[FieldTrip] fieldtrip Digest, Vol 118, Issue 27
RICHARDS, JOHN
RICHARDS at mailbox.sc.edu
Mon Sep 28 17:37:03 CEST 2020
"Unified segmentation"... just happening to be studying this in a MRI neuroimaging class. This is the SPM12 segmenting scheme.
SPM12 segmentation does the following:
Register the head to a MNI avg template
use the MNI avg template priors for GM/WM/"OM" ("OM" is the third class, not-WM not-GM, but not necessarily csf)
Create gm/wm/om/skull/"softtissue" segmented files.
Can be done with linear reg, or nonlinear reg (I think "DARTEL")
These could be used as the segmented head values for the FT methods. You can also get "brain" from bin(gm)+bin(wm)+bin(om).
There are two or three articles on my www site where I have Supplementary Info additions describing the segmenting via FSL and FT calls. We use eLORETA as our inverse constraint.
John
***********************************************
John E. Richards
Carolina Distinguished Professor
Department of Psychology
University of South Carolina
Columbia, SC 29208
Dept Phone: 803 777 2079
Fax: 803 777 9558
Email: richards-john at sc.edu
https://jerlab.sc.edu
*************************************************
-----Original Message-----
From: fieldtrip [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of fieldtrip-request at science.ru.nl
Sent: Monday, September 28, 2020 11:25 AM
To: fieldtrip at science.ru.nl
Subject: fieldtrip Digest, Vol 118, Issue 27
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..."
Today's Topics:
1. Re: eLORETA source analysis (tibor.auer at gmail.com)
2. Re: eLORETA source analysis (Schoffelen, J.M. (Jan Mathijs))
3. Re: eLORETA source analysis (tibor.auer at gmail.com)
4. Re: eLORETA source analysis (Schoffelen, J.M. (Jan Mathijs))
5. Re: eLORETA source analysis (tibor.auer at gmail.com)
----------------------------------------------------------------------
Message: 1
Date: Mon, 28 Sep 2020 12:52:17 +0100
From: <tibor.auer at gmail.com>
To: "'FieldTrip discussion list'" <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] eLORETA source analysis
Message-ID: <064c01d6958d$d1085580$73190080$@gmail.com>
Content-Type: text/plain; charset="utf-8"
Thank you, Jan-Mathijs,
This link is very instructive. I wonder why it eluded me so far. 😊
If I get it right, you recommend using approach based on the cortical sheet because 1) the tutorial for 3D grid is not there yet and 2) I can use results from cortical sheet directly for group analysis.
Kind regards,
Tibor
Auer, Tibor M.D. Ph.D.
Research Fellow
School of Psychology, Faculty of Health and Medical Sciences
University of Surrey, Guildford GU2 7XH
<mailto:T.Auer at surrey.ac.uk> T.Auer at surrey.ac.uk
<https://protect2.fireeye.com/v1/url?k=13286c66-4db66f3d-132822a7-86324fd7403a-07fd78f19c71453b&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=https%3A%2F%2Feur02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Ftwitter.com%252FTiborAuer%26data%3D02%257C01%257Ct.auer%2540surrey.ac.uk%257Cdb32da458c424eedef2908d7d4bd1421%257C6b902693107440aa9e21d89446a2ebb5%257C0%257C0%257C637211780868086968%26sdata%3DzrT5%252FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%253D%26reserved%3D0> @TiborAuer
From: fieldtrip <fieldtrip-bounces at science.ru.nl> On Behalf Of Schoffelen, J.M. (Jan Mathijs)
Sent: Monday, September 28, 2020 10:21 AM
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] eLORETA source analysis
Dear Tibor,
It’s not clear to me what’s special about spm’s ‘unified segmentation’ regarding the creation of source models.
I assume you are aware that source models eventually need to be in the subject’s native space in order for them to be useable.
Documentation about how to create a source model for EEG/MEG source reconstruction can be found at: https://protect2.fireeye.com/v1/url?k=971f155c-c9811607-971f5b9d-86324fd7403a-15ca69c7ec8c729a&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=http%3A%2F%2Fwww.fieldtriptoolbox.org%2Ftutorial%2Fsourcemodel%2F, which might be a good starting point.
Best wishes,
Jan-Mathijs
On 28 Sep 2020, at 10:03, tibor.auer at gmail.com <mailto:tibor.auer at gmail.com> wrote:
Hi Jan-Mathijs,
Thank you for your response. I found that post earlier and noticed that I may need to redo the freqanalysis, however, I still do not know how do I create the sourcemodel from the T1-weighted MRI images already segmented with SPM12.
Kind regards,
Tibor
Auer, Tibor M.D. Ph.D.
Research Fellow
School of Psychology, Faculty of Health and Medical Sciences
University of Surrey, Guildford GU2 7XH
<mailto:T.Auer at surrey.ac.uk> T.Auer at surrey.ac.uk
<https://protect2.fireeye.com/v1/url?k=07ee2e64-59702d3f-07ee60a5-86324fd7403a-f6f044115a9886ab&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=https%3A%2F%2Feur02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Ftwitter.com%252FTiborAuer%26data%3D02%257C01%257Ct.auer%2540surrey.ac.uk%257Cdb32da458c424eedef2908d7d4bd1421%257C6b902693107440aa9e21d89446a2ebb5%257C0%257C0%257C637211780868086968%26sdata%3DzrT5%252FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%253D%26reserved%3D0> @TiborAuer
From: fieldtrip <fieldtrip-bounces at science.ru.nl <mailto:fieldtrip-bounces at science.ru.nl> > On Behalf Of Schoffelen, J.M. (Jan Mathijs)
Sent: Thursday, September 24, 2020 8:12 AM
To: FieldTrip discussion list <fieldtrip at science.ru.nl <mailto:fieldtrip at science.ru.nl> >
Subject: Re: [FieldTrip] eLORETA source analysis
Hi Tibor,
Some of this is discussed (and fixed, there were some small issues in the code) in https://protect2.fireeye.com/v1/url?k=bbf94052-e5674309-bbf90e93-86324fd7403a-f49e8cbd75d6224f&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=https%3A%2F%2Fgithub.com%2Ffieldtrip%2Ffieldtrip%2Fissues%2F1454 and the PR that is linked in the linked issue.
