[FieldTrip] segmented brain seems not fitting the sensor helmet well, (jan-mathijs schoffelen)

Ye Mei frank.ye.mei at gmail.com
Wed Mar 6 22:35:53 CET 2013 

Hi Jan-Mathijs,

Thank you very much for the reply.

I think the problem starts at "mri_sliced = ft_volumereslice([], mri);" 
before using "ft_volumesegment.".

The attached file "beforevolumnslice.png" is the result of 
"imagesc(squeeze(mri.anatomy(:,111,:)))";
The attached file "aftervolumnslice.png" is the result of 
"imagesc(squeeze(mri_sliced.anatomy(:,111,:)))".

We can see part of the head in "aftervolumnslice.png" is already sliced 
away.

Could one do source localization without using "mri_sliced = 
ft_volumereslice([], mri);"?

To circumvent the problem, I am trying to use FreeSurfer instead of 
ft_volumereslice and ft_volumesegment. I had several .mgz files from 
freesurfer.
Can I do the following?
--------
mri=ft_read_mri("brain.mgz"); %brain.mgz is the segmented brain by 
FreeSurfer

cfg = [];
cfg.method  ='fiducial';
cfg.fiducial.nas  = [30 132 96];% position of Nasion
cfg.fiducial.lpa  = [127 113 170];% position of LPA
cfg.fiducial.rpa  = [125 115 18]% position of RPA
cfg.fiducial.zpoint = [125 125 220]
[mri_aligned] = ft_volumerealign(cfg, mri);

cfg = [];
cfg.method = 'singleshell';
vol = ft_prepare_headmodel(cfg, mri_aligned);
...
---------

