Hi,
So when I run bedpostx_datacheck I get the following message:
bedpostx_datacheck: 18: /bin/imtest: not found
[: 18: 1: unexpected operator
home/rajeet/Desktop/new/data does not exist
bedpostx_datacheck: 18: /bin/imtest: not found
[: 18: 1: unexpected operator
home/rajeet/Desktop/new/nodif_brain_mask does not exist
num lines in home/rajeet/Desktop/new/bvals
cat: home/rajeet/Desktop/new/bvals: No such file or directory
0
num words in home/rajeet/Desktop/new/bvals
cat: home/rajeet/Desktop/new/bvals: No such file or directory
0
num lines in home/rajeet/Desktop/new/bvecs
cat: home/rajeet/Desktop/new/bvecs: No such file or directory
0
num words in home/rajeet/Desktop/new/bvecs
cat: home/rajeet/Desktop/new/bvecs: No such file or directory
0
bedpostx_datacheck: 71: /bin/imtest: not found
bedpostx_datacheck: 71: /bin/imtest: not found
[: 71: 1: unexpected operator
However, when I look in the directory, all the files for which it says "No
such file..." are all, in fact, there.
The contents of the Command.txt file are as follows:
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 0
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 1
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 2
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 3
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 4
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 5
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 6
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 7
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 8
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 9
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 10
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 11
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 12
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 13
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 14
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 15
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 16
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 17
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 18
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 19
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 20
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 21
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 22
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 23
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 24
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 25
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 26
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 27
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 28
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 29
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 30
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 31
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 32
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 33
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 34
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 35
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 36
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 37
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 38
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 39
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 40
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 41
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 42
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 43
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 44
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 45
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 46
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 47
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 48
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 49
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 50
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 51
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 52
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 53
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 54
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 55
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 56
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 57
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 58
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 59
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 60
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 61
/usr/share/fsl/bin/bedpostx_single_slice.sh /home/rajeet/Desktop/new 2 1
1000 1250 25 62
As for monitor, they are:
#!/bin/sh
finished=0
logdir=/home/rajeet/Desktop/new.bedpostX/logs
while [ $finished -eq 0 ] ; do
nfin=0
slice=0
while [ "$slice" -le 63 ];do
slicezp=`/usr/share/fsl/bin/zeropad $slice 4`
if [ -f
/home/rajeet/Desktop/new.bedpostX/diff_slices/data_slice_$slicezp/dyads2.nii.gz
];then
nfin=$(($nfin + 1))
fi
slice=$(($slice + 1))
done
if [ $nfin -eq 63 -a -f /home/rajeet/Desktop/new.bedpostX/xfms/eye.mat
] ; then
finished=1
fi
echo "$nfin slices processed"
sleep 600;
done
As for the "file cancel", I'm not quite sure what that is so I'll have to
say probably there was none...
Also, I tried running the feeds test last night and apparently nothing
happens. After giving the run command I just get a flashing cursor without
a command prompt. I wasn't sure if it was doing anything so I left it going
overnight and, sure enough, it was still the same 12 hours later.
Thank you again for all your help.
Rajeet
On Thu, 12 Feb 2009 09:26:28 +0100, Markus Gschwind
<[log in to unmask]> wrote:
>Hi!
>
>It is normal that probtrackx is not working when there are no merged_
>means_ and dyads_in the bedpostx.bedpostX directory!
>The problem is why bedpostx does not work.
>
>Did you check the data with
>
>bedpostx_datacheck <your_bedpostx_directory>?
>
>Could you post the output here?
>
>What is in the files command.txt and monitor? can you post it here also?
>Is there no file cancel?
>
>Hth,
>all the best,
>Markus
>
>
>
>2009/2/11 Rajeet Saluja <[log in to unmask]>
>
>> 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
>>
>
>
>
>--
>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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