] Negative values with debiased weighted phase lag index

Dear Lizzie,

this comes up from time to time on the Mailinglist.
Check for example this response by Martin Vinck:
https://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003892.html<https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fpipermail%2Ffieldtrip%2F2011-June%2F003892.html&data=01%7C01%7Celizabeth.1.shephard%40kcl.ac.uk%7Ccbe12a18f5fd4ba30c9c08d457264f41%7C8370cf1416f34c16b83c724071654356%7C0&sdata=uQ57ydU%2B3nFowiHUDFwvpV2usBijgVUOU8YPTJ%2FCkx8%3D&reserved=0>

Quote: The debiased WPLI estimator gets negative however as a consequence of the debiasing method - different issue.

Cheers,

Julian

Am 17.02.2017 um 12:05 schrieb Shephard, Elizabeth:

Dear all

I am using FieldTrip to explore connectivity in resting-state EEG data and aimed to use the debiased weighted phase lag index (dwPLI) to index this. However, I am finding a lot of negative values in my connectivity matrices when I compute the dwPLI, and I am unsure why this might be - has anyone found this previously, or have an idea of why this might be happening? I do not get this if I compute other connectivity measures (e.g. coherence) and I have a decent amount of clean trials (around 80 per subject) on which to run the connectivity. I am computing the dwPLI from fourier coefficients exported from a straightforward FFT.

Many thanks in advance for any advice
Best wishes
Lizzie

---------------------------------------------------------------------------
Lizzie Shephard, PhD
Postdoctoral researcher
2.21 MRC SGDP Centre
Institute of Psychiatry, Psychology, & Neuroscience
King’s College London
De Crespigny Park
London, SE5 8AF
0207 848 5272
elizabeth.1.shephard at kcl.ac.uk<mailto:elizabeth.1.shephard at kcl.ac.uk>


_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&data=01%7C01%7Celizabeth.1.shephard%40kcl.ac.uk%7Ccbe12a18f5fd4ba30c9c08d457264f41%7C8370cf1416f34c16b83c724071654356%7C0&sdata=%2FoI%2FKqnU4CF2DgSD7TF6qJamCN2ovqL7xZgWacgFYbM%3D&reserved=0>

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From politzerahless at gmail.com  Fri Feb 17 12:49:06 2017
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Fri, 17 Feb 2017 19:49:06 +0800
Subject: [FieldTrip] time windows and number of channels in cluster
	based permutation tests
Message-ID: <CAJT2k_82ouDpdv7+bm+9XxLrGXnbabA6syhcXwe26GtDGGzCyg@mail.gmail.com>

Dear Michele,

The general idea is, when you get a p-value out of the cluster test, it's
evaluated against a permutation distribution---the 'real' cluster is
getting compared against all the fake clusters that pop up when you shuffle
the data randomly. Roughly speaking, when you analyze more timepoints and
more channels, there's more chances for random nonsense clusters to pop up
in each permutation of randomly shuffled data; thus, there's more chances
to get random nonsense clusters that have a bigger test statistic than your
real cluster. Since the p-value is just the proportion of random clusters
that have a bigger test statistic than the real cluster, testing more
timepoints and/or more channels means you might end up with a higher
p-value.

Anyway, the selection of channels and time ranges has to be chosen *a
priori*, not based on the data (choosing which window to analyze after
you've seen where the effect is would be a non-independent / double-dipping
analysis), so since you seem to have found a significant effect based on
the samples you had identified a priori, I don't think you have to worry
about the whole-head analysis.

Best,
Steve

---
Stephen Politzer-Ahles
The Hong Kong Polytechnic University
Department of Chinese and Bilingual Studies
http://www.mypolyuweb.hk/~sjpolit/
<http://www.nyu.edu/projects/politzer-ahles/>

On Fri, Feb 17, 2017 at 7:00 PM, <fieldtrip-request at science.ru.nl> wrote:

> Send fieldtrip mailing list submissions to
>         fieldtrip at science.ru.nl
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
>         fieldtrip-request at science.ru.nl
>
> You can reach the person managing the list at
>         fieldtrip-owner at science.ru.nl
>
>

>
> Message: 3
> Date: Fri, 17 Feb 2017 10:33:52 +0100
> From: Michele Scaltritti <michele.scaltritti at gmail.com>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] time windows and number of channels in cluster
>         based   permutation tests
> Message-ID:
>         <CABGEo=TM-TGqh3bQubOD_29z-cxQ93grvXQHNMo70zqLcpjjEg@
> mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear FieldTrip users,
>
> I have a rather general question regarding cluster-based permutation test.
>
> In the tutorial for Cluster-based permutation tests on event related
> fields, I read that sensitivity of the analysis depends on the length of
> the time interval that is analyzed. Elsewhere, I found a similar reasoning
> regarding channels, in the sense that it the exclusion of the sensors where
> no effect is likely to be present should yield a more sensitive analysis.
>
> In my experiment, I analyzed a limited set of central electrodes (where
> previous evidence suggests that the difference should be located) and found
> a significant positive cluster, and a (smaller) significant negative one.
> When doing the same analysis considering all the electrodes, no significant
> negative cluster is found, just a positive one. Among other things, this
> may reflect a different sensitivity as a function of the number of channels
> considered in the analysis. I explored a bit the different parameters (such
> as neighbors channels definition), but I did not identify the source of the
> difference between the analyses.
>
> Leaving aside my specific case, in more general terms I cannot understand
> how sensitivity is increased by focusing on a smaller time-windows, or on a
> specific set of electrodes. After all, the number of comparisons we make
> should not affect the number of samples surpassing the threshold, nor the
> clustering as a function of the spatial and temporal adjacency of these
> supra-theshold samples. I understand that the same cluster may vary when
> other samples are considered in the analyses (for example, samples from
> other electrodes may get included), but again, I am failing to see how this
> may be related to the sensitivity of the analysis. The cluster-level
> statistics, for example, should not be weakened by this.
>
> I apologize if this message underlies any gross misunderstanding.
>
> Michele Scaltritti
> -------------- next part --------------
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> URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/
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>
> ------------------------------
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> End of fieldtrip Digest, Vol 75, Issue 19
> *****************************************
>
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From michele.scaltritti at gmail.com  Fri Feb 17 13:07:43 2017
From: michele.scaltritti at gmail.com (Michele Scaltritti)
Date: Fri, 17 Feb 2017 13:07:43 +0100
Subject: [FieldTrip] time windows and number of channels in cluster
 based permutation tests
In-Reply-To: <CAJT2k_82ouDpdv7+bm+9XxLrGXnbabA6syhcXwe26GtDGGzCyg@mail.gmail.com>
References: <CAJT2k_82ouDpdv7+bm+9XxLrGXnbabA6syhcXwe26GtDGGzCyg@mail.gmail.com>
Message-ID: <CABGEo=RWSYwBLQtav-TupyfmzjY4Msh6Lkv1WUfq+3vCKTDeJQ@mail.gmail.com>

Dear Stephen,

thank you so much for the clarification. Indeed, I only thought about how
the number of channels/timepoints affects the "real" clusters, without
considering the implications for permutations. Thank you again for your
help, I really appreciate it.

On Fri, Feb 17, 2017 at 12:49 PM, Stephen Politzer-Ahles <
politzerahless at gmail.com> wrote:

