Hi Dave!
Thanks a lot for your explications!
> 1) is this running under SGE?
No, I have 3 single PC running under vmware and fsl-Centos5_32.
> could your run this by hand and see what nslices gets set to (echo
> $nslices)? Is it 40 or 64?
Ideed, you are right: The old data which I am processing with FSL 4.0.2 give
'fslval data.nii.gz dim3' = 40 slices, the other data (which I am
treating with FSL 4.0.1) give 65 (it was another aquisition protocol,
thats correct.)
> All versions 4.0.x should have the monitor function and you should've
> seen a message on the command line telling you that monitor and cancel
> exist and here's how to call them?
Hmm. I have two installations of FSL 4.0.1 on wmvare and neither of
them shows monitor, and neither of them "talks to me" while processing
bedpost.
Only the version FSL 4.0.2 (on a third PC) has monitor and "talks".
This is what the output was after bedposting - I am not sure if
everything is right.
subjectdir is /mnt/hgfs/Windows/CHUV_2006/s2/bedpostx
Making bedpostx directory structure
Queuing preprocessing stages
Queuing parallel processing stage
0 slices processed
10 slices processed
14 slices processed
18 slices processed
21 slices processed
24 slices processed
28 slices processed
32 slices processed
Queuing post processing stage
/usr/local/fsl/bin/bedpostx: line 207: 6225 Terminated
${subjdir}.bedpostX/monitor
subjectdir is /mnt/hgfs/Windows/CHUV_2006/s2/bedpostx
Making bedpostx directory structure
Queuing preprocessing stages
Queuing parallel processing stage
40 slices processed
/usr/local/fsl/bin/bedpostx: line 203: kill: (7908) - No such process
Queuing post processing stage
>> What I don't understand is why the program xfibres, however,
>> continues working (for several hours, c.f. 'top') while monitor and
>> logfiles stopped!
>
> Again there appears to be a discrepancy between your input and the
> output directory. Try cancelling any pending run and moving the output
> directory out of the way and starting afresh. If you still get the
> strange behaviour then something else is wrong.
Yes this is still true.
Here, I found this in ALL bedpostx_preproc.sh.e* files in all my
versions (4.0.1 and 4.0.2):
** ERROR (nifti_image_read): failed to find header file for
'/mnt/hgfs/Windows/C
HUV_2006/s2/bedpostx/nodif'
** ERROR:
nifti_image_open(/mnt/hgfs/Windows/CHUV_2006/s2/bedpostx/nodif): bad h
eader info
Error: failed to open file /mnt/hgfs/Windows/CHUV_2006/s2/bedpostx/nodif
Cannot open volume /mnt/hgfs/Windows/CHUV_2006/s2/bedpostx/nodif for reading!
(NB: as expained on the webpage, I called the 4D volume 'data' and not
'nodif'. There is no 'nodif' in my bedpostx folder).
I am planning to process 16 subjects over holydays, thats why I need
to be sure that it really is not bug ;-)
Thanks a lot for all help!
