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 10:26:03 -0400 (EDT) > To: Hans Johnson hans-johnson@uiowa.edu > Cc: Greg Harris Gregory-Harris@uiowa.edu, Nick Schmansky > nicks@nmr.mgh.harvard.edu, Freesurfer Mailing List > freesurfer@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 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 >>