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