Note: if you want to go from sensor-level to source-level data in the frequency domain, you should either use ‘powandcsd’, or ‘fourier’ as cfg.output argument to ft_freqanalysis.
Best wishes,
Jan-Mathijs
On 23 Sep 2020, at 13:42, tibor.auer at gmail.com <mailto:tibor.auer at gmail.com> wrote:
Dear Community,
I would like to perform an eLORETA source analysis, however, I am unsure about the steps.
I am working on the <https://protect2.fireeye.com/v1/url?k=e6991212-b8071149-e6995cd3-86324fd7403a-22b5e3dddec11468&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=http%3A%2F%2Ffcon_1000.projects.nitrc.org%2Findi%2Fretro%2FMPI_LEMON.html> LEMON data including 62-channel EEG experiment at rest and structural (T1-weighted) MRI of >200 participants.
I have preprocessed the EEG data and performed timefrequency analysis on the 2-second-long epochs with configuration:
* method: 'mtmfft'
* taper: 'hanning'
* foi: [0.9766 1.9531 3.9062 5.8594 7.8125 12.2070 15.1367 20.0195 24.9023 32.2266 40.0391 60.0586 69.8242 80.0781 95.2148 109.8633 120.1172]
* pad: 2.0480
* output: 'pow'
* keeptrials: 'no'
* trials: [233×1 double]
I have also processed the MRI images and normalised-segmented them using SPM12’s unified segmentation outside FieldTrip.
I would appreciate any help including code snippets, pointers to (order of) functions or specific and detailed tutorials.
Kind regards,
Tibor
Auer, Tibor M.D. Ph.D.
Research Fellow
School of Psychology, Faculty of Health and Medical Sciences
University of Surrey, Guildford GU2 7XH
<https://protect2.fireeye.com/v1/url?k=c45fc61f-9ac1c544-c45f88de-86324fd7403a-a791cb1d4ee31f81&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=https%3A%2F%2Feur02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Ftwitter.com%252FTiborAuer%26data%3D02%257C01%257Ct.auer%2540surrey.ac.uk%257Cdb32da458c424eedef2908d7d4bd1421%257C6b902693107440aa9e21d89446a2ebb5%257C0%257C0%257C637211780868086968%26sdata%3DzrT5%252FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%253D%26reserved%3D0> @TiborAuer
dy>_______________________________________________
fieldtrip mailing list
<https://mailman.science.ru.nl/mailman/listinfo/fieldtrip> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
<https://doi.org/10.1371/journal.pcbi.1002202> https://doi.org/10.1371/journal.pcbi.1002202
v>_______________________________________________
fieldtrip mailing list
<https://mailman.science.ru.nl/mailman/listinfo/fieldtrip> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
<https://doi.org/10.1371/journal.pcbi.1002202> https://doi.org/10.1371/journal.pcbi.1002202
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20200928/e1928a28/attachment-0001.htm>
------------------------------
Message: 2
Date: Mon, 28 Sep 2020 12:05:27 +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] eLORETA source analysis
Message-ID: <D14C0BEE-D95F-4779-9C64-F6593B38AB1C at donders.ru.nl>
Content-Type: text/plain; charset="utf-8"
Hi Tibor,
Well, I don’t have a strong recommendation to go for either, apart from the fact that a distributed source reconstruction method (such as eLORETA) benefits from an accurate source model to begin with. Also, it depends on what you aim in your source reconstruction. Limiting yourself to the cortical sheet gets rid subcortical structures/cerebellum.
Regarding 3D grids, there is some stuff that relates to 3D grids, isn’t there?
Best wishes,
JM
On 28 Sep 2020, at 13:52, tibor.auer at gmail.com<mailto:tibor.auer at gmail.com> wrote:
Thank you, Jan-Mathijs,
This link is very instructive. I wonder why it eluded me so far. 😊
If I get it right, you recommend using approach based on the cortical sheet because 1) the tutorial for 3D grid is not there yet and 2) I can use results from cortical sheet directly for group analysis.
Kind regards,
Tibor
Auer, Tibor M.D. Ph.D.
Research Fellow
School of Psychology, Faculty of Health and Medical Sciences University of Surrey, Guildford GU2 7XH T.Auer at surrey.ac.uk<mailto:T.Auer at surrey.ac.uk>
@TiborAuer<https://protect2.fireeye.com/v1/url?k=3d203523-63be3678-3d207be2-86324fd7403a-5f60a742bb3e0206&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=https%3A%2F%2Feur02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Ftwitter.com%252FTiborAuer%26data%3D02%257C01%257Ct.auer%2540surrey.ac.uk%257Cdb32da458c424eedef2908d7d4bd1421%257C6b902693107440aa9e21d89446a2ebb5%257C0%257C0%257C637211780868086968%26sdata%3DzrT5%252FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%253D%26reserved%3D0>
From: fieldtrip <fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>> On Behalf Of Schoffelen, J.M. (Jan Mathijs)
Sent: Monday, September 28, 2020 10:21 AM
To: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Subject: Re: [FieldTrip] eLORETA source analysis
Dear Tibor,
It’s not clear to me what’s special about spm’s ‘unified segmentation’ regarding the creation of source models.
I assume you are aware that source models eventually need to be in the subject’s native space in order for them to be useable.