Cheers Markus
PS: This is the content of the bedpostx.bedpostX/logs/:
-rwxrwxrwx 1 root root 0 Dec 19 10:36 bedpostx.e6226.1
-rwxrwxrwx 1 root root 0 Dec 19 10:55 bedpostx.e6226.10
-rwxrwxrwx 1 root root 0 Dec 19 11:00 bedpostx.e6226.11
-rwxrwxrwx 1 root root 0 Dec 19 11:05 bedpostx.e6226.12
-rwxrwxrwx 1 root root 0 Dec 19 11:11 bedpostx.e6226.13
-rwxrwxrwx 1 root root 0 Dec 19 11:17 bedpostx.e6226.14
-rwxrwxrwx 1 root root 0 Dec 19 11:24 bedpostx.e6226.15
-rwxrwxrwx 1 root root 0 Dec 19 11:31 bedpostx.e6226.16
-rwxrwxrwx 1 root root 0 Dec 19 11:39 bedpostx.e6226.17
-rwxrwxrwx 1 root root 0 Dec 19 11:47 bedpostx.e6226.18
-rwxrwxrwx 1 root root 0 Dec 19 11:55 bedpostx.e6226.19
-rwxrwxrwx 1 root root 0 Dec 19 10:37 bedpostx.e6226.2
-rwxrwxrwx 1 root root 0 Dec 19 12:04 bedpostx.e6226.20
-rwxrwxrwx 1 root root 0 Dec 19 12:13 bedpostx.e6226.21
-rwxrwxrwx 1 root root 0 Dec 19 12:21 bedpostx.e6226.22
-rwxrwxrwx 1 root root 0 Dec 19 12:30 bedpostx.e6226.23
-rwxrwxrwx 1 root root 0 Dec 19 12:38 bedpostx.e6226.24
-rwxrwxrwx 1 root root 0 Dec 19 12:47 bedpostx.e6226.25
-rwxrwxrwx 1 root root 0 Dec 19 12:55 bedpostx.e6226.26
-rwxrwxrwx 1 root root 0 Dec 19 13:04 bedpostx.e6226.27
-rwxrwxrwx 1 root root 0 Dec 19 13:12 bedpostx.e6226.28
-rwxrwxrwx 1 root root 0 Dec 19 13:19 bedpostx.e6226.29
-rwxrwxrwx 1 root root 0 Dec 19 10:38 bedpostx.e6226.3
-rwxrwxrwx 1 root root 0 Dec 19 13:27 bedpostx.e6226.30
-rwxrwxrwx 1 root root 0 Dec 19 13:34 bedpostx.e6226.31
-rwxrwxrwx 1 root root 0 Dec 19 13:40 bedpostx.e6226.32
-rwxrwxrwx 1 root root 0 Dec 19 13:46 bedpostx.e6226.33
-rwxrwxrwx 1 root root 0 Dec 19 13:51 bedpostx.e6226.34
-rwxrwxrwx 1 root root 0 Dec 19 13:56 bedpostx.e6226.35
-rwxrwxrwx 1 root root 0 Dec 19 14:00 bedpostx.e6226.36
-rwxrwxrwx 1 root root 0 Dec 19 14:03 bedpostx.e6226.37
-rwxrwxrwx 1 root root 0 Dec 19 14:06 bedpostx.e6226.38
-rwxrwxrwx 1 root root 0 Dec 19 14:07 bedpostx.e6226.39
-rwxrwxrwx 1 root root 0 Dec 19 10:39 bedpostx.e6226.4
-rwxrwxrwx 1 root root 0 Dec 19 14:08 bedpostx.e6226.40
-rwxrwxrwx 1 root root 0 Dec 19 10:41 bedpostx.e6226.5
-rwxrwxrwx 1 root root 0 Dec 19 10:43 bedpostx.e6226.6
-rwxrwxrwx 1 root root 0 Dec 19 10:46 bedpostx.e6226.7
-rwxrwxrwx 1 root root 0 Dec 19 10:49 bedpostx.e6226.8
-rwxrwxrwx 1 root root 0 Dec 19 10:52 bedpostx.e6226.9
-rwxrwxrwx 1 root root 0 Dec 19 14:11 bedpostx.e7909.1
-rwxrwxrwx 1 root root 0 Dec 19 14:30 bedpostx.e7909.10
