[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: Greg Harris Gregory-Harris@uiowa.edu > Date: Wed, 22 Aug 2007 15:36:59 -0500 > To: Nick Schmansky nicks@nmr.mgh.harvard.edu, Freesurfer Mailing List > freesurfer@nmr.mgh.harvard.edu > Cc: Hans Johnson hans-johnson@uiowa.edu > Conversation: Need an updated mris_annot_to_segmentation program. > Subject: Need an updated mris_annot_to_segmentation program. > > Dear FreeSurfers, > > To produce cortical gray matter ribbon masks for each annotation roi, we > have used in the past the FreeSurfer executable mris_annot_to_segmentation, > and then extracted our 3D masks from the resulting integer code image (in > brains2). > > The current release of mris_annot_to_segmentation works ok on FreeSurfer > studies we ran, for example, on April 15, 2006; however, on FreeSurfer > studies generated with a more modern version of FreeSurfer, for example, on > March 1, 2007, mris_annot_to_segmentation dies with a SegFault and (in gdb) > this sort of message: > > > Program received signal EXC_BAD_ACCESS, Could not access memory. > Reason: KERN_INVALID_ADDRESS at address: 0x804d1000 > 0x00002df2 in ?? () > (gdb) backtrace > #0 0x00002df2 in ?? () > #1 0x01807400 in ?? () > Previous frame inner to this frame (corrupt stack?) > (gdb) > > > Together with the advice from Nick reproduced below, this seems to me to > mean I do not need an earlier version of mris_annot_to_segmentation since > the current version is continuous with data generated last year; instead, I > need to request that someone at FreeSurfer headquarters figure out how to > compile mris_annot_to_segmentation for the contemporary file formats now in > use for surf/lh.white, surf/lh.pial, label/lh.aparc.annot, etc., right? > > Unless the best thing would be to convert these files to the older file > format with something like mris_convert from two distinct releases of > FreeSurfer? I think I see how to convert white and pial, but what converts > aparc.annot to text and back to binary? And isn't my difficulty one that > straddles a version before v.3.0.3 on 5/24/06? Can I even get the earlier > version from January 2006? > > I can ftp a tarball with one of our workups and a TESTME.csh script in it, > but it is 234MB so I am hoping to finesse that if possible. > > Thanks for any and all suggestions. > > Greg Harris > Iowa Psychiatry Brain Imaging Lab > > > On 8/22/07 8:01 AM, "Nick Schmansky" nicks@nmr.mgh.harvard.edu wrote: > >> A new version of Freesurfer is now available for download >> from this page: >> >> https://surfer.nmr.mgh.harvard.edu/fswiki/Download >> >> The list of new features, bug fixes, and known issues is >> found on the ReleaseNotes page: >> >> https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes >> >> Users are reminded that in general, subjects should be >> processed by a single version of Freesurfer (ie. in a group >> study, subjects should not have been processed by different >> versions of Freesurfer). Older versions of Freesurfer are >> available upon request. >> >> The Freesurfer Team. >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >