There is vertex-for-vertex correspondences, but that does not mean that each subject aligns perfectly. There maybe some subjects where a vertex is in the medial wall but not for another subject. They are close, but not in perfect alignment. What I would do is something like this:

a = [subject1fmri.vol(:,:,:,1); subject2fmri.vol(:,:,:,1); subject3fmri.vol(:,:,:,1); ...];

b = a>0;

mask = mean(b)==nsubjects;

On 09/28/2016 05:58 PM, Dorothy Sincasto wrote:

Hi Douglas,

Thanks for your reply.

I thought when individual space data is projected onto fsaverage5 space it get wrapped in a common space, so one vertex would correspond to the same area across subjects, like in MNI.

I tried to create a group subcortical mask by loading each subject fmri surface and selecting the vertex with zero-values and adding one to corresponding element in the 20484 vector . In percentage, 62 vertices are non-zero in half or more of the data size, and 106 in 40% or more. In average, each subject has 120 zero-valued vertices.

If I don't want to account for non-cortical activity in my analysis, do you consider a good approach to discard this 106 vertices that at least in 40% of the subjects are non cortical?

Thanks, Dorothy

On Wed, Sep 28, 2016 at 12:37 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

It is changing with each subject because each subject's brain is
different, and you can't get a subject-specific mask from
fsaverage5. Can you load all your data into matlab and then
compute a mask based on non-zero voxels?


On 9/28/16 1:57 PM, Dorothy Sincasto wrote:

...

Hi freesurfers,

I am doing a connectivity analysis on cortical areas. I load the
2d fmri surface file in fsaverage5 space into matlab and I get
20484 vertices for both hemispheres. Some of which are zero
because I previously specified to get only the cortex vertices.
However, the number of non-cortex vertices changes across subjects.

Is it possible to get from fsaverage5 any overlay mask that
specifies if it is cortical or not, so when I load it into matlab
i can get a logical vector of 20484 elements?

Thanks
Dorothy


_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

_______________________________________________ Freesurfer mailing
list Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> 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
<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. 

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer