Hi Prantik, do you process the data directly from dicoms? If you bring up the orig.mgz in tkmedit does it orient properly?
cheers Bruce On Tue, 11 Aug 2009, Prantik Kundu wrote: > Hello > > In default FS usage, all of the MPRAGE's from this particular study > that I'm analyzing are dying with the error shown below. MPRAGE's from > other studies appear to be processed just fine. The MPRAGEs from the > experiment that FS is failing on are generally of higher quality than > those where FS is succeeding. The failure seems to be happening even > before brainmask.mgz is being created. > When I turn off the automated tlrc checking, then brainmask.mgz is > created but of very poor quality. > This is reproducible on Linux 32 and 64 bit as well as OSX. Please help. > > -Prantik > > FROM recon-all.log : > __________________________________________________________________ > > Mon Aug 10 14:05:54 EDT 2009 > talairach_avi done > > cp transforms/talairach.auto.xfm transforms/talairach.xfm > > #-------------------------------------------- > #...@# Talairach Failure Detection Mon Aug 10 14:05:55 EDT 2009 > /home/kundup/FS_SUBJECTS/BrVi.S06/mri > > talairach_afd -T 0.005 -xfm transforms/talairach.xfm > > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) > Linux cadmium 2.6.28-14-generic #47-Ubuntu SMP Sat Jul 25 01:19:55 UTC > 2009 x86_64 GNU/Linux > > recon-all exited with ERRORS at Mon Aug 10 14:05:55 EDT 2009 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