Documentation about how to create a source model for EEG/MEG source reconstruction can be found at: https://protect2.fireeye.com/v1/url?k=18f2f008-466cf353-18f2bec9-86324fd7403a-c4733859a5237b55&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=http%3A%2F%2Fwww.fieldtriptoolbox.org%2Ftutorial%2Fsourcemodel%2F, which might be a good starting point.
Best wishes,
Jan-Mathijs
On 28 Sep 2020, at 10:03, tibor.auer at gmail.com<mailto:tibor.auer at gmail.com> wrote:
Hi Jan-Mathijs,
Thank you for your response. I found that post earlier and noticed that I may need to redo the freqanalysis, however, I still do not know how do I create the sourcemodel from the T1-weighted MRI images already segmented with SPM12.
Kind regards,
Tibor
Auer, Tibor M.D. Ph.D.
Research Fellow
School of Psychology, Faculty of Health and Medical Sciences University of Surrey, Guildford GU2 7XH T.Auer at surrey.ac.uk<mailto:T.Auer at surrey.ac.uk>
@TiborAuer<https://protect2.fireeye.com/v1/url?k=598b5f68-07155c33-598b11a9-86324fd7403a-d6d14b48e49b38b4&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=https%3A%2F%2Feur02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Ftwitter.com%252FTiborAuer%26data%3D02%257C01%257Ct.auer%2540surrey.ac.uk%257Cdb32da458c424eedef2908d7d4bd1421%257C6b902693107440aa9e21d89446a2ebb5%257C0%257C0%257C637211780868086968%26sdata%3DzrT5%252FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%253D%26reserved%3D0>
From: fieldtrip <fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>> On Behalf Of Schoffelen, J.M. (Jan Mathijs)
Sent: Thursday, September 24, 2020 8:12 AM
To: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Subject: Re: [FieldTrip] eLORETA source analysis
Hi Tibor,
Some of this is discussed (and fixed, there were some small issues in the code) in https://protect2.fireeye.com/v1/url?k=be948000-e00a835b-be94cec1-86324fd7403a-1ba11a05bac0c948&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=https%3A%2F%2Fgithub.com%2Ffieldtrip%2Ffieldtrip%2Fissues%2F1454 and the PR that is linked in the linked issue.
Note: if you want to go from sensor-level to source-level data in the frequency domain, you should either use ‘powandcsd’, or ‘fourier’ as cfg.output argument to ft_freqanalysis.
Best wishes,
Jan-Mathijs
On 23 Sep 2020, at 13:42, tibor.auer at gmail.com<mailto:tibor.auer at gmail.com> wrote:
Dear Community,
I would like to perform an eLORETA source analysis, however, I am unsure about the steps.
I am working on the LEMON data<https://protect2.fireeye.com/v1/url?k=35809974-6b1e9a2f-3580d7b5-86324fd7403a-546b71cc01f17de3&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=http%3A%2F%2Ffcon_1000.projects.nitrc.org%2Findi%2Fretro%2FMPI_LEMON.html> including 62-channel EEG experiment at rest and structural (T1-weighted) MRI of >200 participants.
I have preprocessed the EEG data and performed timefrequency analysis on the 2-second-long epochs with configuration:
* method: 'mtmfft'
* taper: 'hanning'
* foi: [0.9766 1.9531 3.9062 5.8594 7.8125 12.2070 15.1367 20.0195 24.9023 32.2266 40.0391 60.0586 69.8242 80.0781 95.2148 109.8633 120.1172]
* pad: 2.0480
* output: 'pow'
* keeptrials: 'no'
* trials: [233×1 double]
I have also processed the MRI images and normalised-segmented them using SPM12’s unified segmentation outside FieldTrip.
I would appreciate any help including code snippets, pointers to (order of) functions or specific and detailed tutorials.
Kind regards,
Tibor
Auer, Tibor M.D. Ph.D.
Research Fellow
School of Psychology, Faculty of Health and Medical Sciences University of Surrey, Guildford GU2 7XH @TiborAuer<https://protect2.fireeye.com/v1/url?k=daf734ee-846937b5-daf77a2f-86324fd7403a-4a23e0d2d5a8bae3&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=https%3A%2F%2Feur02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Ftwitter.com%252FTiborAuer%26data%3D02%257C01%257Ct.auer%2540surrey.ac.uk%257Cdb32da458c424eedef2908d7d4bd1421%257C6b902693107440aa9e21d89446a2ebb5%257C0%257C0%257C637211780868086968%26sdata%3DzrT5%252FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%253D%26reserved%3D0>
dy>_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202
v>_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202
_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20200928/1ca84196/attachment-0001.htm>
------------------------------
Message: 3
Date: Mon, 28 Sep 2020 15:20:33 +0100
From: <tibor.auer at gmail.com>
To: "'FieldTrip discussion list'" <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] eLORETA source analysis
Message-ID: <003801d695a2$87829190$9687b4b0$@gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi JM,
Thank you for the information.
Regarding 3D grids, the https://protect2.fireeye.com/v1/url?k=aeef8424-f071877f-aeefcae5-86324fd7403a-bc81ef9be11fe8be&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=http%3A%2F%2Fwww.fieldtriptoolbox.org%2Ftutorial%2Fsourcemodel%2F%23construction-of-a-source-model-based-on-a-regular-3-dimensional-grid-of-dipole-positions section says “Content is coming soon!”. Only the steps required for group analysis are detailed.
Kind regards,
Tibor
Auer, Tibor M.D. Ph.D.
