Hello,
I'm new to FSL and I'm trying to use FDT to perform a DTI/tractography
analysis but Im having some trouble at the bedpostx stage. I am running FSL
4.1.2 and Ubuntu 8.04. Everything seems to work okay until the step when I
do the bedpostx process, it only lasts for about 30 minutes then gives me
the following message in the terminal:
bedpostx /home/rajeet/Desktop/new -n 2 -w 1 -b 1000
/usr/share/fsl/bin/bedpostx /home/rajeet/Desktop/new -n 2 -w 1 -b 1000
subjectdir is /home/rajeet/Desktop/new
Making bedpostx directory structure
Queuing preprocessing stages
Queuing parallel processing stage
0 slices processed
Queuing post processing stage
Done!
The GUI states that the process is done and the bedpostx folder was created
but it doesn't contain most of the normal output files (merged, means, and
dyads) are not there. The only files I see are bvals, bvecs, monitor,
commands.txt and the nodif_brain_mask along with the folders diff_slices,
logs, and xfms. If I try to run probtrackx anyway, it gives me a "Errors:
child killed: segmentation violation" message in the GUI with the following
error message coming up in a separate window:
mv: cannot move `/home/rajeet/Desktop/test/fdt_log.tcl' to `fdt.log':
Permission denied
mv: cannot move `/home/rajeet/Desktop/test/fdt_log.tcl' to `fdt.log':
Permission denied
while executing
"exec mv $logfile $copylog"
("probtrackx" arm line 165)
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)
If I go back and look at the display in the terminal window, it says:
mkdir -p /home/rajeet/Desktop/test
/usr/share/fsl/bin/probtrackx --mode=simple
--seedref=/home/rajeet/Desktop/new.bedpostX/nodif_brain_mask -o
/home/rajeet/Desktop/test -x /home/rajeet/Desktop/test/fdt_coordinates.txt
-l -c 0.2 -S 2000 --steplength=0.5 -P 5000 --forcedir --opd -s
/home/rajeet/Desktop/new.bedpostX/merged -m
/home/rajeet/Desktop/new.bedpostX/nodif_brain_mask
--dir=/home/rajeet/Desktop/test
7
175 0 0
Done!
rm /home/rajeet/Desktop/test/fdt_coordinates.txt
mv /home/rajeet/Desktop/test/fdt_log.tcl fdt.log
Can anyone help me out? Thanks in advance
Rajeet