-rwxrwxrwx 1 root root 0 Dec 19 14:35 bedpostx.e7909.11
-rwxrwxrwx 1 root root 0 Dec 19 14:40 bedpostx.e7909.12
-rwxrwxrwx 1 root root 0 Dec 19 14:46 bedpostx.e7909.13
-rwxrwxrwx 1 root root 0 Dec 19 14:52 bedpostx.e7909.14
-rwxrwxrwx 1 root root 0 Dec 19 14:59 bedpostx.e7909.15
-rwxrwxrwx 1 root root 0 Dec 19 15:06 bedpostx.e7909.16
-rwxrwxrwx 1 root root 0 Dec 19 15:14 bedpostx.e7909.17
-rwxrwxrwx 1 root root 0 Dec 19 15:22 bedpostx.e7909.18
-rwxrwxrwx 1 root root 0 Dec 19 15:30 bedpostx.e7909.19
-rwxrwxrwx 1 root root 0 Dec 19 14:11 bedpostx.e7909.2
-rwxrwxrwx 1 root root 0 Dec 19 15:39 bedpostx.e7909.20
-rwxrwxrwx 1 root root 0 Dec 19 15:47 bedpostx.e7909.21
-rwxrwxrwx 1 root root 0 Dec 19 15:56 bedpostx.e7909.22
-rwxrwxrwx 1 root root 0 Dec 19 16:05 bedpostx.e7909.23
-rwxrwxrwx 1 root root 0 Dec 19 16:13 bedpostx.e7909.24
-rwxrwxrwx 1 root root 0 Dec 19 16:22 bedpostx.e7909.25
-rwxrwxrwx 1 root root 0 Dec 19 16:30 bedpostx.e7909.26
-rwxrwxrwx 1 root root 0 Dec 19 16:39 bedpostx.e7909.27
-rwxrwxrwx 1 root root 0 Dec 19 16:47 bedpostx.e7909.28
-rwxrwxrwx 1 root root 0 Dec 19 16:54 bedpostx.e7909.29
-rwxrwxrwx 1 root root 0 Dec 19 14:13 bedpostx.e7909.3
-rwxrwxrwx 1 root root 0 Dec 19 17:02 bedpostx.e7909.30
-rwxrwxrwx 1 root root 0 Dec 19 17:09 bedpostx.e7909.31
-rwxrwxrwx 1 root root 0 Dec 19 17:15 bedpostx.e7909.32
-rwxrwxrwx 1 root root 0 Dec 19 17:21 bedpostx.e7909.33
-rwxrwxrwx 1 root root 0 Dec 19 17:26 bedpostx.e7909.34
-rwxrwxrwx 1 root root 0 Dec 19 17:31 bedpostx.e7909.35
-rwxrwxrwx 1 root root 0 Dec 19 17:35 bedpostx.e7909.36
-rwxrwxrwx 1 root root 0 Dec 19 17:38 bedpostx.e7909.37
-rwxrwxrwx 1 root root 0 Dec 19 17:41 bedpostx.e7909.38
-rwxrwxrwx 1 root root 0 Dec 19 17:42 bedpostx.e7909.39
-rwxrwxrwx 1 root root 0 Dec 19 14:14 bedpostx.e7909.4
-rwxrwxrwx 1 root root 0 Dec 19 17:44 bedpostx.e7909.40
-rwxrwxrwx 1 root root 0 Dec 19 14:16 bedpostx.e7909.5
-rwxrwxrwx 1 root root 0 Dec 19 14:18 bedpostx.e7909.6
-rwxrwxrwx 1 root root 0 Dec 19 14:21 bedpostx.e7909.7
-rwxrwxrwx 1 root root 0 Dec 19 14:23 bedpostx.e7909.8
-rwxrwxrwx 1 root root 0 Dec 19 14:26 bedpostx.e7909.9
-rwxrwxrwx 1 root root 5 Dec 19 10:37 bedpostx.o6226.1
-rwxrwxrwx 1 root root 5 Dec 19 11:00 bedpostx.o6226.10
-rwxrwxrwx 1 root root 5 Dec 19 11:05 bedpostx.o6226.11
-rwxrwxrwx 1 root root 5 Dec 19 11:11 bedpostx.o6226.12
-rwxrwxrwx 1 root root 5 Dec 19 11:17 bedpostx.o6226.13
-rwxrwxrwx 1 root root 5 Dec 19 11:24 bedpostx.o6226.14