>
> Dear Michele,
>
> The general idea is, when you get a p-value out of the cluster test, it's
> evaluated against a permutation distribution---the 'real' cluster is
> getting compared against all the fake clusters that pop up when you shuffle
> the data randomly. Roughly speaking, when you analyze more timepoints and
> more channels, there's more chances for random nonsense clusters to pop up
> in each permutation of randomly shuffled data; thus, there's more chances
> to get random nonsense clusters that have a bigger test statistic than your
> real cluster. Since the p-value is just the proportion of random clusters
> that have a bigger test statistic than the real cluster, testing more
> timepoints and/or more channels means you might end up with a higher
> p-value.
>
> Anyway, the selection of channels and time ranges has to be chosen *a
> priori*, not based on the data (choosing which window to analyze after
> you've seen where the effect is would be a non-independent / double-dipping
> analysis), so since you seem to have found a significant effect based on
> the samples you had identified a priori, I don't think you have to worry
> about the whole-head analysis.
>
> Best,
> Steve
>
> ---
> Stephen Politzer-Ahles
> The Hong Kong Polytechnic University
> Department of Chinese and Bilingual Studies
> http://www.mypolyuweb.hk/~sjpolit/
> <http://www.nyu.edu/projects/politzer-ahles/>
>
> On Fri, Feb 17, 2017 at 7:00 PM, <fieldtrip-request at science.ru.nl> wrote:
>
>> Send fieldtrip mailing list submissions to
>>         fieldtrip at science.ru.nl
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>>         https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> or, via email, send a message with subject or body 'help' to
>>         fieldtrip-request at science.ru.nl
>>
>> You can reach the person managing the list at
>>         fieldtrip-owner at science.ru.nl
>>
>>
>
>>
>> Message: 3
>> Date: Fri, 17 Feb 2017 10:33:52 +0100
>> From: Michele Scaltritti <michele.scaltritti at gmail.com>
>> To: fieldtrip at science.ru.nl
>> Subject: [FieldTrip] time windows and number of channels in cluster
>>         based   permutation tests
>> Message-ID:
>>         <CABGEo=TM-TGqh3bQubOD_29z-cxQ93grvXQHNMo70zqLcpjjEg at mail.
>> gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>>
>> Dear FieldTrip users,
>>
>> I have a rather general question regarding cluster-based permutation test.
>>
>> In the tutorial for Cluster-based permutation tests on event related
>> fields, I read that sensitivity of the analysis depends on the length of
>> the time interval that is analyzed. Elsewhere, I found a similar reasoning
>> regarding channels, in the sense that it the exclusion of the sensors
>> where
>> no effect is likely to be present should yield a more sensitive analysis.
>>
>> In my experiment, I analyzed a limited set of central electrodes (where
>> previous evidence suggests that the difference should be located) and
>> found
>> a significant positive cluster, and a (smaller) significant negative one.
>> When doing the same analysis considering all the electrodes, no
>> significant
>> negative cluster is found, just a positive one. Among other things, this
>> may reflect a different sensitivity as a function of the number of
>> channels
>> considered in the analysis. I explored a bit the different parameters
>> (such
>> as neighbors channels definition), but I did not identify the source of
>> the
>> difference between the analyses.
>>
>> Leaving aside my specific case, in more general terms I cannot understand
>> how sensitivity is increased by focusing on a smaller time-windows, or on
>> a
>> specific set of electrodes. After all, the number of comparisons we make
>> should not affect the number of samples surpassing the threshold, nor the
>> clustering as a function of the spatial and temporal adjacency of these
>> supra-theshold samples. I understand that the same cluster may vary when
>> other samples are considered in the analyses (for example, samples from
>> other electrodes may get included), but again, I am failing to see how
>> this
>> may be related to the sensitivity of the analysis. The cluster-level
>> statistics, for example, should not be weakened by this.
>>
>> I apologize if this message underlies any gross misunderstanding.
>>
>> Michele Scaltritti
>> -------------- next part --------------
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>> s/20170217/c376010b/attachment-0001.html>
>>
>> ------------------------------
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>> End of fieldtrip Digest, Vol 75, Issue 19
>> *****************************************
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From jonas at obleser.de  Fri Feb 17 22:07:29 2017
From: jonas at obleser.de (Jonas Obleser)
Date: Fri, 17 Feb 2017 22:07:29 +0100
Subject: [FieldTrip] =?utf-8?q?open_PhD_student_/_predoctoral_researcher_p?=
 =?utf-8?q?osition_in_the_Obleser_lab_=28L=C3=BCbeck=2C_Germany=29?=
Message-ID: <9BA78314-0381-4A3F-9156-B94628DF3D03@obleser.de>

— Dear colleagues: Thanks for sharing and apologies for any cross-posting — 

The research group “Auditory Cognition” (headed by Jonas Obleser; auditorycognition.com), now at the University of Lübeck, is seeking to hire a predoctoral researcher, with initial funding  for 3 years (DFG, German Science Foundation) for a joint project with the MPI in Leipzig (Gesa Hartwigsen).

Please share or download the full job advert here: https://tinyurl.com/PhDObleserLab2017 <https://t.co/Yau1RbKiZk>

Application deadline is April 1 2017 (postal receipt; additional PDF per email is kindly requested).

Best wishes, Jonas

http://obleserlab.com
http://uni-luebeck.de




Prof. Dr. Jonas Obleser

Universität zu Lübeck
Department of Psychology
MFC 8, Maria-Goeppert-Straße 9a
23562 Lübeck

Tel +49 (0)451 3101 3620
jonas.obleser at uni-luebeck.de <mailto:jonas.obleser at uni-luebeck.de>
http://auditorycognition.com <http://auditorycognition.com/>

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From cmuehl at gmail.com  Sun Feb 19 18:44:26 2017
From: cmuehl at gmail.com (Christian Muehl)
Date: Sun, 19 Feb 2017 17:44:26 +0000
Subject: [FieldTrip] CfPs: Special session on multi-user modeling in ACII
 2017 (Affective Computing and Intelligent Interaction)
Message-ID: <1804ae50d57f440f9e92b5650e896048@EXPRD01.hosting.ru.nl>

** Call for papers **
Brain and physiological signals for multi-user modeling
Special session in ACII 2017 (Affective Computing and Intelligent Interaction)
http://www.affective-sciences.org/en/bps-mum

** Description **
Emotional cues, generated subconsciously by the human body, have always been a crucial part of affective computing. Machines can learn about a person's affective state by analyzing measurements such as autonomic nervous system responses, neurophysiological measurements and gaze behavior. They can then act on the inferred information, adapting their own behavior, response or service based on the user's affective state.

Although emotions can be viewed as a social phenomenon, current physiological computing research is focused on emotions which are triggered by non-social stimuli. In the case of group interactions, emotions do not only develop in one’s mind but rather unfold according to the emotional expressions of the others. Consequently, the behavior, expressions and physiology of interacting people are known to be in synchrony during interactions. This inter-dependency of behavior and emotional expressions can in turn predict several properties of the social interaction such as grounding, mutual understanding, conflict, or social presence. Similarly, researchers in social neuro-science perform hyper-scanning to measure joint brain activities of people interacting with each other. The objective being to uncover brain areas and neural mechanisms supporting social processes.

With this special session we would like to develop research on multi-users’ modeling from neural and physiological sources. Here the concept of user modeling is defined broadly, including emotional, cognitive and social aspects which can be used for intelligent interactions. This special session targets researchers from computer science, neuro-science and psycho-physiology who are interested in the following research questions:

-   What information about the user state and the quality of the interaction between users can be gained from (neuro-)physiological signals?
-   How can that information, combined from several users, be used to interact adaptively with a machine?
-   What is the effect of sharing physiological information with others?
-   Which methods can be developed to reduce inter-users variability and improve user modeling?

The special session topics include but are not limited to:

-   Collaborative brain-computer interfaces
-   Tangible / social display of physiological and neural cues
-   Social bio-feedback
-   Assessment of social processes (conflict, empathy, relationship etc.)
-   Assessment of the quality of interaction and collaboration
-   Social neuroscience and psycho-physiology
-   Emotion assessment, particularly social emotions
-   Domain and transfer learning for building cross-participant models
-   Methods for multiple user modeling (e.g. synchrony measures, dynamic multi-users' models, etc.)
-   Applications of multi-user physiological computing

To facilitate the research on physiological signal classification, several databases are publicly available. Contributions on the physiological data available in such databases are welcome but not obliged. Example databases include:
EATMINT: https://eatmint.unige.ch
RECOLA: https://diuf.unifr.ch/diva/recola
MMDB: http://www.cbi.gatech.edu/mmdb/

Those databases are only examples and work on self-collected or other data are welcome.

** Important dates **
Conference Dates: October 23-26, 2017
Paper Submission Deadline: May 2, 2017
Reviews Provided to Authors: June 16, 2017
Author Rebuttals Due: June 23, 2017
Notification of Acceptance: July 14, 2017
Camera Ready Papers Due: August 18, 2017
Full paper authors should register By: August 7, 2017
Early registration deadline: September 1, 2017

** Submission procedure **
Papers  submitted to this Special Sessions have to be submitted following the same schedule and procedure as regular ACII papers (ACII paper submission). When submitting your paper please check the corresponding box for the Special Session on "Brain and physiological signals for multi-users modeling" in the ACII submission system.

The papers will undergo the same review process by anonymous and independent reviewers as the remaining ACII submissions.

