Two questions for two different subjects during autorecon1:
1. The initial skull strip on this subject left too much extra-cerebral material. Subsequent attempts at using the wsatlas or manual adjustment of the wsthresh have resulted in this error:
*************************WATERSHED************************** preflooding height equal to 25 percent Sorting... T1-weighted MRI image modification of the preflooding height to 15 percent Count how many 110 voxels are present : 1960516
Find the largest 110-component...mriSegmentReallocateVoxels: could not alloc 1048381 voxels for sno 8343 Cannot allocate memory done And identify it as the main brain basin...Segmentation fault Linux rainmaker 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Mon Apr 2 15:02:05 CDT 2007 #--------------------------------------------------------------
Are there too many voxels? I've looked, but couldn't find any information on how to fix this one.
2. This subject continues to fail with errors during intensity normalization. Here is the output:
#-------------------------------------------- #@# Intensity Normalization Mon Apr 2 15:46:47 EDT 2007 /disk/conte_raid1/freesurfer/conte_mprage/021219_5734/mri
mri_normalize -g 1 nu.mgz T1.mgz
using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 0.830 -0.117 -0.004 -3.656; 0.116 0.833 -0.323 -26.577; 0.004 0.028 0.075 84.152; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize: could not find any valid peaks mri_normalize: normalization failed Linux eli 2.6.9-34.0.1.ELsmp #1 SMP Wed May 17 16:59:36 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Mon Apr 2 15:46:49 EDT 2007 #---------------------------------------------
I've checked the talairach.xfm and it is bad. It seems I remember someone on the list saying that a -nold flag could fix this, but I couldn't find any info on the wiki about it. Any suggestions? Can I still salvage this subject?
Thanks for all of your help!
-Derin