-rwxrwxrwx 1 root root 5 Dec 19 11:31 bedpostx.o6226.15
-rwxrwxrwx 1 root root 5 Dec 19 11:39 bedpostx.o6226.16
-rwxrwxrwx 1 root root 5 Dec 19 11:47 bedpostx.o6226.17
-rwxrwxrwx 1 root root 5 Dec 19 11:55 bedpostx.o6226.18
-rwxrwxrwx 1 root root 5 Dec 19 12:04 bedpostx.o6226.19
-rwxrwxrwx 1 root root 5 Dec 19 10:38 bedpostx.o6226.2
-rwxrwxrwx 1 root root 5 Dec 19 12:13 bedpostx.o6226.20
-rwxrwxrwx 1 root root 5 Dec 19 12:21 bedpostx.o6226.21
-rwxrwxrwx 1 root root 5 Dec 19 12:30 bedpostx.o6226.22
-rwxrwxrwx 1 root root 5 Dec 19 12:38 bedpostx.o6226.23
-rwxrwxrwx 1 root root 5 Dec 19 12:47 bedpostx.o6226.24
-rwxrwxrwx 1 root root 5 Dec 19 12:55 bedpostx.o6226.25
-rwxrwxrwx 1 root root 5 Dec 19 13:04 bedpostx.o6226.26
-rwxrwxrwx 1 root root 5 Dec 19 13:12 bedpostx.o6226.27
-rwxrwxrwx 1 root root 5 Dec 19 13:19 bedpostx.o6226.28
-rwxrwxrwx 1 root root 5 Dec 19 13:27 bedpostx.o6226.29
-rwxrwxrwx 1 root root 5 Dec 19 10:39 bedpostx.o6226.3
-rwxrwxrwx 1 root root 5 Dec 19 13:34 bedpostx.o6226.30
-rwxrwxrwx 1 root root 5 Dec 19 13:40 bedpostx.o6226.31
-rwxrwxrwx 1 root root 5 Dec 19 13:46 bedpostx.o6226.32
-rwxrwxrwx 1 root root 5 Dec 19 13:51 bedpostx.o6226.33
-rwxrwxrwx 1 root root 5 Dec 19 13:56 bedpostx.o6226.34
-rwxrwxrwx 1 root root 5 Dec 19 14:00 bedpostx.o6226.35
-rwxrwxrwx 1 root root 5 Dec 19 14:03 bedpostx.o6226.36
-rwxrwxrwx 1 root root 5 Dec 19 14:06 bedpostx.o6226.37
-rwxrwxrwx 1 root root 5 Dec 19 14:07 bedpostx.o6226.38
-rwxrwxrwx 1 root root 5 Dec 19 14:08 bedpostx.o6226.39
-rwxrwxrwx 1 root root 5 Dec 19 10:41 bedpostx.o6226.4
-rwxrwxrwx 1 root root 5 Dec 19 14:09 bedpostx.o6226.40
-rwxrwxrwx 1 root root 5 Dec 19 10:43 bedpostx.o6226.5
-rwxrwxrwx 1 root root 5 Dec 19 10:46 bedpostx.o6226.6
-rwxrwxrwx 1 root root 5 Dec 19 10:49 bedpostx.o6226.7
-rwxrwxrwx 1 root root 5 Dec 19 10:52 bedpostx.o6226.8
-rwxrwxrwx 1 root root 5 Dec 19 10:55 bedpostx.o6226.9
-rwxrwxrwx 1 root root 5 Dec 19 14:11 bedpostx.o7909.1
-rwxrwxrwx 1 root root 5 Dec 19 14:35 bedpostx.o7909.10
-rwxrwxrwx 1 root root 5 Dec 19 14:40 bedpostx.o7909.11
-rwxrwxrwx 1 root root 5 Dec 19 14:46 bedpostx.o7909.12
-rwxrwxrwx 1 root root 5 Dec 19 14:52 bedpostx.o7909.13
-rwxrwxrwx 1 root root 5 Dec 19 14:59 bedpostx.o7909.14
-rwxrwxrwx 1 root root 5 Dec 19 15:06 bedpostx.o7909.15
-rwxrwxrwx 1 root root 5 Dec 19 15:14 bedpostx.o7909.16
-rwxrwxrwx 1 root root 5 Dec 19 15:22 bedpostx.o7909.17
