hello list,
sorry to keep bugging you all, but we are making a lot of progress
with our cluster, thanks to this list, and we are almost fully
functional which is very exciting, as we are seeing some very
impressive speeds on the larger jobs (especially bedpost!)
i implemented the symbolic links which were suggested to me in
earlier posts, and now we can run bedpostx jobs and FEAT jobs fine
from the gui, however we seem to have hit a snag with probtrackx.
here is the information i got from the user in question, please
advise what the problem could be, as it works fine from the command
line (although for some reason this job gets run on the head node
only and never gets submitted through the qsub process to the cluster.)
Running probtrackx from the GUI creates the appropriate output
directory, but only contains fdt_log.tcl and fdt_script.sh
If I open fdt_script.sh and paste only the probtrackx command into
the terminal command line, the job runs perfectly. This is the
command that I paste:
/common/fsl/bin/probtrackx --mode=seedmask -x /Volumes/Clinical/homes/
tyanagihara/sweat/DTI/mask-dump/seed-internalCapsule-mask.hdr -l -c
0.2 -S 2000 --steplength=0.5 -P 5000 --stop=/Volumes/Clinical/homes/
tyanagihara/sweat/DTI/mask-dump/target1-mask.hdr --forcedir --opd -s
This is the error I get when running from the GUI:
usage: at [-q x] [-f file] [-m] time
at -c job [job ...]
at [-f file] -t [[CC]YY]MMDDhhmm[.SS]
at -r job [job ...]
at -l -q queuename
at -l [job ...]
atq [-q x] [-v]
atrm job [job ...]
batch [-f file] [-m]
usage: at [-q x] [-f file] [-m] time
at -c job [job ...]
at [-f file] -t [[CC]YY]MMDDhhmm[.SS]
at -r job [job ...]
at -l -q queuename
at -l [job ...]
atq [-q x] [-v]
atrm job [job ...]
batch [-f file] [-m]
while executing
"exec batch -q long.q ${filebase}_script.sh"
("probtrackx" arm line 144)
invoked from within
"switch -- $probtrack(tool) {
eddy_current {
global eddy
set errorStr ""
if { $eddy(input) == "" } { set errorStr "You need to specify..."
(procedure "fdt:apply" line 5)
invoked from within
"fdt:apply .fdt keep"
invoked from within
".fdt.apply invoke"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list $w invoke]"
(procedure "tk::ButtonUp" line 22)
invoked from within
"tk::ButtonUp .fdt.apply"
(command bound to event)
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