Hello,
I am attempting to run bedpostx, and have run into a problem. The script seems to start properly, and the monitor shows it making progress, but it finishes without having processed all of the slices. Different subjects end up with different number of slices having been processed. For example, one subject with 39 slices ends up with 17 processed. Running monitor after completion gives the following output:
17 slices processed
All slices processed
The commands.txt file has one line for each of the 39 slices. The logs directory has a bedpostx.o6427 and a bedpostx.e6427 file for each of the 39 slices, but only 17 log#### files.
Has anyone encountered this before and/or found a workaround?
Many thanks,
Dallas Card
The output of fslerrorreport is shown below.
######################################################################
#### MACHINE INFORMATION
######################################################################
Uname:
Linux
df:
Filesystem 1K-blocks Used Available Use% Mounted on
/dev/sda5 1324615648 1055235368 202093636 84% /data
quota:
Memory and Swap info:
MemTotal: 8310140 kB
MemFree: 3261424 kB
Buffers: 347732 kB
Cached: 3564976 kB
SwapCached: 32 kB
Active: 3483496 kB
Inactive: 1391464 kB
HighTotal: 7470464 kB
HighFree: 2928448 kB
LowTotal: 839676 kB
LowFree: 332976 kB
SwapTotal: 16386292 kB
SwapFree: 16383532 kB
Dirty: 148 kB
Writeback: 0 kB
Mapped: 936696 kB
Slab: 129460 kB
CommitLimit: 20541360 kB
Committed_AS: 2046804 kB
PageTables: 14820 kB
VmallocTotal: 106488 kB
VmallocUsed: 12160 kB
VmallocChunk: 94020 kB
HugePages_Total: 0
HugePages_Free: 0
Hugepagesize: 2048 kB
######################################################################
#### ENVIRONMENT INFORMATION
######################################################################
FSLMULTIFILEQUIT=TRUE
FSLMACHTYPE=linux_32-gcc3.4
FSLTCLSH=/usr/local/fsl/bin/fsltclsh
FSLMACHINELIST=
FSLREMOTECALL=
FSLCONFDIR=/usr/local/fsl/config
FSLWISH=/usr/local/fsl/bin/fslwish
FSLDIR=/usr/local/fsl
FSLLOCKDIR=
FSLOUTPUTTYPE=NIFTI
MANPATH=/opt/sge/man:/opt/sge/man:/usr/share/man:/usr/local/share/man:/usr/local/man:/usr/X11R6/man
LD_LIBRARY_PATH=/opt/ctf/lib:/opt/ctf/lib:/usr/lib:/usr/local/lib:/usr/X11R6/lib:/usr/local/minc/lib
PATH=/usr/local/fsl/bin:/opt/ctf/bin:/usr/bin/X11:/usr/local/bin:/usr/local/mysql/bin:/opt/sge/bin/lx24-x86:/usr/local/fsl/bi
n:/opt/ctf/bin:/usr/bin/X11:/usr/local/bin:/usr/local/mysql/bin:/usr/kerberos/bin:/opt/sge/bin/lx24-x86:/opt/openoffice.org3/
program:/usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin:/usr/local/afni:/usr/local/afni/bin:/usr/local/minc/bin:/usr/local/fsl/bi
n:/usr/local/scripts:/usr/local/matlab/bin:/usr/local/octave/bin:/usr/local/nil/bin:/usr/local/camino/bin:/usr/java/jdk1.6.0_
06/bin:/usr/local/get11:/usr/local/mri3dx/bx:/usr/local/AIR5.2.6/bin:/usr/local/freesurfer/mni/bin:/usr/local/ANTS:/usr/local
/nil/bin:/home/dallas:/usr/local/bx/:/home/dallas/bin:/usr/local/nil/bin:/home/dallas:/usr/local/bx/:/home/dallas/bin
XUSERFILESEARCHPATH=/home/dallas/%N:/opt/ctf/app-defaults/%N:/home/dallas/%N:/opt/ctf/app-defaults/%N
LD_LIBRARY_PATH=/opt/ctf/lib:/opt/ctf/lib:/usr/lib:/usr/local/lib:/usr/X11R6/lib:/usr/local/minc/lib
######################################################################
#### DIRECTORY INFORMATION
######################################################################
PWD:
/data/jvillafuerte/downsampled_for_tractography/p_ACa.bedpostX
total 52
drwxrwxrwx 5 dallas users 4096 Feb 15 17:47 .
drwxr-xr-x 68 dallas users 4096 Feb 15 17:03 ..
-rw-r--r-- 1 dallas users 182 Feb 15 10:34 bvals
-rw-r--r-- 1 dallas users 1010 Feb 15 10:34 bvecs
-rwxrwxrwx 1 dallas users 30 Feb 15 10:34 cancel
-rw-rw-rw- 1 dallas users 4790 Feb 15 10:34 commands.txt
drwxrwxrwx 19 dallas users 4096 Feb 15 11:42 diff_slices
-rw-rw-rw- 1 dallas users 0 Feb 15 17:49 errorreport.txt
drwxrwxrwx 4 dallas users 4096 Feb 15 11:50 logs
-rwxrwxrwx 1 dallas users 696 Feb 15 10:34 monitor
-rw-r--r-- 1 dallas users 4840 Feb 15 10:34 nodif_brain_mask.nii.gz
drwxrwxrwx 2 dallas users 4096 Feb 15 11:50 xfms
######################################################################
#### FDT INFORMATION
######################################################################
######################################################################
#### Main directory:
total 52
drwxrwxrwx 5 dallas users 4096 Feb 15 17:47 .
drwxr-xr-x 68 dallas users 4096 Feb 15 17:03 ..
-rw-r--r-- 1 dallas users 182 Feb 15 10:34 bvals
-rw-r--r-- 1 dallas users 1010 Feb 15 10:34 bvecs
-rwxrwxrwx 1 dallas users 30 Feb 15 10:34 cancel
-rw-rw-rw- 1 dallas users 4790 Feb 15 10:34 commands.txt
drwxrwxrwx 19 dallas users 4096 Feb 15 11:42 diff_slices
-rw-rw-rw- 1 dallas users 0 Feb 15 17:49 errorreport.txt
drwxrwxrwx 4 dallas users 4096 Feb 15 11:50 logs
-rwxrwxrwx 1 dallas users 696 Feb 15 10:34 monitor
-rw-r--r-- 1 dallas users 4840 Feb 15 10:34 nodif_brain_mask.nii.gz
drwxrwxrwx 2 dallas users 4096 Feb 15 11:50 xfms
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