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.
- 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.**edugreve@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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