Hi Doug and the Freesurfers,
Thanks for your help.  I have 2 questions.:

1) I did the retinotopy analysis on the fsaverage surface as you suggested below and then ran isxconcat-sess for my eccen and polar data:
   e.g. isxconcat-sess -analysis rtopy.fsaverage.lh -contrast polar -sf sessid -o group_polar_lh
    but how do you do this for the fieldsign analysis, since the cess.nii and other files don't exist?

2) So when trying to run a group mri_glmfit on the polar and eccen maps with:
mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surface fsaverage lh --glmdir group_eccen_lh.wls --nii.gz

I got an error, because I have two ces.nii.gz and cesvar.nii.gz files each.  I am not sure how this happened.  I only have one run each of polar and wedge data.  What may have generated these two files and which one do I use?


Thanks.
Michelle


On Thu, Oct 13, 2011 at 11:36 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
When you run preproc-sess use -surface fsaverage lhrh instead of -surface self lhrh. Then create a new analysis with the same parameters, except use -surface fsaverage lh instead of -surface self lh.
doug

Michelle Umali wrote:
Hi Doug,
I'm a little confused as to how to assign functional data to the fsaverage space.
1) Do you mean just change each subject's subjectname file to fsaverage and then do the same thing as before for each person?
2) Also, when I specify the analysis do I change -rtopy.self.lh to rtopy.fsaverage.lh, i.e. will isconcat later be sensitive to analysis name?

e.g. mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold -force

then the same for selxavg3-sess and fieldsign-sess

and then isxconcat-sess would be:
isxconcat-sess -sf sessid -analysis rtopy.fsaverage.lh -o group_lh


Thanks.
Michelle

On Wed, Oct 12, 2011 at 3:54 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

   If you want to combine across subjects, then you need to run the
   analysis on fsaverage (ie, rerun preproc-sess, create a new
   analysis, run selxavg3-sess, and then isxconcat-sess).
   doug

   Michelle Umali wrote:

       Dear Freesurfers,
       I've generated individual polar, eccentricity, and fieldsign
       maps for each of my subjects. I would like to generate group
       average maps of these that I can visualize on the fsaverage brain.

       When I ran:
       isxconcat-sess -sf sessid -analysis rtopy.self.lh -o group_lh

       I got:
       ERROR: analysis space is self surface, not supported

       How do I do a group average for the 3 different maps?

       Thanks.
       Michelle

       For each person I ran recon-all and flattened occipital patches.
       Then:
       mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2
       -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold
       -force
        mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2
       -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold
       -force

       preproc-sess -surface self lhrh -fwhm 5 -per-run -s sjXX -fsd
       bold -force

       selxavg3-sess -a rtopy.self.lh -s sjXX -force
       selxavg3-sess -a rtopy.self.rh -s sjXX -force

       fieldsign-sess -a rtopy.self.lh -occip -fwhm 20 -s sjXX
       fieldsign-sess -a rtopy.self.rh -occip -fwhm 20 -s sjXX

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

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   --     Douglas N. Greve, Ph.D.
   MGH-NMR Center
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