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 -- Hans J. Johnson, Ph.D. [EMAIL PROTECTED] 278 GH The University of Iowa Iowa City, IA 52241 (319) 353 8587 > From: Greg Harris <[EMAIL PROTECTED]> > Date: Wed, 22 Aug 2007 15:36:59 -0500 > To: Nick Schmansky <[EMAIL PROTECTED]>, Freesurfer Mailing List > <[email protected]> > Cc: Hans Johnson <[EMAIL PROTECTED]> > 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" <[EMAIL PROTECTED]> 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 >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
