Hello FSL,
I have encountered difficulties bedposting data, and appreciate any advice you can offer. In summary, when I attempt to bedpost using the GUI, bedposting ends after 10 seconds without producing results. When I attempt to bedpost from the command line, bedposting runs indefinitely without producing results.
(A) When I attempt to bedpost using the GUI (FSL 5.0.4, using tutorial data) and default parameters (fibres=2, weight=1, burn in=1000), FDT runs for about 10 seconds before displaying "0 slices processed." and the "Done" pop-up message. However, there is no data in the .bedpostx directory.
While running, the command line displays the following:
switching from /home/ajames/dti/gui to /home/ajames/dti/gui
bedpostx /home/ajames/dti/gui/. --nf=2 --fudge=1 --bi=1000
/usr/local/fsl/bin/bedpostx /home/ajames/dti/gui/. --nf=2 --fudge=1 --bi=1000
subjectdir is /home/ajames/dti/gui
Making bedpostx directory structure
Queuing preprocessing stages
Queuing parallel processing stage
Queuing post processing stage
Type /home/ajames/dti/gui.bedpostX/monitor to show progress.
Type /home/ajames/dti/gui.bedpostX/cancel to terminate all the queued tasks.
You will get an email at the end of the post-processing stage.
Done!
... and the fslerrorreport reads as follows:
ERROR: Could not open file
######################################################################
#### MACHINE INFORMATION
######################################################################
Uname:
Linux
df:
Filesystem 1K-blocks Used Available Use% Mounted on
/dev/mapper/work-worklv
5160663560 2577201524 2321361152 53% /home
quota:
Memory and Swap info:
MemTotal: 33554432 kB
MemFree: 454348 kB
Buffers: 570036 kB
Cached: 30358108 kB
SwapCached: 0 kB
Active: 8821616 kB
Inactive: 22787576 kB
HighTotal: 0 kB
HighFree: 0 kB
LowTotal: 33554432 kB
LowFree: 454348 kB
SwapTotal: 1020116 kB
SwapFree: 1017036 kB
Dirty: 88428 kB
Writeback: 0 kB
AnonPages: 680792 kB
Mapped: 145704 kB
Slab: 615476 kB
PageTables: 60516 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
CommitLimit: 17797332 kB
Committed_AS: 2427720 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 3236 kB
VmallocChunk: 34359735095 kB
######################################################################
#### ENVIRONMENT INFORMATION
######################################################################
FSLMULTIFILEQUIT=TRUE
FSLMACHTYPE=linux_64-gcc4.1
FSLTCLSH=/usr/local/fsl/bin/fsltclsh
FSLMACHINELIST=
FSLREMOTECALL=
FSLWISH=/usr/local/fsl/bin/fslwish
FSLCONFDIR=/usr/local/fsl/config
FSLDIR=/usr/local/fsl
FSLLOCKDIR=
FSLOUTPUTTYPE=NIFTI_GZ
LD_LIBRARY_PATH=/opt/gridengine/lib/lx26-amd64
PATH=/opt/gridengine/bin/lx26-amd64:/usr/kerberos/bin:/usr/java/latest/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/dtk:/usr/local/AFNI/linux_xorg7_64:/usr/local/AFNI/linux_xorg7_64:/usr/local/fsl/bin:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/openmpi/bin/:/opt/rocks/bin:/opt/rocks/sbin:/opt/sun-ct/bin:/home/ajames/bin
LD_LIBRARY_PATH=/opt/gridengine/lib/lx26-amd64
######################################################################
#### DIRECTORY INFORMATION
######################################################################
PWD:
/home/ajames/dti/gui
total 109968
drwxrwxr-x 2 ajames birc 4096 Jul 1 14:36 .
drwxrwxr-x 6 ajames birc 4096 Jul 1 14:36 ..
-rw-rw-r-- 1 ajames birc 60 Jul 1 14:36 bedpostcom_log.tcl
-rwxr-xr-x 1 ajames birc 1041 Jul 1 14:35 bvals
-rwxr-xr-x 1 ajames birc 2988 Jul 1 14:35 bvecs
-rwxr-xr-x 1 ajames birc 110756192 Jul 1 14:35 data.nii
-rw-r--r-- 1 ajames birc 1704288 Jul 1 14:35 nodif_brain_mask.nii
######################################################################
#### IMAGE INFORMATION
######################################################################
This error report is saved in the file: /tmp/fsl_iT7iNF.gz
(B) When I attempt to bedpost using the command line (using command "bedpostx /home/ajames/dti/commandline/ -n 1", all default options), the bedposting runs indefinitely with no results. After 3 days, the monitor command still reads "0 slices processed."