** Organizers **
Guillaume Chanel, Swiss Center for Affective Sciences, Switzerland
guillaume.chanel[at]unige.ch<http://unige.ch>
http://www.affective-sciences.ch/user/chanel

Christian Mühl, German Aerospace Center, Germany
cmuehl[at]gmail.com<http://gmail.com>
https://www.linkedin.com/in/cmuhl

Jérémy Frey, Ullo, France
jfrey[at]ullo.fr<http://ullo.fr>
http://phd.jfrey.info

Anton Nijholt, University of Twente, The Netherlands
anijholt[at]cs.utwente.nl<http://cs.utwente.nl>
http://wwwhome.cs.utwente.nl/~anijholt/<http://wwwhome.cs.utwente.nl/%7Eanijholt/>
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From sarang at cfin.au.dk  Mon Feb 20 15:13:40 2017
From: sarang at cfin.au.dk (Sarang S. Dalal)
Date: Mon, 20 Feb 2017 14:13:40 +0000
Subject: [FieldTrip] MEG Nord conference in Aarhus - May 9-10
Message-ID: <D9DC18A9-1E53-4C99-8B47-6B6C6F51CBF3@cfin.au.dk>

On behalf of the Center of Functionally Integrative Neurosciece (CFIN, Aarhus University, Denmark), we would like to welcome you to the first Nordic MEG conference (MEG Nord 2017) – the first international meeting dedicated to development of magnetoencephalographic science and technology in Northern Europe and Scandinavia. With the growing number of MEG groups in Northern Europe, the conference will serve to create stronger ties between them, exchange ideas and techniques, have more collaborative projects, create common standards and jointly apply for funding.

CFIN and Aarhus University are pleased to host the first meeting in what will hopefully become a regular series of international events. The meeting will take place at AU on May 9-10, 2017 (preceded by MEG-related satellite events on May 8), and will gather together scientists from all main MEG centres in Northern Europe as well as collaborators and guests from across the world.

The meeting programme will feature dedicated slots for oral presentations by the main Nordic MEG sites. However, researchers from anywhere in the world are invited to attend, and will have the opportunity to submit abstracts for the poster session or a short talk.

We are striving to keep the conference participation free of any fees or charges to the participants, but note that registration is obligatory (see below). We hope you will enjoy a stimulating conference, a company of friendly colleagues, and the beautiful old Danish city of Aarhus, European Capital of Culture for 2017.

You can find our preliminary program online here:
http://cfin.au.dk/meg-nord-2017/

We look forward to seeing you here!

Yury Shtyrov / Sarang Dalal / Chris Bailey



From skelly2 at ccny.cuny.edu  Wed Feb 22 23:52:14 2017
From: skelly2 at ccny.cuny.edu (Simon Kelly)
Date: Wed, 22 Feb 2017 22:52:14 +0000
Subject: [FieldTrip] PhD opening in the neural mechanisms of decision making
	- Dublin
Message-ID: <591122f2582149a7b2543b0ebb64eb0f@EXPRD04.hosting.ru.nl>

​Applications are invited for a fully funded 4-year PhD position in the Cognitive Neural Systems lab (https://cogneusys.com/), led by Simon Kelly, to study the neural mechanisms of decision making. This position is part of a project funded by Science Foundation Ireland, which involves a combination of psychophysics, computational modelling, non-invasive electrophysiology of human brain and muscle, and analyses of existing single-cell neurophysiological data. The funded research is specifically focused on the impact of value (i.e., how much decision outcomes are worth) on the dynamics of decision formation in sensory, decision, and motor areas of the brain. However, the overall PhD can be significantly broader in scope (including e.g. biomedical/translational applications), depending on the student’s interests within the broader research themes of the lab.

The Cognitive Neural Systems lab is situated within the School of Electrical and Electronic Engineering in University College Dublin, Ireland, and has strong collaborative links to basic cognitive and clinical neuroscience research groups both locally (e.g. Trinity College Institute of Neuroscience) and internationally (e.g. City College and Columbia University in New York). The successful applicant will have ample opportunities for wider collaborations and the learning of a broad range of experimental, conceptual, analytic and computational skills.

Applicants should have a BSc/B.E. or Masters degree in neuroscience, psychology, electrical/biomedical engineering, computer science, or other related discipline and a demonstrable interest in cognitive neuroscience. The ideal candidate will be highly motivated and have excellent communication skills. Any prior experience in programming, psychophysics, EEG and/or modelling, especially in the area of cognitive neuroscience, is a definite advantage.

To apply, submit a CV, short cover letter and contact information for at least two referees to Dr Simon Kelly (simon.kelly at ucd.edu). Candidates should explain in their cover letter how their own research interests fit specifically with those of the Kelly lab.

-----------------------------------------------------------
Simon Kelly, Ph.D.
Associate Professor
School of Electrical and Electronic Engineering
University College Dublin
t: +353 (1) 716 1803
e: simon.kelly at ucd.ie
-----------------------------------------------------------

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From r.oostenveld at donders.ru.nl  Thu Feb 23 17:14:29 2017
From: r.oostenveld at donders.ru.nl (Robert Oostenveld)
Date: Thu, 23 Feb 2017 17:14:29 +0100
Subject: [FieldTrip] Donders Neuroimaging Tool-kits - registration now open
References: <90D0A92901510646B5CD061AE2F9AC0350535A51@exprd04.hosting.ru.nl>
Message-ID: <5E650174-6457-48F1-BEF9-E430B094C799@donders.ru.nl>

On 23 Feb 2017, at 14:07, Stijns, M.H. (Tildie) <tildie.stijns at donders.ru.nl> wrote:

Are you interested in learning neuroimaging techniques directly from the experts?
Do you like courses that take a practical hands-on approach to training?

To help you become proficient in modern neuroimaging methods, the Donders Institute offers “Tool-kits” of Cognitive Neuroscience, held annually at Radboud University, Nijmegen, the Netherlands.

Donders Tool-kits in 2017 <http://www.ru.nl/donders/agenda-news/donders-tool-kits/>:

Advanced MEG/EEG <http://www.ru.nl/donders/agenda-news/donders-tool-kits/vm-tool-kits/donders-meg-eeg-tool-kit/>: (3-7 April 2017)
Advanced (f)MRI: <http://www.ru.nl/donders/agenda-news/donders-tool-kits/vm-tool-kits/donders-fmri-tool-kit/>(15-18 May 2017)
Brain Stimulation <http://www.ru.nl/donders/agenda-news/donders-tool-kits/vm-tool-kits/donders-brain-stimulation-tool-kit/>: (30 May-2 June 2017)
Neuroimaging <http://www.ru.nl/donders/agenda-news/donders-tool-kits/vm-tool-kits/donders-neuroimaging-tool-kit/>: (28 August-1 September 2017)

Best regards,
Tildie Stijns

 
===================================================
 
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging (DCCN)
Radboud University
 
P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands
 
Visiting address:
Kapittelweg 29
Office 01.120
6525 EN Nijmegen
 
Tel. 00 31 (0)24 - 3610651
Fax 00 31 (0)24 - 3610652
www.ru.nl/donders <http://www.ru.nl/donders>

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From sophiechen33 at gmail.com  Fri Feb 24 12:04:32 2017
From: sophiechen33 at gmail.com (sophie chen)
Date: Fri, 24 Feb 2017 12:04:32 +0100
Subject: [FieldTrip] Fwd: job opening : PhD position in MEG signal
 processing in Marseille, France
In-Reply-To: <58b00b9a.2f8fdf0a.6bc7b.4f06SMTPIN_ADDED_BROKEN@mx.google.com>
References: <CAOdCn2xxSe55QcS2Qf+VePVwxjTy_xs3wTnDe2CwRqg3raLTGQ@mail.gmail.com>
 <58b00b9a.2f8fdf0a.6bc7b.4f06SMTPIN_ADDED_BROKEN@mx.google.com>
Message-ID: <CAOdCn2wNLMyMRYmptL74=U+wC88E2uHa9Pq-JdSGwYma7bGiyA@mail.gmail.com>

---------- Forwarded message ----------
From: Christian-G. Bénar <christian.benar at univ-amu.fr>
Date: 2017-02-24 11:31 GMT+01:00
Subject: RE: job opening : PhD position in MEG signal processing in
Marseille, France
To: sophie chen <sophie.chen at univ-amu.fr>
Cc: "Christian-G. Bénar" <christian.benar at univ-amu.fr>


Dear all,



Please find below an announcement for a PhD position in MEG signal
processing, located in Aix-Marseille University (Marseille, France).

The project will be in collaboration between the "Institut de Neurosciences
des Systèmes" (C. Bénar) and the "Institut de Mathématiques de Marseille"
(B. Torrésani). Please check eligibility criteria.