Research Fellow
School of Psychology, Faculty of Health and Medical Sciences
University of Surrey, Guildford GU2 7XH
<mailto:T.Auer at surrey.ac.uk> T.Auer at surrey.ac.uk
<https://protect2.fireeye.com/v1/url?k=607892b2-3ee691e9-6078dc73-86324fd7403a-42795158b0dd1f88&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=https%3A%2F%2Feur02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Ftwitter.com%252FTiborAuer%26data%3D02%257C01%257Ct.auer%2540surrey.ac.uk%257Cdb32da458c424eedef2908d7d4bd1421%257C6b902693107440aa9e21d89446a2ebb5%257C0%257C0%257C637211780868086968%26sdata%3DzrT5%252FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%253D%26reserved%3D0> @TiborAuer
From: fieldtrip <fieldtrip-bounces at science.ru.nl> On Behalf Of Schoffelen, J.M. (Jan Mathijs)
Sent: Monday, September 28, 2020 1:05 PM
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] eLORETA source analysis
Hi Tibor,
Well, I don’t have a strong recommendation to go for either, apart from the fact that a distributed source reconstruction method (such as eLORETA) benefits from an accurate source model to begin with. Also, it depends on what you aim in your source reconstruction. Limiting yourself to the cortical sheet gets rid subcortical structures/cerebellum.
Regarding 3D grids, there is some stuff that relates to 3D grids, isn’t there?
Best wishes,
JM
On 28 Sep 2020, at 13:52, tibor.auer at gmail.com <mailto:tibor.auer at gmail.com> wrote:
Thank you, Jan-Mathijs,
This link is very instructive. I wonder why it eluded me so far. 😊
If I get it right, you recommend using approach based on the cortical sheet because 1) the tutorial for 3D grid is not there yet and 2) I can use results from cortical sheet directly for group analysis.
Kind regards,
Tibor
Auer, Tibor M.D. Ph.D.
Research Fellow
School of Psychology, Faculty of Health and Medical Sciences
University of Surrey, Guildford GU2 7XH
<mailto:T.Auer at surrey.ac.uk> T.Auer at surrey.ac.uk
<https://protect2.fireeye.com/v1/url?k=64f9a249-3a67a112-64f9ec88-86324fd7403a-56f02a632367217c&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=https%3A%2F%2Feur02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Ftwitter.com%252FTiborAuer%26data%3D02%257C01%257Ct.auer%2540surrey.ac.uk%257Cdb32da458c424eedef2908d7d4bd1421%257C6b902693107440aa9e21d89446a2ebb5%257C0%257C0%257C637211780868086968%26sdata%3DzrT5%252FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%253D%26reserved%3D0> @TiborAuer
From: fieldtrip <fieldtrip-bounces at science.ru.nl <mailto:fieldtrip-bounces at science.ru.nl> > On Behalf Of Schoffelen, J.M. (Jan Mathijs)
Sent: Monday, September 28, 2020 10:21 AM
To: FieldTrip discussion list <fieldtrip at science.ru.nl <mailto:fieldtrip at science.ru.nl> >
Subject: Re: [FieldTrip] eLORETA source analysis
Dear Tibor,
It’s not clear to me what’s special about spm’s ‘unified segmentation’ regarding the creation of source models.
I assume you are aware that source models eventually need to be in the subject’s native space in order for them to be useable.
Documentation about how to create a source model for EEG/MEG source reconstruction can be found at: https://protect2.fireeye.com/v1/url?k=026a1a9a-5cf419c1-026a545b-86324fd7403a-7fb37d7fda491c6f&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=http%3A%2F%2Fwww.fieldtriptoolbox.org%2Ftutorial%2Fsourcemodel%2F, which might be a good starting point.
Best wishes,
Jan-Mathijs
On 28 Sep 2020, at 10:03, tibor.auer at gmail.com <mailto:tibor.auer at gmail.com> wrote:
Hi Jan-Mathijs,
Thank you for your response. I found that post earlier and noticed that I may need to redo the freqanalysis, however, I still do not know how do I create the sourcemodel from the T1-weighted MRI images already segmented with SPM12.
Kind regards,
Tibor
Auer, Tibor M.D. Ph.D.
Research Fellow
School of Psychology, Faculty of Health and Medical Sciences
University of Surrey, Guildford GU2 7XH
<mailto:T.Auer at surrey.ac.uk> T.Auer at surrey.ac.uk
<https://protect2.fireeye.com/v1/url?k=ace40823-f27a0b78-ace446e2-86324fd7403a-d27868113f91ea71&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=https%3A%2F%2Feur02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Ftwitter.com%252FTiborAuer%26data%3D02%257C01%257Ct.auer%2540surrey.ac.uk%257Cdb32da458c424eedef2908d7d4bd1421%257C6b902693107440aa9e21d89446a2ebb5%257C0%257C0%257C637211780868086968%26sdata%3DzrT5%252FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%253D%26reserved%3D0> @TiborAuer
From: fieldtrip <fieldtrip-bounces at science.ru.nl <mailto:fieldtrip-bounces at science.ru.nl> > On Behalf Of Schoffelen, J.M. (Jan Mathijs)
Sent: Thursday, September 24, 2020 8:12 AM
To: FieldTrip discussion list <fieldtrip at science.ru.nl <mailto:fieldtrip at science.ru.nl> >
Subject: Re: [FieldTrip] eLORETA source analysis
Hi Tibor,
Some of this is discussed (and fixed, there were some small issues in the code) in https://protect2.fireeye.com/v1/url?k=673ab1e0-39a4b2bb-673aff21-86324fd7403a-4bcc281cfa66a185&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=https%3A%2F%2Fgithub.com%2Ffieldtrip%2Ffieldtrip%2Fissues%2F1454 and the PR that is linked in the linked issue.
Note: if you want to go from sensor-level to source-level data in the frequency domain, you should either use ‘powandcsd’, or ‘fourier’ as cfg.output argument to ft_freqanalysis.
Best wishes,
Jan-Mathijs
On 23 Sep 2020, at 13:42, tibor.auer at gmail.com <mailto:tibor.auer at gmail.com> wrote:
Dear Community,
I would like to perform an eLORETA source analysis, however, I am unsure about the steps.