When I run fslerrorreport, I get this message:
/usr/local/fsl/bin/fslerrorreport: line 232: /usr/local/fsl/bin/bedpost_datacheck: No such file or directory
######################################################################
#### MACHINE INFORMATION
######################################################################
Uname:
Linux
df:
Filesystem 1K-blocks Used Available Use% Mounted on
/dev/mapper/work-worklv
5160663560 2576385512 2322177164 53% /home
quota:
Memory and Swap info:
MemTotal: 33554432 kB
MemFree: 919644 kB
Buffers: 624452 kB
Cached: 30014452 kB
SwapCached: 0 kB
Active: 16034928 kB
Inactive: 15114520 kB
HighTotal: 0 kB
HighFree: 0 kB
LowTotal: 33554432 kB
LowFree: 919644 kB
SwapTotal: 1020116 kB
SwapFree: 1017036 kB
Dirty: 32 kB
Writeback: 0 kB
AnonPages: 510248 kB
Mapped: 125964 kB
Slab: 614140 kB
PageTables: 54932 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
CommitLimit: 17797332 kB
Committed_AS: 2169488 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 3236 kB
VmallocChunk: 34359735095 kB
######################################################################
#### ENVIRONMENT INFORMATION
######################################################################
FSLMULTIFILEQUIT=TRUE
FSLMACHTYPE=linux_64-gcc4.1
FSLTCLSH=/usr/local/fsl/bin/fsltclsh
FSLMACHINELIST=
FSLREMOTECALL=
FSLWISH=/usr/local/fsl/bin/fslwish
FSLCONFDIR=/usr/local/fsl/config
FSLDIR=/usr/local/fsl
FSLLOCKDIR=
FSLOUTPUTTYPE=NIFTI_GZ
LD_LIBRARY_PATH=/opt/gridengine/lib/lx26-amd64
PATH=/opt/gridengine/bin/lx26-amd64:/usr/kerberos/bin:/usr/java/latest/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/dtk:/usr/local/AFNI/linux_xorg7_64:/usr/local/AFNI/linux_xorg7_64:/usr/local/fsl/bin:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/openmpi/bin/:/opt/rocks/bin:/opt/rocks/sbin:/opt/sun-ct/bin:/home/ajames/bin
LD_LIBRARY_PATH=/opt/gridengine/lib/lx26-amd64
######################################################################
#### DIRECTORY INFORMATION
######################################################################
PWD:
/home/ajames/dti/commandline.bedpostX
total 40
drwxrwxr-x 5 ajames birc 4096 Jul 1 14:43 .
drwxrwxr-x 8 ajames birc 4096 Jul 1 14:43 ..
-rwxrwxr-x 1 ajames birc 39 Jul 1 14:43 cancel
-rw-rw-r-- 1 ajames birc 9270 Jul 1 14:43 commands.txt
drwxrwxr-x 2 ajames birc 4096 Jul 1 14:43 diff_slices
drwxrwxr-x 3 ajames birc 4096 Jul 1 14:43 logs
-rwxrwxr-x 1 ajames birc 621 Jul 1 14:43 monitor
drwxrwxr-x 2 ajames birc 4096 Jul 1 14:43 xfms
######################################################################
#### FDT INFORMATION
######################################################################
######################################################################
#### Main directory:
total 40
drwxrwxr-x 5 ajames birc 4096 Jul 1 14:43 .
drwxrwxr-x 8 ajames birc 4096 Jul 1 14:43 ..
-rwxrwxr-x 1 ajames birc 39 Jul 1 14:43 cancel
-rw-rw-r-- 1 ajames birc 9270 Jul 1 14:43 commands.txt
drwxrwxr-x 2 ajames birc 4096 Jul 1 14:43 diff_slices
drwxrwxr-x 3 ajames birc 4096 Jul 1 14:43 logs
-rwxrwxr-x 1 ajames birc 621 Jul 1 14:43 monitor
drwxrwxr-x 2 ajames birc 4096 Jul 1 14:43 xfms
This error report is saved in the file: /tmp/fsl_xyx5Gj.gz
(C) I noticed in the command line fslerrorreport:
/usr/local/fsl/bin/fslerrorreport: line 232: /usr/local/fsl/bin/bedpost_datacheck: No such file or directory
Checking the /usr/local/fsl/bin/ directory, I have a bedpostx_datacheck file but not a bedpost_datacheck. Could this be an incomplete installation issue?. I am new to FSL and could not get bedposting to work using v4.something, so I upgraded last week to v5.0.4 (running the self-install from root). How can I check that I have all the necessary files - and if not, replace them?
Strangely, everything else works. We can process data up to bedposting, and we can process pre-bedposted data to completion. But this step keeps failing.
Thank you,
Andy James
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