Topic : " *CHARACTERIZING BRAIN NETWORKS IN REAL TIME ACROSS FREQUENCIES
BASED ON A COMBINATION OF TIME FREQUENCY AND SOURCE LOCALIZATION METHODS*"



More details can be found at:



http://doc2amu.univ-amu.fr/en/characterizing-brain-networks-
in-real-time-across-frequencies-based-on-a-combination-of-time-1

Best regards,



Christian Bénar

Institut de Neurosciences des Systèmes-  INS

UMR 1106, Faculté de Médecine La timone

27 bd Jean Moulin 13005 Marseille

http://ins.univ-amu.fr/research-teams/dynamical-brain-mapping-dynamap/

http://meg.univ-amu.fr/wiki/Main_Page

https://www.researchgate.net/profile/Christian_Benar












------------------------------
[image: Avast logo] <https://www.avast.com/antivirus>

L'absence de virus dans ce courrier électronique a été vérifiée par le
logiciel antivirus Avast.
www.avast.com <https://www.avast.com/antivirus>
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From davide.tabarelli at unitn.it  Fri Feb 24 16:43:38 2017
From: davide.tabarelli at unitn.it (Davide Tabarelli)
Date: Fri, 24 Feb 2017 16:43:38 +0100
Subject: [FieldTrip] Databrowser magscale
Message-ID: <6C5211AF-C65B-4B4A-A9B0-D400BAA3E0FC@unitn.it>

Hi to all,

I’m using Fieldtrip version 20170223 and I’m trying to visualize some MEG data from a Neuromag dataset.
I’ve set the cfg for ft_databrowser as:

cfg=[];
cfg.channel = 'MEG';
cfg.viewmode = 'vertical';
cfg.blocksize = 10;
cfg.magscale = 25;

but magnetometers data are not scaled ...

Any suggestion?

Thanks !


From stephen.whitmarsh at gmail.com  Fri Feb 24 17:26:02 2017
From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh)
Date: Fri, 24 Feb 2017 17:26:02 +0100
Subject: [FieldTrip] Databrowser magscale
In-Reply-To: <6C5211AF-C65B-4B4A-A9B0-D400BAA3E0FC@unitn.it>
References: <6C5211AF-C65B-4B4A-A9B0-D400BAA3E0FC@unitn.it>
Message-ID: <CAFrxm=zaFTB+b=dsCyZs-oqw911N8fX=DqtxLEfwOsanLWjvvw@mail.gmail.com>

Hi Davide,

Ft_databrowser only has the option of (auto) scaling all displayed channels
at once. So since magnetometers and gradiometers have different scales,
with the latter larger than the former, only display the magnetometers and
you're fine.

Cheers,
Stephen

On 24 February 2017 at 16:43, Davide Tabarelli <davide.tabarelli at unitn.it>
wrote:

> Hi to all,
>
> I’m using Fieldtrip version 20170223 and I’m trying to visualize some MEG
> data from a Neuromag dataset.
> I’ve set the cfg for ft_databrowser as:
>
> cfg=[];
> cfg.channel = 'MEG';
> cfg.viewmode = 'vertical';
> cfg.blocksize = 10;
> cfg.magscale = 25;
>
> but magnetometers data are not scaled ...
>
> Any suggestion?
>
> Thanks !
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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From thomas.hartmann at th-ht.de  Fri Feb 24 18:33:52 2017
From: thomas.hartmann at th-ht.de (Thomas Hartmann)
Date: Fri, 24 Feb 2017 18:33:52 +0100
Subject: [FieldTrip] simulating a dipole with a real headmodel and using
 DICS to locate it misplaces the source
Message-ID: <8610b87c-d0cd-9678-902b-795da6445d73@th-ht.de>

hi,

i wanted to see whether i can simulate a dipole with the data provided 
by the tutorial and use the DICS beamformer to see where the source gets 
projected.

the code i used is in the attached file.

it expects the data you can download from here: 
ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer/

in a folder called "beamformer".

the puzzling thing is that i do not seem to manage to have it project 
the sources anywhere near to the original dipole in the simulation. the 
center of the head bias come out nicely if neither baseline correction 
or NAI calculation is used. i also checked whether the the coordinate 
system of the volume and the grid i generate match. i also checked 
whether the chosen dipole shows up at the correct location when i plot 
it on the head model.

so, my question is: what do i not get here? maybe there is something 
wrong with my script? maybe ft_dipolesimulate is not supposed to be used 
that way?

i would really appreciate any suggestions.

best,
thomas

ps: i also tried with eloreta and a simple dipole fit. the results look 
slightly different but not really any better...

-- 
Dr. Thomas Hartmann

Centre for Cognitive Neuroscience
FB Psychologie
Universität Salzburg
Hellbrunnerstraße 34/II
5020 Salzburg

Tel: +43 662 8044 5109
Email: thomas.hartmann at th-ht.de

"I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan Doyle)

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From mona at sdsc.edu  Sat Feb 25 02:16:47 2017
From: mona at sdsc.edu (Wong-Barnum, Mona)
Date: Sat, 25 Feb 2017 01:16:47 +0000
Subject: [FieldTrip] problem getting frequency bands
In-Reply-To: <CACXO-RPX388dNSPnfmsbG31a2Og5cbrMyEuWxbnDWKCg41OEpw@mail.gmail.com>
References: <380251EF-CC46-44D1-8D5B-FBA1DB12A962@mail.ucsd.edu>
 <CACXO-RPX388dNSPnfmsbG31a2Og5cbrMyEuWxbnDWKCg41OEpw@mail.gmail.com>
Message-ID: <AFE9A4FD-51A2-45E8-8A07-CB906D406EDD@mail.ucsd.edu>


Yes that worked (:  Thank you Julian for catching my typo!

cheers,
Mona


On Feb 10, 2017, at 11:10 PM, Julian Keil <julian.keil at gmail.com<mailto:julian.keil at gmail.com>> wrote:

Hi Mona,
You have a typo in you cfg call.
Check thr cfg.bpfilter='yes' setting.

Hope that hepls,

Julian

*********************************************
    Mona Wong
    Web & Mobile Application Developer
    San Diego Supercomputer Center

    Believing we are in control is an
    illusion that brings suffering.
*********************************************






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From mona at sdsc.edu  Sat Feb 25 02:29:37 2017
From: mona at sdsc.edu (Wong-Barnum, Mona)
Date: Sat, 25 Feb 2017 01:29:37 +0000
Subject: [FieldTrip] error in filter_with_correction
Message-ID: <7AC17F80-7F8D-4EC9-87F5-1B3279AC8DE1@mail.ucsd.edu>

Hello fellow FieldTrip'er:

Can someone help me understand and hopefully fix the following runtime error message I am seeing (I searched a bit on the website documentation but didn’t find anything):

Error using filter_with_correction (line 51)
Calculated filter coefficients have poles on or outside the unit circle and
will not be stable. Try a higher cutoff frequency or a different type/order of
filter.

Error in filter_with_correction (line 51)
  error('Calculated filter coefficients have poles on or outside the unit
  circle and will not be stable. Try a higher cutoff frequency or a different
  type/order of filter.');

Error in ft_preproc_bandpassfilter (line 286)
  filt = filter_with_correction(B,A,dat,dir,usefftfilt);

Error in preproc (line 324)
  if strcmp(cfg.bpfilter, 'yes'),     dat = ft_preproc_bandpassfilter(dat,
  fsample, cfg.bpfreq, cfg.bpfiltord, cfg.bpfilttype, cfg.bpfiltdir,
  cfg.bpinstabilityfix, cfg.bpfiltdf, cfg.bpfiltwintype, cfg.bpfiltdev,
  cfg.plotfiltresp, cfg.usefftfilt); end

Error in ft_preprocessing (line 592)
      [cutdat{i}, label, time{i}, cfg] = preproc(dat, hdr.label(rawindx), tim,
      cfg, begpadding, endpadding);

Error in test (line 25)
data = ft_preprocessing ( cfg );

Error in run (line 96)
evalin('caller', [script ';']);

Here is my script:

addpath /path/to/my/fieldtrip
ft_defaults

% 1. MEG
disp ( 'Reading 1.fif...' )
cfg = [];
cfg.dataset = '1.fif';
data = ft_preprocessing ( cfg );

disp ( 'Getting MEG channel 1...' )
meg_channel = ft_channelselection ( 'MEG0111', data.label );
cfg = [];
cfg.channel = meg_channel;
meg = ft_selectdata ( cfg, data );
disp ( 'Saving meg...' )
save meg.mat meg -v7.3;
clearvars cfg meg;

% 2. Low delta MEG
disp ( 'Low delta MEG...' )
cfg = [];
cfg.bpfilter = 'yes';
cfg.bpfreq = [0.1 2];
cfg.dataset = '1.fif';
data = ft_preprocessing ( cfg );

cfg = [];
cfg.channel = meg_channel;
cfg.frequency = [0.1 2];
meg = ft_selectdata ( cfg, data );
disp ( 'Saving low delta meg...' )
save low_delta_meg.mat meg -v7.3;
clearvars cfg meg;

Line #25 is the last “data = ft_preprocessing ( cfg );” line.

