Re: [Freesurfer] Re: Need an updated mris_annot_to_segmentation program.

-- Hans J. Johnson, Ph.D. Hans-johnson@uiowa.edu 278 GH The University of Iowa Iowa City, IA 52241 (319) 353 8587 > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > Date: Fri, 24 Aug 2007 14:53:58 -0400 (EDT) > To: Doug Greve greve@nmr.mgh.harvard.edu > Cc: Hans Johnson hans-johnson@UIOWA.EDU, Greg Harris > Gregory-Harris@UIOWA.EDU, Freesurfer Mailing List > freesurfer@nmr.mgh.harvard.edu, Nick Schmansky nicks@nmr.mgh.harvard.edu, > "H. Jeremy Bockholt" jbockholt@themindinstitute.org > Subject: Re: [Freesurfer] Re: Need an updated mris_annot_to_segmentation > program. > > Hi Hans, > > I think mris_annot_to_segmentation is deprecated. Did I tell you to use > it at some point? > > Bruce > On Fri, 24 Aug 2007, Doug Greve wrote: > >> >> Hi Hans, >> >> have you tried using mri_aparc2aseg instead of mris_annot_to_segmentation? >> >> doug >> >> >> >> Bruce Fischl wrote: >> >>> Hi Hans, >>> >>> I fixed this last night, Nick can give you a new version if you tell him >>> what hardware/software platform you are using. However, looking at the data >>> it seems that you already stripped the cerebellum from the orig.mgz volume. >>> This will mess everything up, as the subsequent atlas alignment will try to >>> match a (non-existent) cerebellum in the data and the aseg will do >>> something strange. Are you stripping it using something else before putting >>> the data through recon-all? >>> >>> cheers, >>> Bruce >>> >>> >>> >>> >>> On Thu, 23 Aug 2007, Hans Johnson wrote: >>> >>>> Nick and Freesurfer Team, >>>> >>>> This is a followup to the message sent by Greg Harris yesterday. Greg has >>>> put together a tarball and shell script that demonstrates the problem. >>>> >>>> wget http://www.psychiatry.uiowa.edu/users/hjohnson/ftp/tempFScase.tgz >>>> tar -xzvf /iplweb/html/users/hjohnson/ftp/tempFScase.tgz >>>> cd tempFScase/ >>>> csh TESTME.csh >>>> >>>> I am hoping that if this were run through a debugger that the problem is >>>> going to be quite easy to fix. Will you please let us know if there is >>>> anything that we can do to help address this issue? >>>> >>>> Thanks, >>>> Hans >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> >>