I'm a little lost here. Why would you run mris_preproc with the average subject as input? That is not one of the options I listed below. It sounds like you would run mris_preproc with fsaverage as the target and your list of subjects for a group as input. Then take the mean of the output stack to give you the group mean (mri_concat y.mgh --mean --o y.mean.mgh). Do this for each group. You can then display it on the average subject
doug On 04/17/2014 11:22 AM, Jonathan Holt wrote: > Anyone have any input? > On Apr 16, 2014, at 11:27 AM, Jonathan Holt <whats...@umich.edu> wrote: > >> 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. >>> > > -- 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
