[Mne_analysis] morph maps, vertex missing/mismatch

Björn Herrmann herrmann.b at gmail.com
Fri Jan 13 13:52:42 EST 2017
Search archives: 
Thank you Alex and Hari,

Regarding the indexing, this is not the problem. I only read the morph
map (i.e., the matrix) into matlab and look at the size of the matrix.
The matrix size for the dimension of the "from" brain is one too short
with respect to the actual number of vertices of the surface (for
some, but not all subjects). Regarding the 'mindist' command for
source space building, I was wondering whether you referred to early
steps in the freesurfer pipeline? I would like to obtain the morphing
from the ~130,000 vertices of one brain to the ~130,000 vertices of a
different brain. It should have nothing to do with for example a
source space created by mne_setup_source_space? I believe the command

mne_make_morph_maps --from subjID --to fsurfavr

uses all ~130,000 vertices of the sphere. So, basically, I run
mne_make_morph_maps as soon as all the freesurfer calculations are
done (no mne_setup_source_space or other functions have been run), and
then I have the problem already (and it also occurs for other than the
standard freesurfer brain).
Do you have any other ideas what the problem could be, and how to fix it?
Thank you in advance,

Bjorn



----------
Björn Herrmann

Brain and Mind Institute
The University of Western Ontario
London, Ontario N6A 5B7
Canada

