If you want to display the group mean on the average anatomy of your group, then you use make_average_subject. This is different that just creating an average map of cortical thickness (as is done with mris_preproc). make_average_subject actually creates surfaces, the whole freesurfer subject tree, etc. mris_preproc just creates a single file.
doug On 04/17/2014 03:18 PM, Jon Holt wrote: > Doug > > thank you for your patience. for you what seems natural can be a bit > confusing for me. I'll do what you suggests, but I have to ask where does > make_average_subject come into play. you recommended it as an option, but now > it doesn't seem to be > a part of the process > > Jon >> On Apr 17, 2014, at 3:08 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> >> wrote: >> >> >> 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/ >> > -- 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