-rwxrwxrwx 1 root root 5 Dec 19 15:30 bedpostx.o7909.18
-rwxrwxrwx 1 root root 5 Dec 19 15:39 bedpostx.o7909.19
-rwxrwxrwx 1 root root 5 Dec 19 14:13 bedpostx.o7909.2
-rwxrwxrwx 1 root root 5 Dec 19 15:47 bedpostx.o7909.20
-rwxrwxrwx 1 root root 5 Dec 19 15:56 bedpostx.o7909.21
-rwxrwxrwx 1 root root 5 Dec 19 16:05 bedpostx.o7909.22
-rwxrwxrwx 1 root root 5 Dec 19 16:13 bedpostx.o7909.23
-rwxrwxrwx 1 root root 5 Dec 19 16:22 bedpostx.o7909.24
-rwxrwxrwx 1 root root 5 Dec 19 16:30 bedpostx.o7909.25
-rwxrwxrwx 1 root root 5 Dec 19 16:39 bedpostx.o7909.26
-rwxrwxrwx 1 root root 5 Dec 19 16:47 bedpostx.o7909.27
-rwxrwxrwx 1 root root 5 Dec 19 16:54 bedpostx.o7909.28
-rwxrwxrwx 1 root root 5 Dec 19 17:02 bedpostx.o7909.29
-rwxrwxrwx 1 root root 5 Dec 19 14:14 bedpostx.o7909.3
-rwxrwxrwx 1 root root 5 Dec 19 17:09 bedpostx.o7909.30
-rwxrwxrwx 1 root root 5 Dec 19 17:15 bedpostx.o7909.31
-rwxrwxrwx 1 root root 5 Dec 19 17:21 bedpostx.o7909.32
-rwxrwxrwx 1 root root 5 Dec 19 17:26 bedpostx.o7909.33
-rwxrwxrwx 1 root root 5 Dec 19 17:31 bedpostx.o7909.34
-rwxrwxrwx 1 root root 5 Dec 19 17:35 bedpostx.o7909.35
-rwxrwxrwx 1 root root 5 Dec 19 17:38 bedpostx.o7909.36
-rwxrwxrwx 1 root root 5 Dec 19 17:41 bedpostx.o7909.37
-rwxrwxrwx 1 root root 5 Dec 19 17:42 bedpostx.o7909.38
-rwxrwxrwx 1 root root 5 Dec 19 17:44 bedpostx.o7909.39
-rwxrwxrwx 1 root root 5 Dec 19 14:16 bedpostx.o7909.4
-rwxrwxrwx 1 root root 5 Dec 19 17:44 bedpostx.o7909.40
-rwxrwxrwx 1 root root 5 Dec 19 14:18 bedpostx.o7909.5
-rwxrwxrwx 1 root root 5 Dec 19 14:21 bedpostx.o7909.6
-rwxrwxrwx 1 root root 5 Dec 19 14:23 bedpostx.o7909.7
-rwxrwxrwx 1 root root 5 Dec 19 14:26 bedpostx.o7909.8
-rwxrwxrwx 1 root root 5 Dec 19 14:30 bedpostx.o7909.9
-rwxrwxrwx 1 root root 0 Dec 19 14:09 bedpostx_postproc.sh.e7348
-rwxrwxrwx 1 root root 0 Dec 19 17:44 bedpostx_postproc.sh.e9043
-rwxrwxrwx 1 root root 55 Dec 19 14:11 bedpostx_postproc.sh.o7348
-rwxrwxrwx 1 root root 55 Dec 19 17:46 bedpostx_postproc.sh.o9043
-rwxrwxrwx 1 root root 350 Dec 19 10:36 bedpostx_preproc.sh.e6042
-rwxrwxrwx 1 root root 350 Dec 19 14:11 bedpostx_preproc.sh.e7724
-rwxrwxrwx 1 root root 40 Dec 19 10:36 bedpostx_preproc.sh.o6042
-rwxrwxrwx 1 root root 40 Dec 19 14:11 bedpostx_preproc.sh.o7724
-rwxrwxrwx 1 root root 3051 Dec 19 14:11 log0000
-rwxrwxrwx 1 root root 5131 Dec 19 14:13 log0001
-rwxrwxrwx 1 root root 6699 Dec 19 14:14 log0002
-rwxrwxrwx 1 root root 9098 Dec 19 14:16 log0003
