doug- When i try to do this it still brings up an error with the make_average_subject regarding the --no-aseg as a subject to be averaged. I went ahead and ran make_average_surface and make_average_volume with a --no-aseg flag. This should recreate the process of the make_average_subject correct?
michael On 6/4/12, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > you should be able to run make_average_subject with --no-aseg > > On 06/04/2012 06:25 PM, mdkrue...@uwalumni.com wrote: >> so what i should be able to do is run make_average_surface and >> make_average_volume separately with a --no-aseg flag on >> make_average_volume. >> >> On 6/4/12, Gregory Kirk<gk...@wisc.edu> wrote: >>> so it seems that i ran make_average_volume which does have a --no-aseg >>> flag >>> >>> make_average_subject really just runs 2 other commands >>> make_average_surface and make_average_volume. >>> >>> bruce the reason i did this is that mike was running a `super` average, >>> i.e. >>> the average >>> subject of 2 different syudies, i.e. ave_study1, ave_study2 >>> >>> and he was running make_average_subject --subjects ave_study1 ave_study2 >>> --out superave. >>> >>> we were doing this so we could map labels from one study to another >>> and we were getting an error in the log file from make_average_volume >>> that indicated it was having a problem with the aseg after the >>> make_average_surface had already finished without error. >>> >>> really we could just skip it i think as we are not actually doing >>> anything >>> with the average volume. >>> >>> greg >>> >>> On 06/04/12, Bruce Fischl wrote: >>>> Hi Michael >>>> >>>> a couple of typos. It should be "make_average_subject" (note no "s"), >>>> and >>>> it should be --subjects (note the ending "s"). I also don't see a flag >>>> named --no-aseg, which I think is why it's being included as a subject. >>>> What are you trying to do? >>>> >>>> cheers >>>> Bruce >>>> >>>> On Mon, 4 Jun 2012, michael kruepke wrote: >>>> >>>>> Hi all - >>>>> Having a bit of an issue with trying to run a make_average with the >>>>> flag >>>>> --no-aseg. When written >>>>> >>>>> make_average_subjects --subject subject1 subject2 --no-aseg --out >>>>> superaverage >>>>> >>>>> the propt runs as if --no-aseg and --out superaverage are subjects i >>>>> wish >>>>> to >>>>> average in with subjects1 and subject2. This is obviously and issue, >>>>> hoping >>>>> someone might have an idea of a solution. I have tried moving these >>>>> flags >>>>> to >>>>> somewhere else in the prompt seeing if that would solve it, no luck >>>>> there. >>>>> >>>>> Best- >>>>> Michael >>>>> >>>>> -- >>>>> Michael D. Kruepke >>>>> PhD - University of Illinois at Urbana-Champaign >>>>> BA - Psych - University of Wisconsin-Madison >>>>> mdkrue...@gmail.com >>>>> (262)-483-7449 >>>>> >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> 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: 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 > -- Michael D. Kruepke BA-Psychology University of Wisconsin-Madison mdkrue...@uwalumni.com (262)-483-7449 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
