Hi Marcus.
With regards to the feeds, I did in fact run it in the feeds directory with
the script as you wrote it. It just doesn't do anything for me.
As for the datacheck, I think you are asking if I ran it on the input folder
or the output folder. Am I correct? If so, the answer would be both. I
initially ran it on the output folder, realized my mistake and ran it on the
input folder and both ended up giving me similar messages with multiple
files not being found. What I posted, however, was the output it gave me
when I ran it on the input folder.
In terms of file extensions, the only one that has .txt on it is the
command.txt file, all the rest are simply bvals or bvecs, etc.
Could it be that I am having difficulty because I am using Ubuntu. Should I
be trying it with another Linux OS?
Thank you in advance.
Rajeet
On Thu, 12 Feb 2009 19:53:17 +0100, Markus Gschwind
<[log in to unmask]> wrote:
>Hi Rajeet!
>
>Yes, the feeds test is a very good idea! Make sure that you have write
>wights for the feeds directory.
>The command would be (being INSIDE the feeds_directory)
>/usr/bin/time ./RUN all
>
>did you do so? It should then start quite soon (giving out what it is doing)
>and run between 30 and 60 min (depending on your system).
>
>did you rand bedpostx_datacheck like this?:
>cd subjectdir
>bedpostx_datacheck bedpostx
>(not bedpostx.bedpostX)
>
>Note that the files must have names exactly like indicated on the FDT site
>(bvals/bvecs without ".txt"-extension)
>(http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html)
>
>All the best,
>Markus
>
>
>
>
>
>
>
>2009/2/12 Rajeet Saluja <[log in to unmask]>
>
>> 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
>> >
>>
>
>
>
>--
>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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