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:
#--------------------------------------------
[EMAIL PROTECTED] 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
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