Re: [Freesurfer] Group Average of Retinotopy Results

Hi Doug, Thank you for your help with this. So when I looked at the maps, two issues arose.

1) The fieldsign map looks like it needs lots of smoothing. When I ran the individual subjects on the surface, I smoothed by 20 during fieldsign-sess. Is it still appropriate/can one smooth at the mri_fieldsign step below?

2)Results ended up on the lateral side and way anterior from the occipital lobe. Do I perform a separate registration between the individual subject and fsaverage somewhere along the line? Is this because I ran the individual subject analyses on a flattened fsaverage occipital patch and not on lh.sphere?

Thanks! Michelle

On Wed, Oct 19, 2011 at 7:34 PM, Michelle Umali mumali01@gmail.com wrote:

Hi Doug, Two problems happened (I'm attaching a picture).

1. The fieldsign map looks like it needs lots of smoothing. When I ran the

individual subjects on the surface, I smoothed by 20 during fieldsign-sess. Is it still appropriate/can one smooth at the mri_fieldsign step below?

2)Results ended up on the lateral side and way anterior from the occipital lobe. Do I perform a separate registration between the individual subject and fsaverage somewhere along the line? Is this because I ran the individual subject analyses on a flattened fsaverage occipital patch and not on lh.sphere?

Thanks! Michelle

On Wed, Oct 19, 2011 at 5:30 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:

...

Hi Michelle, try this:

isxconcat-sess -sf sessidlist -a rtopy.fsaverage.lh -call -o retgroup cd retgroup/rtopy.fsaverage.lh

mri_glmfit --y eccen/ces.000.nii.gz --osgm --o eccen/glm.real --surface fsaverage lh mri_glmfit --y eccen/ces.001.nii.gz --osgm --o eccen/glm.imag --surface fsaverage lh mri_glmfit --y polar/ces.000.nii.gz --osgm --o polar/glm.real --surface fsaverage lh mri_glmfit --y polar/ces.001.nii.gz --osgm --o polar/glm.imag --surface fsaverage lh

mri_fieldsign --fs lh.fieldsign.mgh \ --eccen eccen/glm.real/osgm/gamma.mgh eccen/glm.imag/osgm/gamma.mgh \ --polar polar/glm.real/osgm/gamma.mgh polar/glm.imag/osgm/gamma.mgh \ --s fsaverage --hemi lh --sphere --old

tksurfer fsaverage lh inflated -aparc -ov lh.fieldsign.mgh -fthresh .5

Michelle Umali wrote:

...

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 <mailto:greve@nmr.mgh.harvard.**edugreve@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<greve@nmr.mgh.harvard.edu>

...

    <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>

   <mailto:greve@nmr.mgh.harvard.**edu <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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