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