thanks ahead,
Ye


On 13-02-28 05:10 PM, fieldtrip-request at science.ru.nl wrote:
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>     1. Re: NIHC-BrainGain Tutorial Day - March 21, 2013
>        (Robert Oostenveld)
>     2. Re: segmented brain seems not fitting the sensor helmet	well
>        (jan-mathijs schoffelen)
>     3. Re: segmented brain seems not fitting the sensor helmet	well
>        (Ye Mei)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 28 Feb 2013 17:46:39 +0100
> From: Robert Oostenveld <r.oostenveld at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] NIHC-BrainGain Tutorial Day - March 21, 2013
> Message-ID: <9741C083-F00A-4BC9-86EF-FB99715576A7 at donders.ru.nl>
> Content-Type: text/plain; charset=windows-1252
>
> Dear FieldTrip users,
>
> The NIHC-BrainGain Tutorial Day marks the end of the BrainGain project. For the last 6 years, the development and continued support of FieldTrip for normal/offline and realtime/online analysis has received support from the BrainGain project.
>
> There is now more information available online on this tutorial day, please see
> https://www.hersenenencognitie.nl/contents/1876
> https://www.hersenenencognitie.nl/contents/1915
>
> If you happen to be close to Nijmegen, you might also want to come to the "Breinfest"  on Tuesday evening 19 March in the city centre with talks by international speakers and BCI demo's for the general public. Personally, I will be demonstrating how real-time data streaming and processing can be done using the FieldTrip buffer to various platforms (OS X, WIndows, Linux), to the Raspberry Pi and even to an Arduino (yes, fieldtrip runs on an arduino! ... well, a small part of it runs on an arduino). See http://www.ru.nl/breinfest for details on the evening.
>
> best regards,
> Robert
>
>
>
> On 19 Feb 2013, at 14:30, Robert Oostenveld wrote:
>
>> NIHC-BrainGain Tutorial Day:
>> Tools and novelties in neurotechnology research
>>   
>> We invite PhD students, post-docs and senior researchers working in the fields of brain-computer interfacing (BCI), neurofeedback, cognitive neuroscience, neuroinformatics, neurosurgery and related topics to our Tutorial Day on March 21st, 2013 in the Sanadome Nijmegen.
>> The day marks the end of the BrainGain consortium, a six-year joint-effort project on Brain-Computer Interfacing and related technologies. More information on BrainGain can be found here.
>>   
>> The Tutorial Day will consist of a 'tools' track and a 'novelties? track. The 'tools' track is intended to provide both newcomers to the field and experienced researchers with an overview of the tools needed to integrate cognitive neuroscience and advanced invasive and non-invasive technology. Topics range from data streaming to modelling and statistics, and from online fMRI decoding to a crash course in neuroethics., You will also receive some helpful insights for a future career, in case you are interested in applying for a grant in the near future or considering setting up your own company.
>> The 'novelties' track covers a wide range of topics indicating some of the possible topics to be further explored in BCI and neurotechnology research, including genetics, robotics and intracranial recordings.
>> There is no need to stick to one of the two tracks the whole day: you are free to switch between tracks any time.
>>   
>> In parallel to the lectures, there will be several interesting demonstrations.
>>   
>> The full programme and registration form can be found on the NIHC website (https://www.hersenenencognitie.nl). Please register before 1 March 2013. Participation is free. Lunch and drinks will be provided.
>>   
>> We hope to welcome you on March 21st in Nijmegen!
>>   
>> Susanna Bicknell
>> Radboud University Nijmegen
>> ____________________________________________________________________
>> Faculty of Science | Finance and Economic Affairs | Project Management | LC-IMPACT
>> Faculty of Social Sciences | Donders Centre for Cognition | BRAINGAIN | Project Manager
>> T +31 24 3653300 | HG00.616 (Monday, Thursday)
>> Faculty of Science | IMAPP | T +31 24 3652972 | HG07.315 (Tuesday, Wednesday)
>> Postal address: P.O. Box 9010, 6500 GL Nijmegen, The Netherlands
>> Visiting and courier service address: Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 28 Feb 2013 18:54:14 +0100
> From: jan-mathijs schoffelen <jan.schoffelen at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] segmented brain seems not fitting the sensor
> 	helmet	well
> Message-ID: <B86193FA-0829-494E-A52B-69955F3EAEBF at donders.ru.nl>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Ye,
>
> Looks like a coregistration problem to me. In other words, something went wrong in ft_volumesegment, because the images were not sufficiently aligned. You need to investigate the input and output of ft_volumesegment.
> Do you use ft_volumerealign after calling ft_volumesegment? This should be the other way around.
>
> Best,
>
> Jan-Mathijs
>
>
> On Feb 28, 2013, at 5:38 PM, Ye Mei wrote:
>
>> Hello FieldtripList,
>>
>> After segmentation and alignment using
>> 'ft_volumesegment' and 'ft_volumerealign', one of the subjects' segmented
>> brain seems rotated forward in the sensor helmet(brain.png) and the
>> cerebellum part seems to be segmented out. However, his head MRI seems
>> fitting the sensor helmet well(head.jpg). My another subject's brain
>> seem to be correctly segmented without missing the cerebellum part. And
>> the brain is not rotated forward.
>>
>> Could might be the problem?
>>
>> thanks ahead,
>> Ye
>> <brain.png><head.jpg>_______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> Jan-Mathijs Schoffelen, MD PhD
>
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
>
> Max Planck Institute for Psycholinguistics,
> Nijmegen, The Netherlands
>
> J.Schoffelen at donders.ru.nl
> Telephone: +31-24-3614793
>
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> ------------------------------
>
> Message: 3
> Date: Thu, 28 Feb 2013 17:09:57 -0500
> From: Ye Mei <frank.ye.mei at gmail.com>
> To: fieldtrip at science.ru.nl
> Subject: Re: [FieldTrip] segmented brain seems not fitting the sensor
> 	helmet	well
> Message-ID: <512FD5B5.8080700 at gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> Hello All,
>
> I found the problem I mentioned in the previous email was caused by
> using "mri_sliced = ft_volumereslice([], mri);" before using
> ft_volumesegment.
> After erasing the line "mri_sliced = ft_volumereslice([], mri);", the
> segmented brain seems to be normal and fits the sensor helmet well now,
> as show in the attached figure(notvolumnsliced.jpg).
> For another of my subject, if the "ft_volumereslice" is included, the
> brain looks sliced on the top(subject2vs.jpg). If no "ft_volumreslice"
> it looks normal(subject2.jpg).
>
> I notice in the fieldtrip headmodel tutorial
> (http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg),
> "ft_volumereslice" is not used. but in the field trip beamformer
> tutorial(http://fieldtrip.fcdonders.nl/tutorial/beamformer), it is used.
>
> I am wondering if I should include "ft_volumereslice" in my source
> localization code. Can anyone give me some suggestions?
>
>
>
> thanks ahead,
> Ye
>
>
>
>
> On 13-02-28 11:45 AM, fieldtrip-request at science.ru.nl wrote:
>> Send fieldtrip mailing list submissions to
>> 	fieldtrip at science.ru.nl
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>> 	http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> or, via email, send a message with subject or body 'help' to
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>> When replying, please edit your Subject line so it is more specific
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>>
>> Today's Topics:
>>
>>      1. segmented brain seems not fitting the sensor helmet well (Ye Mei)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Thu, 28 Feb 2013 11:38:21 -0500
>> From: Ye Mei <frank.ye.mei at gmail.com>
>> To: fieldtrip at science.ru.nl
>> Subject: [FieldTrip] segmented brain seems not fitting the sensor
>> 	helmet well
>> Message-ID: <512F87FD.80500 at gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>>
>> Hello FieldtripList,
>>
>> After segmentation and alignment using
>> 'ft_volumesegment' and 'ft_volumerealign', one of the subjects' segmented
>> brain seems rotated forward in the sensor helmet(brain.png) and the
>> cerebellum part seems to be segmented out. However, his head MRI seems
>> fitting the sensor helmet well(head.jpg). My another subject's brain
>> seem to be correctly segmented without missing the cerebellum part. And
>> the brain is not rotated forward.
>>
>> Could might be the problem?
>>
>> thanks ahead,
>> Ye
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>> ------------------------------
>>
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