I am working on the <https://protect2.fireeye.com/v1/url?k=ebb599f3-b52b9aa8-ebb5d732-86324fd7403a-44cf6ac076e44450&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=http%3A%2F%2Ffcon_1000.projects.nitrc.org%2Findi%2Fretro%2FMPI_LEMON.html> LEMON data including 62-channel EEG experiment at rest and structural (T1-weighted) MRI of >200 participants.
I have preprocessed the EEG data and performed timefrequency analysis on the 2-second-long epochs with configuration:
* method: 'mtmfft'
* taper: 'hanning'
* foi: [0.9766 1.9531 3.9062 5.8594 7.8125 12.2070 15.1367 20.0195 24.9023 32.2266 40.0391 60.0586 69.8242 80.0781 95.2148 109.8633 120.1172]
* pad: 2.0480
* output: 'pow'
* keeptrials: 'no'
* trials: [233×1 double]
I have also processed the MRI images and normalised-segmented them using SPM12’s unified segmentation outside FieldTrip.
I would appreciate any help including code snippets, pointers to (order of) functions or specific and detailed tutorials.
Kind regards,
Tibor
Auer, Tibor M.D. Ph.D.
Research Fellow
School of Psychology, Faculty of Health and Medical Sciences
University of Surrey, Guildford GU2 7XH
<https://protect2.fireeye.com/v1/url?k=bf1b5dde-e1855e85-bf1b131f-86324fd7403a-1e63c65109523720&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=https%3A%2F%2Feur02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Ftwitter.com%252FTiborAuer%26data%3D02%257C01%257Ct.auer%2540surrey.ac.uk%257Cdb32da458c424eedef2908d7d4bd1421%257C6b902693107440aa9e21d89446a2ebb5%257C0%257C0%257C637211780868086968%26sdata%3DzrT5%252FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%253D%26reserved%3D0> @TiborAuer
dy>_______________________________________________
fieldtrip mailing list
<https://mailman.science.ru.nl/mailman/listinfo/fieldtrip> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
<https://doi.org/10.1371/journal.pcbi.1002202> https://doi.org/10.1371/journal.pcbi.1002202
v>_______________________________________________
fieldtrip mailing list
<https://mailman.science.ru.nl/mailman/listinfo/fieldtrip> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
<https://doi.org/10.1371/journal.pcbi.1002202> https://doi.org/10.1371/journal.pcbi.1002202
_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20200928/e1f7c356/attachment-0001.htm>
------------------------------
Message: 4
Date: Mon, 28 Sep 2020 14:27:53 +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] eLORETA source analysis
Message-ID: <4984D303-1950-40FD-B3CC-BD46BC669A8B at donders.ru.nl>
Content-Type: text/plain; charset="utf-8"
Well, the group analysis section should be sufficient.
Best wishes,
JM
On 28 Sep 2020, at 16:20, tibor.auer at gmail.com<mailto:tibor.auer at gmail.com> wrote:
Hi JM,
Thank you for the information.
Regarding 3D grids, the https://protect2.fireeye.com/v1/url?k=10aa0807-4e340b5c-10aa46c6-86324fd7403a-4ae3bd78860fd58a&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=http%3A%2F%2Fwww.fieldtriptoolbox.org%2Ftutorial%2Fsourcemodel%2F%23construction-of-a-source-model-based-on-a-regular-3-dimensional-grid-of-dipole-positions section says “Content is coming soon!”. Only the steps required for group analysis are detailed.
Kind regards,
Tibor
Auer, Tibor M.D. Ph.D.
Research Fellow
School of Psychology, Faculty of Health and Medical Sciences University of Surrey, Guildford GU2 7XH T.Auer at surrey.ac.uk<mailto:T.Auer at surrey.ac.uk>
@TiborAuer<https://protect2.fireeye.com/v1/url?k=137d5c86-4de35fdd-137d1247-86324fd7403a-edd8dfa0bb169b1f&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=https%3A%2F%2Feur02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Ftwitter.com%252FTiborAuer%26data%3D02%257C01%257Ct.auer%2540surrey.ac.uk%257Cdb32da458c424eedef2908d7d4bd1421%257C6b902693107440aa9e21d89446a2ebb5%257C0%257C0%257C637211780868086968%26sdata%3DzrT5%252FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%253D%26reserved%3D0>
From: fieldtrip <fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>> On Behalf Of Schoffelen, J.M. (Jan Mathijs)
Sent: Monday, September 28, 2020 1:05 PM
To: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Subject: Re: [FieldTrip] eLORETA source analysis
Hi Tibor,
Well, I don’t have a strong recommendation to go for either, apart from the fact that a distributed source reconstruction method (such as eLORETA) benefits from an accurate source model to begin with. Also, it depends on what you aim in your source reconstruction. Limiting yourself to the cortical sheet gets rid subcortical structures/cerebellum.
Regarding 3D grids, there is some stuff that relates to 3D grids, isn’t there?
Best wishes,
JM
On 28 Sep 2020, at 13:52, tibor.auer at gmail.com<mailto:tibor.auer at gmail.com> wrote:
Thank you, Jan-Mathijs,
This link is very instructive. I wonder why it eluded me so far. 😊
If I get it right, you recommend using approach based on the cortical sheet because 1) the tutorial for 3D grid is not there yet and 2) I can use results from cortical sheet directly for group analysis.
Kind regards,
Tibor
Auer, Tibor M.D. Ph.D.
