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
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