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
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
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-
Bruce Fischl -
Prantik Kundu