Research Fellow
School of Psychology, Faculty of Health and Medical Sciences University of Surrey, Guildford GU2 7XH T.Auer at surrey.ac.uk<mailto:T.Auer at surrey.ac.uk>
@TiborAuer<https://protect2.fireeye.com/v1/url?k=8a1b9ba0-d48598fb-8a1bd561-86324fd7403a-d9c7b17c8f390c5f&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=https%3A%2F%2Feur02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Ftwitter.com%252FTiborAuer%26data%3D02%257C01%257Ct.auer%2540surrey.ac.uk%257Cdb32da458c424eedef2908d7d4bd1421%257C6b902693107440aa9e21d89446a2ebb5%257C0%257C0%257C637211780868086968%26sdata%3DzrT5%252FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%253D%26reserved%3D0>
From: fieldtrip <fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>> On Behalf Of Schoffelen, J.M. (Jan Mathijs)
Sent: Monday, September 28, 2020 10:21 AM
To: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Subject: Re: [FieldTrip] eLORETA source analysis
Dear Tibor,
It’s not clear to me what’s special about spm’s ‘unified segmentation’ regarding the creation of source models.
I assume you are aware that source models eventually need to be in the subject’s native space in order for them to be useable.
Documentation about how to create a source model for EEG/MEG source reconstruction can be found at: https://protect2.fireeye.com/v1/url?k=ea6ed61b-b4f0d540-ea6e98da-86324fd7403a-3560ac155aaadc31&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=http%3A%2F%2Fwww.fieldtriptoolbox.org%2Ftutorial%2Fsourcemodel%2F, which might be a good starting point.
Best wishes,
Jan-Mathijs
On 28 Sep 2020, at 10:03, tibor.auer at gmail.com<mailto:tibor.auer at gmail.com> wrote:
Hi Jan-Mathijs,
Thank you for your response. I found that post earlier and noticed that I may need to redo the freqanalysis, however, I still do not know how do I create the sourcemodel from the T1-weighted MRI images already segmented with SPM12.
Kind regards,
Tibor
Auer, Tibor M.D. Ph.D.
Research Fellow
School of Psychology, Faculty of Health and Medical Sciences University of Surrey, Guildford GU2 7XH T.Auer at surrey.ac.uk<mailto:T.Auer at surrey.ac.uk>
@TiborAuer<https://protect2.fireeye.com/v1/url?k=2eb5abb1-702ba8ea-2eb5e570-86324fd7403a-0a0e4e8080bd6775&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=https%3A%2F%2Feur02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Ftwitter.com%252FTiborAuer%26data%3D02%257C01%257Ct.auer%2540surrey.ac.uk%257Cdb32da458c424eedef2908d7d4bd1421%257C6b902693107440aa9e21d89446a2ebb5%257C0%257C0%257C637211780868086968%26sdata%3DzrT5%252FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%253D%26reserved%3D0>
From: fieldtrip <fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>> On Behalf Of Schoffelen, J.M. (Jan Mathijs)
Sent: Thursday, September 24, 2020 8:12 AM
To: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Subject: Re: [FieldTrip] eLORETA source analysis
Hi Tibor,
Some of this is discussed (and fixed, there were some small issues in the code) in https://protect2.fireeye.com/v1/url?k=7e74789e-20ea7bc5-7e74365f-86324fd7403a-7b64d5ae3ee03906&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=https%3A%2F%2Fgithub.com%2Ffieldtrip%2Ffieldtrip%2Fissues%2F1454 and the PR that is linked in the linked issue.
Note: if you want to go from sensor-level to source-level data in the frequency domain, you should either use ‘powandcsd’, or ‘fourier’ as cfg.output argument to ft_freqanalysis.
Best wishes,
Jan-Mathijs
On 23 Sep 2020, at 13:42, tibor.auer at gmail.com<mailto:tibor.auer at gmail.com> wrote:
Dear Community,
I would like to perform an eLORETA source analysis, however, I am unsure about the steps.
I am working on the LEMON data<https://protect2.fireeye.com/v1/url?k=2522ae05-7bbcad5e-2522e0c4-86324fd7403a-7b2a0f7132b3f62b&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=http%3A%2F%2Ffcon_1000.projects.nitrc.org%2Findi%2Fretro%2FMPI_LEMON.html> including 62-channel EEG experiment at rest and structural (T1-weighted) MRI of >200 participants.
I have preprocessed the EEG data and performed timefrequency analysis on the 2-second-long epochs with configuration:
* method: 'mtmfft'
* taper: 'hanning'
* foi: [0.9766 1.9531 3.9062 5.8594 7.8125 12.2070 15.1367 20.0195 24.9023 32.2266 40.0391 60.0586 69.8242 80.0781 95.2148 109.8633 120.1172]
* pad: 2.0480
* output: 'pow'
* keeptrials: 'no'
* trials: [233×1 double]
I have also processed the MRI images and normalised-segmented them using SPM12’s unified segmentation outside FieldTrip.
I would appreciate any help including code snippets, pointers to (order of) functions or specific and detailed tutorials.
Kind regards,
Tibor
Auer, Tibor M.D. Ph.D.
Research Fellow
School of Psychology, Faculty of Health and Medical Sciences University of Surrey, Guildford GU2 7XH @TiborAuer<https://protect2.fireeye.com/v1/url?k=6ab401e1-342a02ba-6ab44f20-86324fd7403a-e6be7bdbc0cdf7ef&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=https%3A%2F%2Feur02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Ftwitter.com%252FTiborAuer%26data%3D02%257C01%257Ct.auer%2540surrey.ac.uk%257Cdb32da458c424eedef2908d7d4bd1421%257C6b902693107440aa9e21d89446a2ebb5%257C0%257C0%257C637211780868086968%26sdata%3DzrT5%252FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%253D%26reserved%3D0>
dy>_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202
v>_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202
_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202
div>_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20200928/034b16bd/attachment-0001.htm>
------------------------------
Message: 5
Date: Mon, 28 Sep 2020 16:25:09 +0100
From: <tibor.auer at gmail.com>
To: "'FieldTrip discussion list'" <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] eLORETA source analysis
Message-ID: <006301d695ab$8d6d38e0$a847aaa0$@gmail.com>
Content-Type: text/plain; charset="utf-8"
Do you mean I could simply use <fieldtrip>/template/sourcemodel/standard_sourcemodel3d10mm.mat?