If I do cfg.bpfreq = [2 4] then there is no error but I really like to get this low [0.1 2] range…any tips?

Mona

*********************************************
    Mona Wong
    Web & Mobile Application Developer
    San Diego Supercomputer Center

    Believing we are in control is an
    illusion that brings suffering.
*********************************************






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From r.oostenveld at donders.ru.nl  Sat Feb 25 14:46:03 2017
From: r.oostenveld at donders.ru.nl (Robert Oostenveld)
Date: Sat, 25 Feb 2017 14:46:03 +0100
Subject: [FieldTrip] MEG/EEG FieldTrip toolkit course in Nijmegen:
	pre-registration still open
In-Reply-To: <F45C6F34-0F6B-449D-8A4E-F727CC0DD15C@donders.ru.nl>
References: <F45C6F34-0F6B-449D-8A4E-F727CC0DD15C@donders.ru.nl>
Message-ID: <46196986-747B-4A37-8852-8C14BF1844FB@donders.ru.nl>

Dear All,

— Please disseminate to PhD students and postdoctoral researchers working with MEG, EEG and ECoG data analysis. ---

Please note that pre-registration closes on 1 March!

On 3-6 April we will host the "Toolkit of Cognitive Neuroscience: advanced data analysis and source modelling of EEG and MEG data" at the Donders Institute in Nijmegen. 

This intense 4-day toolkit course will teach you advanced MEG and EEG data analysis skills. Preprocessing, frequency analysis, source reconstruction, connectivity and various statistical methods will be covered. The toolkit will consist of a number of lectures, followed by hands-on sessions in which you will be tutored through the complete analysis of a MEG data set using the FieldTrip toolbox. The lectures and tutoring will be provided by the core FieldTrip development team, and there will also be plenty of opportunity to interact and ask questions to us about your research and data. On the final day you will have the opportunity to work on your own dataset under supervision of the tutors.

We can host a limited number of participants. From past experience we expect the course to be oversubscribed, hence we will start with pre-registration. The final selection of the participants will be based on the motivation, background experience and research interests that are provided in the registration form. The deadline for pre-registration is March 1, 2017.

More information, including a preliminary program, can be found at http://www.ru.nl/donders/agenda-news/donders-tool-kits/vm-tool-kits/donders-meg-eeg-tool-kit/ <http://www.ru.nl/donders/agenda-news/donders-tool-kits/vm-tool-kits/donders-meg-eeg-tool-kit/> 


Looking forward to welcoming you in Nijmegen,
Robert Oostenveld and Jan-Mathijs Schoffelen.


-----------------------------------------------------------
Robert Oostenveld, PhD

Senior Researcher & MEG Physicist
Donders Institute for Brain, Cognition and Behaviour
Radboud University, Nijmegen, The Netherlands

Visiting Professor
NatMEG - the Swedish National MEG facility
Karolinska Institute, Stockholm, Sweden

tel.: +31 (0)24 3619695
e-mail: r.oostenveld at donders.ru.nl <mailto:r.oostenveld at donders.ru.nl>
web: http://www.ru.nl/donders <http://www.ru.nl/donders>
skype: r.oostenveld
-----------------------------------------------------------


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From changa5 at mcmaster.ca  Sat Feb 25 16:39:17 2017
From: changa5 at mcmaster.ca (Andrew Chang)
Date: Sat, 25 Feb 2017 10:39:17 -0500
Subject: [FieldTrip] 96 channel ActiCap sensor locations
Message-ID: <CAJquwbogdf+pKhh5fNE72vdV8gDOsoNnStrZJGbwmTS6FH1WKQ@mail.gmail.com>

Dear FieldTrip users,

I am wondering whether anyone would like to share the Fieldtrip layout file
of the "*actiCap 96Ch Standard 2*" EEG cap with me. I have checked around
the websites of Fieldtrip and Easycap, but failed to find anything useful.
So far I only got it's top-view map and it's Theta/Phi Coordinates (see the
attached PDFs in the links below).
https://www.dropbox.com/s/wlshxqb93tn4duz/actiCAP-96-channel-Standard-2.pdf?dl=0
https://www.dropbox.com/s/6bva7az6ydc6hvh/actiCap-96Ch-Standard%202%20Theta_Phi_CAP.pdf?dl=0

It would be very appreciated if anyone can share the Fieldtrip layout file
with me, or teach me how to create a layout in Fieldtrip from Theta/Phi
Coordinates.
Thank you all in advance!

Sincerely,
Andrew


-- 
Andrew Chang, Ph.D. Candidate
Vanier Canada Graduate Scholar
http://changa5.wordpress.com/

Auditory Development Lab
Department of Psychology, Neuroscience & Behaviour
McMaster University
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From julian.keil at gmail.com  Sat Feb 25 20:31:58 2017
From: julian.keil at gmail.com (Julian Keil)
Date: Sat, 25 Feb 2017 20:31:58 +0100
Subject: [FieldTrip] 96 channel ActiCap sensor locations
In-Reply-To: <CAJquwbogdf+pKhh5fNE72vdV8gDOsoNnStrZJGbwmTS6FH1WKQ@mail.gmail.com>
References: <CAJquwbogdf+pKhh5fNE72vdV8gDOsoNnStrZJGbwmTS6FH1WKQ@mail.gmail.com>
Message-ID: <85CF9A72-EF24-4498-98B6-567A1C167BCD@gmail.com>

Hi Andrew,

I attached you a function to convert the theta/phi coordinates to xyz-coordinates you can use in FieldTrip (Written by Stephan Moratti @UCM).
To actually use the result, you need to build an electrode structure, so do something like this:

cap=importdata('128_channel_easycap.elp'); % Import the Vendor-Provided 3d Positions

%% Step 2.1. Make an electrode file

elec.pnt=elp2coor(cap.data',100)';
elec.label=cap.textdata;

%% Check the positiosn on the head surface. They don't look good, do they?

 figure
  triplot(vol.bnd(1).pnt, vol.bnd(1).tri,  [], 'edges');
 hold
 plot3(elec.pnt(:,1),elec.pnt(:,2),elec.pnt(:,3),'r*')

%% Step 3 Move the electrodes to match the head

  cfg=[];
  cfg.method='interactive';
  cfg.elec=elec;
  cfg.headshape=vol.bnd(1);

  elec_new=ft_electroderealign(cfg);

Good luck,

Julian



********************
Dr. Julian Keil

AG Multisensorische Integration
Klinik für Psychiatrie und Psychotherapie
der Charité im St. Hedwig-Krankenhaus
Große Hamburger Straße 5-11, Haus 2
10115 Berlin

Telefon: +49-30-2311-1879
Fax:        +49-30-2311-2209
www.multisensorymind.com



Am 25.02.2017 um 16:39 schrieb Andrew Chang:

> Dear FieldTrip users,
> 
> I am wondering whether anyone would like to share the Fieldtrip layout file of the "actiCap 96Ch Standard 2" EEG cap with me. I have checked around the websites of Fieldtrip and Easycap, but failed to find anything useful. So far I only got it's top-view map and it's Theta/Phi Coordinates (see the attached PDFs in the links below).
> https://www.dropbox.com/s/wlshxqb93tn4duz/actiCAP-96-channel-Standard-2.pdf?dl=0
> https://www.dropbox.com/s/6bva7az6ydc6hvh/actiCap-96Ch-Standard%202%20Theta_Phi_CAP.pdf?dl=0
> 
> It would be very appreciated if anyone can share the Fieldtrip layout file with me, or teach me how to create a layout in Fieldtrip from Theta/Phi Coordinates.
> Thank you all in advance!
> 
> Sincerely,
> Andrew
> 
> 
> --
> Andrew Chang, Ph.D. Candidate
> Vanier Canada Graduate Scholar
> http://changa5.wordpress.com/
> 
> Auditory Development Lab
> Department of Psychology, Neuroscience & Behaviour
> McMaster University
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From changa5 at mcmaster.ca  Sat Feb 25 21:38:34 2017
From: changa5 at mcmaster.ca (Andrew Chang)
Date: Sat, 25 Feb 2017 15:38:34 -0500
Subject: [FieldTrip] 96 channel ActiCap sensor locations
In-Reply-To: <85CF9A72-EF24-4498-98B6-567A1C167BCD@gmail.com>
References: <CAJquwbogdf+pKhh5fNE72vdV8gDOsoNnStrZJGbwmTS6FH1WKQ@mail.gmail.com>
 <85CF9A72-EF24-4498-98B6-567A1C167BCD@gmail.com>
Message-ID: <CAJquwbqEVUzKKvxYPVtRizjijM_m76gOvGY7Oy9yVdKdMv+tvA@mail.gmail.com>

Thank you, Julian! Your comments are very helpful. It's working well!

