Hello everyone,
I'm trying to process a diffusion tensor dataset with 32 directions. I've
successfully run DTIFit on the data, bedpost_datacheck doesn't complain.
When I run bedpost, though, I get the message "0 slices processed" over and
over, and there doesn't seem to be any output in the .bedpost directory.
Instead, the processes run by the bedpost script seem to exit (processor
load drops to zero after having been at 100% for a few minutes and there's
no active thread in the ps output), only the timestamping mechanism keeps
working:
USER PID %CPU %MEM VSZ RSS TTY STAT START TIME COMMAND
johannes 32091 0.0 0.1 4704 1684 pts/6 S Nov05 0:00 bash
johannes 32461 3.2 0.1 3520 1748 pts/6 S Nov05 126:29 \_
/usr/X11R6/bi
johannes 32464 0.7 0.0 1816 924 pts/6 S Nov05 27:53 \_ top
johannes 31606 0.0 0.1 4712 1704 pts/3 S Nov05 0:00 -bash
johannes 32161 0.0 0.9 13224 9432 pts/3 T Nov05 0:01 \_
/data3/fsl3.2
johannes 32177 0.0 0.1 4484 1236 pts/3 T Nov05 0:03 | \_
/bin/sh /
johannes 19070 0.0 0.0 3932 524 pts/3 T 13:42 0:00 | \_
sleep
johannes 19073 0.0 0.0 2524 636 pts/3 R 13:43 0:00 \_ ps fu
I've attached the bedpost_datacheck output, a directory listing and the
command line log. I'm running on a 4 processor linux host (SuSE) in
parallelized mode.
I'd appreciate any suggestions where to look for mistakes.
Thanks
Johannes
fdt/data
dim1 128
dim2 128
dim3 60
dim4 33
datatype 16
pixdim1 1.7500000000
pixdim2 1.7500000000
pixdim3 2.0000000000
pixdim4 1.0000000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
fdt/nodif
dim1 128
dim2 128
dim3 60
dim4 1
datatype 16
pixdim1 1.7500000000
pixdim2 1.7500000000
pixdim3 2.0000000000
pixdim4 1.0000000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
fdt/nodif_brain_mask
dim1 128
dim2 128
dim3 60
dim4 1
datatype 16
pixdim1 1.7500000000
pixdim2 1.7500000000
pixdim3 2.0000000000
pixdim4 1.0000000000
cal_max 1.0000
cal_min 0.0000
file_type NIFTI-1+
num lines in fdt/bvals
1
num words in fdt/bvals
33
num lines in fdt/bvecs
3
num words in fdt/bvecs
99
johannes@heinzel7:/data3/fsl3.2/XXXXXXXX/fdt.bedpost> ls -R
.:
bvals bvecs diff_slices logs nodif.nii.gz nodif_brain.nii.gz nodif_brain_mask.nii.gz
./diff_slices:
./logs:
pid_19239
./logs/pid_19239:
johannes@heinzel7:/data3/fsl3.2/XXXXXXXX> Fdt
rm -rf /data3/fsl3.2/XXXXXXXX/fdt.bedpost
bedpost /data3/fsl3.2/XXXXXXXX/fdt
/data3/fsl3.2/fsl/bin/bedpost /data3/fsl3.2/XXXXXXXX/fdt
subjectdir is /data3/fsl3.2/XXXXXXXX/fdt
making bedpost directory
copying files to bedpost directory
processing data on hosts: heinzel7 heinzel7 heinzel7 heinzel7
0 slices processed
0 slices processed
0 slices processed
0 slices processed
0 slices processed
0 slices processed
0 slices processed
0 slices processed
0 slices processed
0 slices processed
0 slices processed
0 slices processed
0 slices processed
0 slices processed
0 slices processed
0 slices processed
0 slices processed
0 slices processed
0 slices processed
0 slices processed
0 slices processed
0 slices processed
0 slices processed
[ about 100 repetitions removed to reduce file size ]
0 slices processed
0 slices processed
0 slices processed
0 slices processed
0 slices processed
0 slices processed
0 slices processed
0 slices processed
0 slices processed
0 slices processed
0 slices processed
0 slices processed
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