Kind regards,
Tibor
Auer, Tibor M.D. Ph.D.
Research Fellow
School of Psychology, Faculty of Health and Medical Sciences
University of Surrey, Guildford GU2 7XH
<mailto:T.Auer at surrey.ac.uk> T.Auer at surrey.ac.uk
<https://protect2.fireeye.com/v1/url?k=626240ec-3cfc43b7-62620e2d-86324fd7403a-8457e1393355a4ce&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=https%3A%2F%2Feur02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Ftwitter.com%252FTiborAuer%26data%3D02%257C01%257Ct.auer%2540surrey.ac.uk%257Cdb32da458c424eedef2908d7d4bd1421%257C6b902693107440aa9e21d89446a2ebb5%257C0%257C0%257C637211780868086968%26sdata%3DzrT5%252FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%253D%26reserved%3D0> @TiborAuer
From: fieldtrip <fieldtrip-bounces at science.ru.nl> On Behalf Of Schoffelen, J.M. (Jan Mathijs)
Sent: Monday, September 28, 2020 3:28 PM
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] eLORETA source analysis
Well, the group analysis section should be sufficient.
Best wishes,
JM
On 28 Sep 2020, at 16:20, tibor.auer at gmail.com <mailto:tibor.auer at gmail.com> wrote:
Hi JM,
Thank you for the information.
Regarding 3D grids, the https://protect2.fireeye.com/v1/url?k=225c4713-7cc24448-225c09d2-86324fd7403a-cfbe1a46040bf23f&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=http%3A%2F%2Fwww.fieldtriptoolbox.org%2Ftutorial%2Fsourcemodel%2F%23construction-of-a-source-model-based-on-a-regular-3-dimensional-grid-of-dipole-positions section says “Content is coming soon!”. Only the steps required for group analysis are detailed.
Kind regards,
Tibor
Auer, Tibor M.D. Ph.D.
Research Fellow
School of Psychology, Faculty of Health and Medical Sciences
University of Surrey, Guildford GU2 7XH
<mailto:T.Auer at surrey.ac.uk> T.Auer at surrey.ac.uk
<https://protect2.fireeye.com/v1/url?k=fb7edb71-a5e0d82a-fb7e95b0-86324fd7403a-16a5255414bf52c4&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=https%3A%2F%2Feur02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Ftwitter.com%252FTiborAuer%26data%3D02%257C01%257Ct.auer%2540surrey.ac.uk%257Cdb32da458c424eedef2908d7d4bd1421%257C6b902693107440aa9e21d89446a2ebb5%257C0%257C0%257C637211780868086968%26sdata%3DzrT5%252FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%253D%26reserved%3D0> @TiborAuer
From: fieldtrip <fieldtrip-bounces at science.ru.nl <mailto:fieldtrip-bounces at science.ru.nl> > On Behalf Of Schoffelen, J.M. (Jan Mathijs)
Sent: Monday, September 28, 2020 1:05 PM
To: FieldTrip discussion list <fieldtrip at science.ru.nl <mailto:fieldtrip at science.ru.nl> >
Subject: Re: [FieldTrip] eLORETA source analysis
Hi Tibor,
Well, I don’t have a strong recommendation to go for either, apart from the fact that a distributed source reconstruction method (such as eLORETA) benefits from an accurate source model to begin with. Also, it depends on what you aim in your source reconstruction. Limiting yourself to the cortical sheet gets rid subcortical structures/cerebellum.
Regarding 3D grids, there is some stuff that relates to 3D grids, isn’t there?
Best wishes,
JM
On 28 Sep 2020, at 13:52, tibor.auer at gmail.com <mailto:tibor.auer at gmail.com> wrote:
Thank you, Jan-Mathijs,
This link is very instructive. I wonder why it eluded me so far. 😊
If I get it right, you recommend using approach based on the cortical sheet because 1) the tutorial for 3D grid is not there yet and 2) I can use results from cortical sheet directly for group analysis.
Kind regards,
Tibor
Auer, Tibor M.D. Ph.D.
Research Fellow
School of Psychology, Faculty of Health and Medical Sciences
University of Surrey, Guildford GU2 7XH
<mailto:T.Auer at surrey.ac.uk> T.Auer at surrey.ac.uk
<https://protect2.fireeye.com/v1/url?k=b74e6976-e9d06a2d-b74e27b7-86324fd7403a-14eab881cda19cbc&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=https%3A%2F%2Feur02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Ftwitter.com%252FTiborAuer%26data%3D02%257C01%257Ct.auer%2540surrey.ac.uk%257Cdb32da458c424eedef2908d7d4bd1421%257C6b902693107440aa9e21d89446a2ebb5%257C0%257C0%257C637211780868086968%26sdata%3DzrT5%252FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%253D%26reserved%3D0> @TiborAuer
From: fieldtrip <fieldtrip-bounces at science.ru.nl <mailto:fieldtrip-bounces at science.ru.nl> > On Behalf Of Schoffelen, J.M. (Jan Mathijs)
Sent: Monday, September 28, 2020 10:21 AM
To: FieldTrip discussion list <fieldtrip at science.ru.nl <mailto:fieldtrip at science.ru.nl> >
Subject: Re: [FieldTrip] eLORETA source analysis
Dear Tibor,
It’s not clear to me what’s special about spm’s ‘unified segmentation’ regarding the creation of source models.
I assume you are aware that source models eventually need to be in the subject’s native space in order for them to be useable.