For the future reference of other Fieldtrip users, here are my codes of
implementing it.

sphcoor = [Theta,Phi]'; % combining theta and phi coordinates
cartcoor = elp2coor(sphcoor)'; % converting theta/phi coorfinates into xyz

data.elec.elecpos = cartcoor;
data.elec.chanpos = cartcoor;
data.elec.label = ChannelName; % 'ChannelName' is a cell array of channel
labels
data.elec.unit = 'm';
%
plot3(data.elec.elecpos(:,1),data.elec.elecpos(:,2),data.elec.elecpos(:,3),'r*')
% just check the positions

% make a fieldtrip layout file
cfg = [];
layout = ft_prepare_layout(cfg,data);
cfg.layout    = layout;
ft_layoutplot(cfg,layout); % check the layout


Here is the function converting the theta/phi coordinates to
xyz-coordinates you can use in FieldTrip (Written by Stephan Moratti @UCM).

% Convert electrode positions in polar coordinates (theta, phi like from
*.elp-files)
% into cartesion coordinates
% Electrode positions are assumed to lie on a sphere with radius "radius"
(=1 if not specified)
% sphcoor(2, number of sensors), cartcoor(3, number of sensors)
% Written by Stephan Moratti moratti at med.ucm.es

function cartcoor = elp2coor(sphcoor, radius);

factor = pi/180;

if nargin == 1
radius = 1.0;
end;

[m n] = size(sphcoor);

for i=1:n
projxy = sin(factor*sphcoor(1,i));
cartcoor(3,i) = cos(factor*sphcoor(1,i));

cartcoor(1,i) = projxy*cos(factor*sphcoor(2,i));
cartcoor(2,i) = projxy*sin(factor*sphcoor(2,i));
end;

cartcoor = radius*cartcoor;


Best,
Andrew

On Sat, Feb 25, 2017 at 2:31 PM, Julian Keil <julian.keil at gmail.com> wrote:

> Hi Andrew,
>
> I attached you a function to convert the theta/phi coordinates to
> xyz-coordinates you can use in FieldTrip (Written by Stephan Moratti @UCM).
> To actually use the result, you need to build an electrode structure, so
> do something like this:
>
> cap=importdata('128_channel_easycap.elp'); % Import the Vendor-Provided 3d
> Positions
>
> %% Step 2.1. Make an electrode file
>
> elec.pnt=elp2coor(cap.data',100)';
> elec.label=cap.textdata;
>
> %% Check the positiosn on the head surface. They don't look good, do they?
>
>  figure
>   triplot(vol.bnd(1).pnt, vol.bnd(1).tri,  [], 'edges');
>  hold
>  plot3(elec.pnt(:,1),elec.pnt(:,2),elec.pnt(:,3),'r*')
>
>
> %% Step 3 Move the electrodes to match the head
>
>   cfg=[];
>   cfg.method='interactive';
>   cfg.elec=elec;
>   cfg.headshape=vol.bnd(1);
>
>
>   elec_new=ft_electroderealign(cfg);
>
>
> Good luck,
>
> Julian
>
>
>
>
> ********************
> *Dr. Julian Keil*
>
> AG Multisensorische Integration
> Klinik für Psychiatrie und Psychotherapie
> der Charité im St. Hedwig-Krankenhaus
> Große Hamburger Straße 5-11, Haus 2
> 10115 Berlin
>
> Telefon: +49-30-2311-1879 <+49%2030%2023111879>
> Fax:        +49-30-2311-2209 <+49%2030%2023112209>
> www.multisensorymind.com
>
>
>
> Am 25.02.2017 um 16:39 schrieb Andrew Chang:
>
> Dear FieldTrip users,
>
> I am wondering whether anyone would like to share the Fieldtrip layout
> file of the "*actiCap 96Ch Standard 2*" EEG cap with me. I have checked
> around the websites of Fieldtrip and Easycap, but failed to find anything
> useful. So far I only got it's top-view map and it's Theta/Phi Coordinates
> (see the attached PDFs in the links below).
> https://www.dropbox.com/s/wlshxqb93tn4duz/actiCAP-96-
> channel-Standard-2.pdf?dl=0
> https://www.dropbox.com/s/6bva7az6ydc6hvh/actiCap-96Ch-
> Standard%202%20Theta_Phi_CAP.pdf?dl=0
>
> It would be very appreciated if anyone can share the Fieldtrip layout file
> with me, or teach me how to create a layout in Fieldtrip from Theta/Phi
> Coordinates.
> Thank you all in advance!
>
> Sincerely,
> Andrew
>
>
> --
> Andrew Chang, Ph.D. Candidate
> Vanier Canada Graduate Scholar
> http://changa5.wordpress.com/
>
> Auditory Development Lab
> Department of Psychology, Neuroscience & Behaviour
> McMaster University
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
Andrew Chang, Ph.D. Candidate
Vanier Canada Graduate Scholar
http://changa5.wordpress.com/

Auditory Development Lab
Department of Psychology, Neuroscience & Behaviour
McMaster University
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From marek-b at wp.pl  Sat Feb 25 22:00:04 2017
From: marek-b at wp.pl (Marek)
Date: Sat, 25 Feb 2017 22:00:04 +0100
Subject: [FieldTrip] ft_redefinetrial does not yield correct number of trials
Message-ID: <58b1f0542074c1.66825227@wp.pl>

Hello,
I've got the following problem. When I want to reduce the number of trials in my dataset using syntax: 

cfg = [];
cfg.trials = [1 1 1 1 1 1 1 1 1];
fdata_freq_stim = ft_redefinetrial(cfg, data_freq_stim);

I get the output messages:
the input is raw data with 40 channels and 30 trials
selecting 9 trials
the call to "ft_selectdata" took 0 seconds
the call to "ft_redefinetrial" took 0 seconds

but the resulting variable contains only one trial. In fact, the same output occurs with any setting of cfg.trials, if it contains only ones. The resulting variable contains only one trial, while the message correctly reports the number of selected trials.

When using 

cfg.trials = [1 0 0 1 1];

an error message appears:
the input is raw data with 40 channels and 30 trials
selecting 9 trials
Subscript indices must either be real positive integers or logicals.

What is wrong here? Any help would be appreciated.

MATLAB Version: 8.6.0.267246 (R2015b)
FieldTrip version: fieldtrip-20170224

Thanks,
Marek






From jb.eichenlaub at gmail.com  Sat Feb 25 23:03:57 2017
From: jb.eichenlaub at gmail.com (Jean-Baptiste Eichenlaub)
Date: Sat, 25 Feb 2017 17:03:57 -0500
Subject: [FieldTrip] ft_redefinetrial does not yield correct number of
	trials
In-Reply-To: <58b1f0542074c1.66825227@wp.pl>
References: <58b1f0542074c1.66825227@wp.pl>
Message-ID: <CAPtiWEc88=+k_SE8qpSPpiEx-x5_3OEKxwwk7n+mpR4K4rfqcQ@mail.gmail.com>

The documentation says:

cfg.trials       = 'all' or a selection given as a 1xN vector (default = 'all')

In your case, cfg.trials should be as 1xN vector containing trials' index
e.g. cfg.trials = [1:9] or cfg.trials = [1,2,3,6,8,45,67,69,89].

