Michelle Umali wrote: > 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? Yes, the smoothing applied during the individual fieldsign creations does not apply to the group. > > 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? The individuals were run on the full fsaverage surface. The field sign created at the individual level is not used at all in the group analysis. There is not any additional registration that you should use. Try the smoothing in mri_fieldsign (--fwhm); if that does not fix the problem, send me a snapshot.
doug > > Thanks! > Michelle > > On Wed, Oct 19, 2011 at 7:34 PM, Michelle Umali <mumal...@gmail.com > <mailto: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 <mailto: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> > <mailto: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>> > <mailto: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>> > <mailto: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>> > <mailto: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>> > <tel: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>> > <tel: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> > 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> > > > > > 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> > <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> > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > 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> > 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