Documentation about how to create a source model for EEG/MEG source reconstruction can be found at: https://protect2.fireeye.com/v1/url?k=16eb4e10-48754d4b-16eb00d1-86324fd7403a-70cb9a3df2868fce&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=http%3A%2F%2Fwww.fieldtriptoolbox.org%2Ftutorial%2Fsourcemodel%2F, which might be a good starting point.
Best wishes,
Jan-Mathijs
On 28 Sep 2020, at 10:03, tibor.auer at gmail.com <mailto:tibor.auer at gmail.com> wrote:
Hi Jan-Mathijs,
Thank you for your response. I found that post earlier and noticed that I may need to redo the freqanalysis, however, I still do not know how do I create the sourcemodel from the T1-weighted MRI images already segmented with SPM12.
Kind regards,
Tibor
Auer, Tibor M.D. Ph.D.
Research Fellow
School of Psychology, Faculty of Health and Medical Sciences
University of Surrey, Guildford GU2 7XH
<mailto:T.Auer at surrey.ac.uk> T.Auer at surrey.ac.uk
<https://protect2.fireeye.com/v1/url?k=103e91b2-4ea092e9-103edf73-86324fd7403a-83a4166428416cf6&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=https%3A%2F%2Feur02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Ftwitter.com%252FTiborAuer%26data%3D02%257C01%257Ct.auer%2540surrey.ac.uk%257Cdb32da458c424eedef2908d7d4bd1421%257C6b902693107440aa9e21d89446a2ebb5%257C0%257C0%257C637211780868086968%26sdata%3DzrT5%252FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%253D%26reserved%3D0> @TiborAuer
From: fieldtrip <fieldtrip-bounces at science.ru.nl <mailto:fieldtrip-bounces at science.ru.nl> > On Behalf Of Schoffelen, J.M. (Jan Mathijs)
Sent: Thursday, September 24, 2020 8:12 AM
To: FieldTrip discussion list <fieldtrip at science.ru.nl <mailto:fieldtrip at science.ru.nl> >
Subject: Re: [FieldTrip] eLORETA source analysis
Hi Tibor,
Some of this is discussed (and fixed, there were some small issues in the code) in https://protect2.fireeye.com/v1/url?k=772eca1b-29b0c940-772e84da-86324fd7403a-073a5f8a5e268aa6&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=https%3A%2F%2Fgithub.com%2Ffieldtrip%2Ffieldtrip%2Fissues%2F1454 and the PR that is linked in the linked issue.
Note: if you want to go from sensor-level to source-level data in the frequency domain, you should either use ‘powandcsd’, or ‘fourier’ as cfg.output argument to ft_freqanalysis.
Best wishes,
Jan-Mathijs
On 23 Sep 2020, at 13:42, tibor.auer at gmail.com <mailto:tibor.auer at gmail.com> wrote:
Dear Community,
I would like to perform an eLORETA source analysis, however, I am unsure about the steps.
I am working on the <https://protect2.fireeye.com/v1/url?k=af7fbb38-f1e1b863-af7ff5f9-86324fd7403a-935ab088716b5525&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=http%3A%2F%2Ffcon_1000.projects.nitrc.org%2Findi%2Fretro%2FMPI_LEMON.html> LEMON data including 62-channel EEG experiment at rest and structural (T1-weighted) MRI of >200 participants.
I have preprocessed the EEG data and performed timefrequency analysis on the 2-second-long epochs with configuration:
* method: 'mtmfft'
* taper: 'hanning'
* foi: [0.9766 1.9531 3.9062 5.8594 7.8125 12.2070 15.1367 20.0195 24.9023 32.2266 40.0391 60.0586 69.8242 80.0781 95.2148 109.8633 120.1172]
* pad: 2.0480
* output: 'pow'
* keeptrials: 'no'
* trials: [233×1 double]
I have also processed the MRI images and normalised-segmented them using SPM12’s unified segmentation outside FieldTrip.
I would appreciate any help including code snippets, pointers to (order of) functions or specific and detailed tutorials.
Kind regards,
Tibor
Auer, Tibor M.D. Ph.D.
Research Fellow
School of Psychology, Faculty of Health and Medical Sciences
University of Surrey, Guildford GU2 7XH
<https://protect2.fireeye.com/v1/url?k=725d2357-2cc3200c-725d6d96-86324fd7403a-6127d665e1b6773c&q=1&e=722d1cda-14b9-46de-a1c0-ff5eb51ce01f&u=https%3A%2F%2Feur02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Ftwitter.com%252FTiborAuer%26data%3D02%257C01%257Ct.auer%2540surrey.ac.uk%257Cdb32da458c424eedef2908d7d4bd1421%257C6b902693107440aa9e21d89446a2ebb5%257C0%257C0%257C637211780868086968%26sdata%3DzrT5%252FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%253D%26reserved%3D0> @TiborAuer
dy>_______________________________________________
fieldtrip mailing list
<https://mailman.science.ru.nl/mailman/listinfo/fieldtrip> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
<https://doi.org/10.1371/journal.pcbi.1002202> https://doi.org/10.1371/journal.pcbi.1002202
v>_______________________________________________
fieldtrip mailing list
<https://mailman.science.ru.nl/mailman/listinfo/fieldtrip> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
<https://doi.org/10.1371/journal.pcbi.1002202> https://doi.org/10.1371/journal.pcbi.1002202
_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202
div>_______________________________________________
fieldtrip mailing list
<https://mailman.science.ru.nl/mailman/listinfo/fieldtrip> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
<https://doi.org/10.1371/journal.pcbi.1002202> https://doi.org/10.1371/journal.pcbi.1002202
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20200928/fe32428e/attachment.htm>
------------------------------
Subject: Digest Footer
_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202
------------------------------
End of fieldtrip Digest, Vol 118, Issue 27
******************************************
More information about the fieldtrip
mailing list