Thanks,

jb


On Sat, Feb 25, 2017 at 4:00 PM, Marek <marek-b at wp.pl> wrote:

> Hello,
> I've got the following problem. When I want to reduce the number of trials
> in my dataset using syntax:
>
> cfg = [];
> cfg.trials = [1 1 1 1 1 1 1 1 1];
> fdata_freq_stim = ft_redefinetrial(cfg, data_freq_stim);
>
> I get the output messages:
> the input is raw data with 40 channels and 30 trials
> selecting 9 trials
> the call to "ft_selectdata" took 0 seconds
> the call to "ft_redefinetrial" took 0 seconds
>
> but the resulting variable contains only one trial. In fact, the same
> output occurs with any setting of cfg.trials, if it contains only ones. The
> resulting variable contains only one trial, while the message correctly
> reports the number of selected trials.
>
> When using
>
> cfg.trials = [1 0 0 1 1];
>
> an error message appears:
> the input is raw data with 40 channels and 30 trials
> selecting 9 trials
> Subscript indices must either be real positive integers or logicals.
>
> What is wrong here? Any help would be appreciated.
>
> MATLAB Version: 8.6.0.267246 (R2015b)
> FieldTrip version: fieldtrip-20170224
>
> Thanks,
> Marek
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
Jean-Baptiste Eichenlaub, PhD
MGH - Harvard Medical School
Boston, US
jb.eichenlaub at gmail.com
(1)857-654-3879
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From tzvetan.popov at uni-konstanz.de  Mon Feb 27 14:23:42 2017
From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov)
Date: Mon, 27 Feb 2017 14:23:42 +0100
Subject: [FieldTrip] simulating a dipole with a real headmodel and using
	DICS to locate it misplaces the source
In-Reply-To: <8610b87c-d0cd-9678-902b-795da6445d73@th-ht.de>
References: <8610b87c-d0cd-9678-902b-795da6445d73@th-ht.de>
Message-ID: <4D1A2E5F-9D06-4F6D-89AF-C7375DCD1DDC@uni-konstanz.de>

Hi Thomas,

you might have solved it. In case not, I changed :
cfg.relnoise = 5;

and the amplitude of the baseline signal to

cfg.dip.amplitude = .1; 

and it worked. You simulate the location at 9 0 6 and it comes out (NAI) at 90.5 -.5 59.5 (see attached). 

best 
tzvetan




> hi,
> 
> i wanted to see whether i can simulate a dipole with the data provided by the tutorial and use the DICS beamformer to see where the source gets projected.
> 
> the code i used is in the attached file.
> 
> it expects the data you can download from here: ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer/
> 
> in a folder called "beamformer".
> 
> the puzzling thing is that i do not seem to manage to have it project the sources anywhere near to the original dipole in the simulation. the center of the head bias come out nicely if neither baseline correction or NAI calculation is used. i also checked whether the the coordinate system of the volume and the grid i generate match. i also checked whether the chosen dipole shows up at the correct location when i plot it on the head model.
> 
> so, my question is: what do i not get here? maybe there is something wrong with my script? maybe ft_dipolesimulate is not supposed to be used that way?
> 
> i would really appreciate any suggestions.
> 
> best,
> thomas
> 
> ps: i also tried with eloreta and a simple dipole fit. the results look slightly different but not really any better...
> 
> -- 
> Dr. Thomas Hartmann
> 
> Centre for Cognitive Neuroscience
> FB Psychologie
> Universität Salzburg
> Hellbrunnerstraße 34/II
> 5020 Salzburg
> 
> Tel: +43 662 8044 5109
> Email: thomas.hartmann at th-ht.de
> 
> "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan Doyle)
> 
> <test_for_list.m>_______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From thomas.hartmann at th-ht.de  Mon Feb 27 15:57:23 2017
From: thomas.hartmann at th-ht.de (Thomas Hartmann)
Date: Mon, 27 Feb 2017 15:57:23 +0100
Subject: [FieldTrip] simulating a dipole with a real headmodel and using
 DICS to locate it misplaces the source
In-Reply-To: <4D1A2E5F-9D06-4F6D-89AF-C7375DCD1DDC@uni-konstanz.de>
References: <8610b87c-d0cd-9678-902b-795da6445d73@th-ht.de>
 <4D1A2E5F-9D06-4F6D-89AF-C7375DCD1DDC@uni-konstanz.de>
Message-ID: <ab5a118a-7dc1-9a4e-aca5-e7107a1acf44@th-ht.de>

thanks a lot, tzvetan! i seem to have misinterpreted the meaning of 
cfg.absnoise. i thought it had the same scale as the cfg.dip.amplitude.

thanks again and all the best,
thomas


Am 27.02.2017 um 14:23 schrieb Tzvetan Popov:
> Hi Thomas,
>
> you might have solved it. In case not, I changed :
> cfg.relnoise = 5;
>
> and the amplitude of the baseline signal to
>
> cfg.dip.amplitude = .1;
>
> and it worked. You simulate the location at 9 0 6 and it comes out 
> (NAI) at 90.5 -.5 59.5 (see attached).
>
> best
> tzvetan
>
>
>
>> hi,
>>
>> i wanted to see whether i can simulate a dipole with the data 
>> provided by the tutorial and use the DICS beamformer to see where the 
>> source gets projected.
>>
>> the code i used is in the attached file.
>>
>> it expects the data you can download from here: 
>> ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer/
>>
>> in a folder called "beamformer".
>>
>> the puzzling thing is that i do not seem to manage to have it project 
>> the sources anywhere near to the original dipole in the simulation. 
>> the center of the head bias come out nicely if neither baseline 
>> correction or NAI calculation is used. i also checked whether the the 
>> coordinate system of the volume and the grid i generate match. i also 
>> checked whether the chosen dipole shows up at the correct location 
>> when i plot it on the head model.
>>
>> so, my question is: what do i not get here? maybe there is something 
>> wrong with my script? maybe ft_dipolesimulate is not supposed to be 
>> used that way?
>>
>> i would really appreciate any suggestions.
>>
>> best,
>> thomas
>>
>> ps: i also tried with eloreta and a simple dipole fit. the results 
>> look slightly different but not really any better...
>>
>> -- 
>> Dr. Thomas Hartmann
>>
>> Centre for Cognitive Neuroscience
>> FB Psychologie
>> Universität Salzburg
>> Hellbrunnerstraße 34/II
>> 5020 Salzburg
>>
>> Tel: +43 662 8044 5109
>> Email: thomas.hartmann at th-ht.de <mailto:thomas.hartmann at th-ht.de>
>>
>> "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur 
>> Conan Doyle)
>>
>> <test_for_list.m>_______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip

-- 
Dr. Thomas Hartmann

Centre for Cognitive Neuroscience
FB Psychologie
Universität Salzburg
Hellbrunnerstraße 34/II
5020 Salzburg

Tel: +43 662 8044 5109
Email: thomas.hartmann at th-ht.de

"I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan Doyle)

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From michak at is.umk.pl  Tue Feb 28 01:24:05 2017
From: michak at is.umk.pl (=?UTF-8?Q?Micha=C5=82_Komorowski?=)
Date: Tue, 28 Feb 2017 01:24:05 +0100
Subject: [FieldTrip] Clustering algorithm used in sourcestatistics
	(montecarlo)
Message-ID: <CAEJSOqh7J7-ioMFvQVvcfFoHN1fW8FNBTKa9esWES1S9BYyWXQ@mail.gmail.com>

Dear Fieldtrippers,

Does anybody know what clustering algorithm is used
in ft_statistics_montecarlo (ft_sourcestatistics with cfg.correctm =
'cluster') when analysing data from ft_sourceanalysis?

It seems like spm_bwlabel function is used, but I have not found an open
source.

Any help would be greatly appreciated.

-- 
Michał Komorowski, MSc
Nicolaus Copernicus University in Toruń
Faculty of Physics, Astronomy and Informatics
Department of Informatics
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From maity_winky at yahoo.es  Tue Feb 28 11:13:15 2017
From: maity_winky at yahoo.es (=?UTF-8?Q?Mait=C3=A9_Crespo_Garc=C3=ADa?=)
Date: Tue, 28 Feb 2017 10:13:15 +0000 (UTC)
Subject: [FieldTrip] Clustering algorithm used in
	sourcestatistics	(montecarlo)
In-Reply-To: <CAEJSOqh7J7-ioMFvQVvcfFoHN1fW8FNBTKa9esWES1S9BYyWXQ@mail.gmail.com>
References: <CAEJSOqh7J7-ioMFvQVvcfFoHN1fW8FNBTKa9esWES1S9BYyWXQ@mail.gmail.com>
Message-ID: <868712641.4147303.1488276795779@mail.yahoo.com>

Hi Michal,
The 'ft_statistics_montecarlo' uses as default the maxsum statistic and the algorithms for clustering are in the 'clusterstat' function, inside the private folder. Is that what you mean?
Best wishes,Maité
 

    El Martes 28 de febrero de 2017 1:40, Michał Komorowski <michak at is.umk.pl> escribió:
 

 

Dear Fieldtrippers,
Does anybody know what clustering algorithm is used in ft_statistics_montecarlo (ft_sourcestatistics with cfg.correctm = 'cluster') when analysing data from ft_sourceanalysis?

