Hi Corey,
something is very strange with that volume. Is it really only 77 slices? It doesn't show properly in tkmedit, which means that the direction cosines are probably messed up. The voxel sizes may be wrong too, as it looks very odd. Do you have dicoms for it? Bruce
On Tue, 12 May 2009 ckeller@nmr.mgh.harvard.edu wrote:
When trying to perform an auto recon on MRI_1.nii in /space/annecy/12/users/adykstra/cashlab/MRI/BW10/mri/, I get the following error during autorecon1:
Tue May 12 10:34:18 EDT 2009 talairach_avi done
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#-------------------------------------------- #@# Talairach Failure Detection Tue May 12 10:34:19 EDT 2009 /autofs/space/annecy_012/users/adykstra/cashlab/MRI/BW10_SURFER_OUTPUT/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 gate 2.6.9-78.0.5.ELsmp #1 SMP Wed Oct 8 07:12:03 EDT 2008 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Tue May 12 10:34:19 EDT 2009
So far I've identified and ruled out three possible reasons why this could be happening.
- The localizer slice as the first slice in the volume. I removed that
slice in the volume and tried again.
- The field of view did not encompass the whole head in the
anterior/posterior dimension, so I zero padded the edges - still didn't work.
- The in-plane resolution of each slice is 512x512, which I learned from
the help archive may be problematic. So, I tried both downsampling the volume and re-running autorecon1 as well as keeping the native resolution and giving autorecon1 the -cw256. This still didn't work.
Please help.
Thanks, Corey
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