Doug, Thanks for the quick reply.
At this point all I want to do is calculate average thickness, per group, then visualize the average whole brain thickness for each group. I’m thinking I’m probably going to need the latter option, but to clarify when I’m going to run mris_preproc the target is fsaverage and by --s will be averagesubject? so mris_preproc --s averagesubject --target fsaverage --hemi ?h --meas thickness --out new_averagesubject ? jon On Apr 16, 2014, at 11:17 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > I'm not sure I understand what you mean. If you follow the group > analysis wiki, it does not give you an option to even create an average > subject, and you have to generate the average subject from > make_average_subject. The proper path depends on what you want to do > exactly. > > If you want to do a full analysis on an average subject, then you'll > need to create the average subject with make_average_subject. Then you > will need to register your individuals to this subject with surfreg --s > individual --t averagesubject ... Then run mris_preproc with --target > averagesubject --surfreg averagesubject.sphere.reg > > If you want to simply display the results on the average group anatomy, > then run make_average_subject to create the average. Run mris_preproc > using fsaverage. When you go to display the final result (eg, with > tksurfer or freeview), specify the averagesubject instead of fsaverage > > doug > > On 04/16/2014 11:03 AM, Jonathan Holt wrote: >> Hi all, >> >> I’m currently trying to generate an average subject for two groups so that I >> might be able to display average thickness for both groups. I’m confused as >> to whether I should be following the GroupAnalysis workflow in the wiki, or >> if I should use make_average_subject and mris_preproc in tandem, but for the >> latter option (if it is the appropriate one) how should I use the two >> together, if that’s the right approach? >> >> jon >> _______________________________________________ >> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
