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 <mumal...@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 < > gr...@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 < >>> gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.**edu<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<gr...@nmr.mgh.harvard.edu> >>> > >>> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu> >>> >>> <mailto:gr...@nmr.mgh.harvard.**edu <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:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >>> > >>> >>> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >>> >>> >>> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >>> >> >>> >>> https://mail.nmr.mgh.harvard.** >>> edu/mailman/listinfo/**freesurfer<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 <gr...@nmr.mgh.harvard.edu>> >>> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu> >>> >>> <mailto:gr...@nmr.mgh.harvard.**edu <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<http://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<http://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<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<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> >>> >>> <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<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<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<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> >> >> >
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