-rwxrwxrwx 1 root root 10698 Dec 19 14:18 log0004
-rwxrwxrwx 1 root root 12098 Dec 19 14:21 log0005
-rwxrwxrwx 1 root root 13138 Dec 19 14:23 log0006
-rwxrwxrwx 1 root root 14888 Dec 19 14:26 log0007
-rwxrwxrwx 1 root root 18708 Dec 19 14:30 log0008
-rwxrwxrwx 1 root root 23378 Dec 19 14:35 log0009
-rwxrwxrwx 1 root root 27768 Dec 19 14:40 log0010
-rwxrwxrwx 1 root root 30428 Dec 19 14:46 log0011
-rwxrwxrwx 1 root root 31988 Dec 19 14:52 log0012
-rwxrwxrwx 1 root root 34358 Dec 19 14:59 log0013
-rwxrwxrwx 1 root root 37038 Dec 19 15:06 log0014
-rwxrwxrwx 1 root root 39118 Dec 19 15:14 log0015
-rwxrwxrwx 1 root root 41408 Dec 19 15:22 log0016
-rwxrwxrwx 1 root root 43248 Dec 19 15:30 log0017
-rwxrwxrwx 1 root root 44278 Dec 19 15:39 log0018
-rwxrwxrwx 1 root root 44918 Dec 19 15:47 log0019
-rwxrwxrwx 1 root root 45058 Dec 19 15:56 log0020
-rwxrwxrwx 1 root root 44948 Dec 19 16:05 log0021
-rwxrwxrwx 1 root root 44648 Dec 19 16:13 log0022
-rwxrwxrwx 1 root root 44348 Dec 19 16:22 log0023
-rwxrwxrwx 1 root root 43718 Dec 19 16:30 log0024
-rwxrwxrwx 1 root root 42928 Dec 19 16:39 log0025
-rwxrwxrwx 1 root root 41868 Dec 19 16:47 log0026
-rwxrwxrwx 1 root root 40328 Dec 19 16:54 log0027
-rwxrwxrwx 1 root root 38178 Dec 19 17:02 log0028
-rwxrwxrwx 1 root root 35888 Dec 19 17:09 log0029
-rwxrwxrwx 1 root root 33148 Dec 19 17:15 log0030
-rwxrwxrwx 1 root root 30018 Dec 19 17:21 log0031
-rwxrwxrwx 1 root root 26968 Dec 19 17:26 log0032
-rwxrwxrwx 1 root root 23878 Dec 19 17:31 log0033
-rwxrwxrwx 1 root root 20188 Dec 19 17:35 log0034
-rwxrwxrwx 1 root root 16268 Dec 19 17:38 log0035
-rwxrwxrwx 1 root root 12688 Dec 19 17:41 log0036
-rwxrwxrwx 1 root root 7611 Dec 19 17:42 log0037
-rwxrwxrwx 1 root root 4379 Dec 19 17:44 log0038
-rwxrwxrwx 1 root root 1659 Dec 19 17:44 log0039
drwxrwxrwx 1 root root 0 Dec 19 10:36 pid_5981
drwxrwxrwx 1 root root 0 Dec 19 14:11 pid_7663
> --
> Cheers, Dave
>
> Dave Flitney, IT Manager
> Oxford Centre for Functional MRI of the Brain
> E:[log in to unmask] W:+44-1865-222713 F:+44-1865-222717
> URL: http://www.fmrib.ox.ac.uk/~flitney
--
Dr. med. Markus Gschwind, M.D.
Laboratory for Neurology and Imaging of Cognition
Dept of Neurosciences
University Medical Center (CMU)
1 Michel-Servet - 1211 GENEVA - CH
Tel 0041 (0) 22 379 5324
Fax 0041 (0) 22 379 5402
email: [log in to unmask]
http://labnic.unige.ch
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