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 > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@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 > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > 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. > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 > <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
