Re: [Freesurfer] Group Average of Retinotopy Results
First thing you can do is to look at each individual in the ces file, tksurfer fsaverage lh inflated -ov eccen/ces.000.nii.gz Bring up the functional configuration window. You may need to adjust the thresholds. Then scroll through each time point. The pattern itself might not be meaningful, but you should be able to see that each subject has the right brain coverage. Actually, before you do that, view the individual field sign maps for the fsaverage analysis. doug Michelle Umali wrote: Hi Doug, I tried smoothing by 20 but it didn't make a difference. I'm attaching a picture, and as you can see the map is misplaced? How should I troubleshoot? Thanks. Michelle On Thu, Oct 20, 2011 at 11:20 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: 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 mailto: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 mailto: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
Re: [Freesurfer] Group Average of Retinotopy Results
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
Re: [Freesurfer] Group Average of Retinotopy Results
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
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 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.**edugr...@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.**edugr...@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
Re: [Freesurfer] Group Average of Retinotopy Results
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 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.**edugr...@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.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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.**edugr...@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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://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/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to
Re: [Freesurfer] Group Average of Retinotopy Results
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 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 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.
[Freesurfer] Group Average of Retinotopy Results
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] Group Average of Retinotopy Results
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
