When I run recon-all -base 1_template -tp 1_first -tp 1_secon -all
-debug. It crash during CA Reg Thu Sep 12 19:59:01 CEST 2013. I can send
the rest of the log.
Knut J
#--------------------------------------
#@# CA Reg Thu Sep 12 19:59:01 CEST 2013
/cluster/home/kjbjuland/freesurfer/long/NTNU_PRE_023_template/mri
mri_ca_register -nobigventricles -T transforms/talairach.lta
-align-after -mask
brainmask.mgz norm.mgz
/cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_a
ll_2008-03-26.gca transforms/talairach.m3z
not handling expanded ventricles...
using previously computed transform transforms/talairach.lta
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-regularize_mean 0.500
-regularize 0.500
using MR volume brainmask.mgz to mask input volume...
reading 1 input volumes...
logging results to talairach.log
======= NUMBER OF OPENMP THREADS = 1 =======
reading input volume 'norm.mgz'...
reading GCA
'/cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_all_2008-03-26.gca'...
label assignment complete, 0 changed (0.00%)
det(m_affine) = 1.55 (predicted orig area = 5.2)
label assignment complete, 0 changed (0.00%)
freeing gibbs priors...done.
average std[0] = 5.0
**************** pass 1 of 1 ************************
setting smoothness coefficient to 0.039
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.932, neg=0, invalid=96777
On 09/12/2013 10:14 AM, Knut J Bjuland wrote:
Hi,
I have run recon-al longitudinal process on abel cluster with this
command recon-all -base @filename@_template -tp @filename@ -tp
@filename@v2 -all -debug. However, it crashed or is killed when it ran
mri_ca_register.
I have looked through the log, and I have not found a reason for it
being killed even tough I added -debug. The cluster is running sbatch
and CentOS release 6.4. Are there any debug options I can add or are
there any debugversion of mri_ca_register I can download? This happen
every time I run the program. I have asked for 8g ram when ran the
program.
Best regards
Knut Jørgen Bjuland
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