email: herrmann.b at gmail.com
web: www.bjoernherrmann.com


On Fri, Jan 13, 2017 at 11:37 AM,
<mne_analysis-request at nmr.mgh.harvard.edu> wrote:
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> Today's Topics:
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>    1. morph maps, vertex missing/mismatch (Bj?rn Herrmann)
>    2. Re: morph maps, vertex missing/mismatch (Alexandre Gramfort)
>    3. Re: morph maps, vertex missing/mismatch (Bharadwaj, Hari M)
>    4. plotting whitened raw data (Olaf Hauk)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 12 Jan 2017 14:09:56 -0500
> From: Bj?rn Herrmann <herrmann.b at gmail.com>
> Subject: [Mne_analysis] morph maps, vertex missing/mismatch
> To: mne_analysis at nmr.mgh.harvard.edu
> Message-ID:
>         <CAKzHZe6sKi2o_OistvD=MP2OvgtLGSJKDzG2FdocjDD9pvBEhQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear list,
>
> I was wondering whether someone has advice on a problem I encountered.
> I use the morph maps in matlab to morph brain activity from one
> individual to another brain.
>
> I calculate the morph maps in the linux shell:
> mne_make_morph_maps --from subjID --to fsurfavr
>
> that works all fine, but when I open the morph maps in matlab
> (mne_read_morph_map), then in a handful of my subjects, the number of
> vertices of the source subject is one to small. The source space
> (mne_read_source_spaces) of that individual shows the correct number
> of vertices. Also the output in the linux shell while the morph map is
> calculated shows the right number of vertices.
>
> When I morph the individuals brain (subjID above) to a different brain
> (not the freesurfer standard brain) then it might work properly with
> the correct number of vertices for this subject in the morph map
> matrix, but not for others. It seems to be a specific interaction
> between source and target brain whether one vertex (so far it was
> always just one) cannot not be properly morphed and just gets dropped.
>
> Has someone encountered this problem before and is there a way to
> solve it. I currently cannot morph a handful of participants to a
> common brain space.
>
> Thank you in advance for any input you may have,
> Cheers,
>
> Bjorn
>
>
>
> ----------
> Bj?rn Herrmann
>
> Brain and Mind Institute
> The University of Western Ontario
> London, Ontario N6A 5B7
> Canada
>
> email: herrmann.b at gmail.com
> web: www.bjoernherrmann.com
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 13 Jan 2017 10:10:52 +0100
> From: Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr>
> Subject: Re: [Mne_analysis] morph maps, vertex missing/mismatch
> To: Discussion and support forum for the users of MNE Software
>         <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
>         <CADeotZqkNq6msx7K_qHYWAFYx+esfBfmS8bYArLaEwz41gHfCA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> hi Bjorn,
>
> I see 2 possible problems:
>
> - 0 vs 1 indexing in matlab
> - use of mindist in source space building
>
> but maybe it's something else...
>
> Alex
>
>
>
>
> On Thu, Jan 12, 2017 at 8:09 PM, Bj?rn Herrmann <herrmann.b at gmail.com> wrote:
>> Dear list,
>>
>> I was wondering whether someone has advice on a problem I encountered.
>> I use the morph maps in matlab to morph brain activity from one
>> individual to another brain.
>>
>> I calculate the morph maps in the linux shell:
>> mne_make_morph_maps --from subjID --to fsurfavr
>>
>> that works all fine, but when I open the morph maps in matlab
>> (mne_read_morph_map), then in a handful of my subjects, the number of
>> vertices of the source subject is one to small. The source space
>> (mne_read_source_spaces) of that individual shows the correct number
>> of vertices. Also the output in the linux shell while the morph map is
>> calculated shows the right number of vertices.
>>
>> When I morph the individuals brain (subjID above) to a different brain
>> (not the freesurfer standard brain) then it might work properly with
>> the correct number of vertices for this subject in the morph map
>> matrix, but not for others. It seems to be a specific interaction
>> between source and target brain whether one vertex (so far it was
>> always just one) cannot not be properly morphed and just gets dropped.
>>
>> Has someone encountered this problem before and is there a way to
>> solve it. I currently cannot morph a handful of participants to a
>> common brain space.
>>
>> Thank you in advance for any input you may have,
>> Cheers,
>>
>> Bjorn
>>
>>
>>
>> ----------
>> Bj?rn Herrmann
>>
>> Brain and Mind Institute
>> The University of Western Ontario
>> London, Ontario N6A 5B7
>> Canada
>>
>> email: herrmann.b at gmail.com
>> web: www.bjoernherrmann.com
>>
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in error
>> but does not contain patient information, please contact the sender and properly
>> dispose of the e-mail.
>
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 13 Jan 2017 12:28:57 +0000
> From: "Bharadwaj, Hari M" <hbharadw at purdue.edu>
> Subject: Re: [Mne_analysis] morph maps, vertex missing/mismatch
> To: Discussion and support forum for the users of MNE Software
>         <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID: <1484310537415.38846 at purdue.edu>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Bjorn,
>
> Is it an issue specific to fsaverage, i.e., does the issue occur with any pair of subjects when neither is fsaverage?
>
> This old thread may be relevant: https://mail.nmr.mgh.harvard.edu/pipermail//mne_analysis/2011-March/000542.html
>
> - Hari
> ________________________________________
> From: mne_analysis-bounces at nmr.mgh.harvard.edu <mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Bj?rn Herrmann <herrmann.b at gmail.com>
> Sent: Thursday, January 12, 2017 2:09 PM
> To: mne_analysis at nmr.mgh.harvard.edu
> Subject: [Mne_analysis] morph maps, vertex missing/mismatch
>
> Dear list,
>
> I was wondering whether someone has advice on a problem I encountered.
> I use the morph maps in matlab to morph brain activity from one
> individual to another brain.
>
> I calculate the morph maps in the linux shell:
> mne_make_morph_maps --from subjID --to fsurfavr
>
> that works all fine, but when I open the morph maps in matlab
> (mne_read_morph_map), then in a handful of my subjects, the number of
> vertices of the source subject is one to small. The source space
> (mne_read_source_spaces) of that individual shows the correct number
> of vertices. Also the output in the linux shell while the morph map is
> calculated shows the right number of vertices.
>
> When I morph the individuals brain (subjID above) to a different brain
> (not the freesurfer standard brain) then it might work properly with
> the correct number of vertices for this subject in the morph map
> matrix, but not for others. It seems to be a specific interaction
> between source and target brain whether one vertex (so far it was
> always just one) cannot not be properly morphed and just gets dropped.
>
> Has someone encountered this problem before and is there a way to
> solve it. I currently cannot morph a handful of participants to a
> common brain space.
>
> Thank you in advance for any input you may have,
> Cheers,
>
> Bjorn
>
>
>
> ----------
> Bj?rn Herrmann
>
> Brain and Mind Institute
> The University of Western Ontario
> London, Ontario N6A 5B7
> Canada
>
> email: herrmann.b at gmail.com
> web: www.bjoernherrmann.com
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and properly
> dispose of the e-mail.
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 13 Jan 2017 16:35:54 +0000
> From: Olaf Hauk <Olaf.Hauk at mrc-cbu.cam.ac.uk>
> Subject: [Mne_analysis] plotting whitened raw data
> To: Discussion and support forum for the users of MNE Software
>         <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
>         <F5E982DF9D0D224D95974018326FF307010C81B9A1 at WSR-EX-01.mrc-cbsu.local>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
> is there an equivalent of evoked.plot_white() for raw data? I would like to compare different covariance methods for whitening empty room data.
>
> Thanks,
>
> Olaf
>
>
> Olaf Hauk, PhD
> MRC Cognition and Brain Sciences Unit
> Phone: +44(0)1223 273702
> Fax: +44(0)1223 359062
> Web: http://www.mrc-cbu.cam.ac.uk/people/olaf.hauk/
>
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