It seems like spm_bwlabel function is used, but I have not found an open source.
Any help would be greatly appreciated.

-- 
Michał Komorowski, MScNicolaus Copernicus University in ToruńFaculty of Physics, Astronomy and Informatics
Department of Informatics
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip

   
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From michak at is.umk.pl  Tue Feb 28 11:39:06 2017
From: michak at is.umk.pl (=?UTF-8?Q?Micha=C5=82_Komorowski?=)
Date: Tue, 28 Feb 2017 11:39:06 +0100
Subject: [FieldTrip] Clustering algorithm used in sourcestatistics
	(montecarlo)
In-Reply-To: <868712641.4147303.1488276795779@mail.yahoo.com>
References: <CAEJSOqh7J7-ioMFvQVvcfFoHN1fW8FNBTKa9esWES1S9BYyWXQ@mail.gmail.com>
 <868712641.4147303.1488276795779@mail.yahoo.com>
Message-ID: <CAEJSOqiGRNVfMXBFp3X2H7XzPuCA4WiPDuYA1ZiJuVXDF341QQ@mail.gmail.com>

Hey,

Not exactly.
Function 'clusterstat' takes advantage of 'spm_bwlabel' function to
clusterize data, then it computes a cluster-level statistic.

I want to know what algorithm is used: k-means? DBSCAN? Other ?

Thank you for your fast reply.

2017-02-28 11:13 GMT+01:00 Maité Crespo García <maity_winky at yahoo.es>:

> Hi Michal,
>
> The 'ft_statistics_montecarlo' uses as default the maxsum statistic and
> the algorithms for clustering are in the 'clusterstat' function, inside the
> private folder. Is that what you mean?
>
> Best wishes,
> Maité
>
>
> El Martes 28 de febrero de 2017 1:40, Michał Komorowski <michak at is.umk.pl>
> escribió:
>
>
>
>
> Dear Fieldtrippers,
>
> Does anybody know what clustering algorithm is used
> in ft_statistics_montecarlo (ft_sourcestatistics with cfg.correctm =
> 'cluster') when analysing data from ft_sourceanalysis?
>
> It seems like spm_bwlabel function is used, but I have not found an open
> source.
>
> Any help would be greatly appreciated.
>
> --
> Michał Komorowski, MSc
> Nicolaus Copernicus University in Toruń
> Faculty of Physics, Astronomy and Informatics
> Department of Informatics
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
Michał Komorowski, MSc
Nicolaus Copernicus University in Toruń
Faculty of Physics, Astronomy and Informatics
Department of Informatics
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From jan.schoffelen at donders.ru.nl  Tue Feb 28 11:45:55 2017
From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Tue, 28 Feb 2017 10:45:55 +0000
Subject: [FieldTrip] Clustering algorithm used in
	sourcestatistics	(montecarlo)
In-Reply-To: <CAEJSOqiGRNVfMXBFp3X2H7XzPuCA4WiPDuYA1ZiJuVXDF341QQ@mail.gmail.com>
References: <CAEJSOqh7J7-ioMFvQVvcfFoHN1fW8FNBTKa9esWES1S9BYyWXQ@mail.gmail.com>
 <868712641.4147303.1488276795779@mail.yahoo.com>
 <CAEJSOqiGRNVfMXBFp3X2H7XzPuCA4WiPDuYA1ZiJuVXDF341QQ@mail.gmail.com>
Message-ID: <E57892AC-3503-44E1-B43B-D3A54727AE4C@donders.ru.nl>

spm_bwlabel is inspired by the image toolbox function bwlabeln. So it looks for spatial contiguity in an n-dimensional volume.

JM


J.M.Schoffelen, MD PhD
Senior Researcher, VIDI-fellow
Telephone: +31-24-3614793
Physical location: room 00.028
Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands



On 28 Feb 2017, at 11:39, Michał Komorowski <michak at is.umk.pl<mailto:michak at is.umk.pl>> wrote:

Hey,

Not exactly.
Function 'clusterstat' takes advantage of 'spm_bwlabel' function to clusterize data, then it computes a cluster-level statistic.

I want to know what algorithm is used: k-means? DBSCAN? Other ?

Thank you for your fast reply.

2017-02-28 11:13 GMT+01:00 Maité Crespo García <maity_winky at yahoo.es<mailto:maity_winky at yahoo.es>>:
Hi Michal,

The 'ft_statistics_montecarlo' uses as default the maxsum statistic and the algorithms for clustering are in the 'clusterstat' function, inside the private folder. Is that what you mean?

Best wishes,
Maité


El Martes 28 de febrero de 2017 1:40, Michał Komorowski <michak at is.umk.pl<mailto:michak at is.umk.pl>> escribió:




Dear Fieldtrippers,

Does anybody know what clustering algorithm is used in ft_statistics_montecarlo (ft_sourcestatistics with cfg.correctm = 'cluster') when analysing data from ft_sourceanalysis?

It seems like spm_bwlabel function is used, but I have not found an open source.

Any help would be greatly appreciated.

--
Michał Komorowski, MSc
Nicolaus Copernicus University in Toruń
Faculty of Physics, Astronomy and Informatics
Department of Informatics

_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip


_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip



--
Michał Komorowski, MSc
Nicolaus Copernicus University in Toruń
Faculty of Physics, Astronomy and Informatics
Department of Informatics
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip




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From mmagnuski at swps.edu.pl  Tue Feb 28 11:58:53 2017
From: mmagnuski at swps.edu.pl (=?UTF-8?Q?Miko=C5=82aj_Magnuski?=)
Date: Tue, 28 Feb 2017 11:58:53 +0100
Subject: [FieldTrip] Clustering algorithm used in sourcestatistics
	(montecarlo)
In-Reply-To: <CAEJSOqiGRNVfMXBFp3X2H7XzPuCA4WiPDuYA1ZiJuVXDF341QQ@mail.gmail.com>
References: <CAEJSOqh7J7-ioMFvQVvcfFoHN1fW8FNBTKa9esWES1S9BYyWXQ@mail.gmail.com>
 <868712641.4147303.1488276795779@mail.yahoo.com>
 <CAEJSOqiGRNVfMXBFp3X2H7XzPuCA4WiPDuYA1ZiJuVXDF341QQ@mail.gmail.com>
Message-ID: <CAN75O0ULMQ=BpQ41wFmnmxUNasoMA7UbfxZgKhKiGFmP+4ojwg@mail.gmail.com>

Hey Michał,

by default it clusters effects that are adjacent (in time, space, frequency
- depending on your search space) above some treshold. The adjacency in
space is defined by adjacency matrix (or more precisely cfg.neighbours
structure).
Take a look at fieldtrip tutorials about nonparametric cluster-based
permitation tests - there should be a reference to the Maris, Oostenveld
2007 paper too.

28.02.2017 11:47 AM "Michał Komorowski" <michak at is.umk.pl> napisał(a):

> Hey,
>
> Not exactly.
> Function 'clusterstat' takes advantage of 'spm_bwlabel' function to
> clusterize data, then it computes a cluster-level statistic.
>
> I want to know what algorithm is used: k-means? DBSCAN? Other ?
>
> Thank you for your fast reply.
>
> 2017-02-28 11:13 GMT+01:00 Maité Crespo García <maity_winky at yahoo.es>:
>
>> Hi Michal,
>>
>> The 'ft_statistics_montecarlo' uses as default the maxsum statistic and
>> the algorithms for clustering are in the 'clusterstat' function, inside the
>> private folder. Is that what you mean?
>>
>> Best wishes,
>> Maité
>>
>>
>> El Martes 28 de febrero de 2017 1:40, Michał Komorowski <michak at is.umk.pl>
>> escribió:
>>
>>
>>
>>
>> Dear Fieldtrippers,
>>
>> Does anybody know what clustering algorithm is used
>> in ft_statistics_montecarlo (ft_sourcestatistics with cfg.correctm =
>> 'cluster') when analysing data from ft_sourceanalysis?
>>
>> It seems like spm_bwlabel function is used, but I have not found an open
>> source.
>>
>> Any help would be greatly appreciated.
>>
>> --
>> Michał Komorowski, MSc
>> Nicolaus Copernicus University in Toruń
>> Faculty of Physics, Astronomy and Informatics
>> Department of Informatics
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
>
> --
> Michał Komorowski, MSc
> Nicolaus Copernicus University in Toruń
> Faculty of Physics, Astronomy and Informatics
> Department of Informatics
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>

-- 

------------------------------
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