Hi Natalia,
I had a quick look on your data. The bvals entries are wrong, they have the value 1.118, I am assuming these should be 1118.
Please correct the bvals file and rerun, that should resolve the problem.
Cheers
Stam
On 11 Dec 2012, at 21:21, Natalia Sanchez wrote:
> I am running bedpost on a cluster using the following code:
>
>
>
>
> ############################################################
> #!/bin/bash
> ##script written in Bash. Comments at the beginning should be prefaced with two number signs.
> ## output files from the job will go into the output_files folder. error files go into the error_files folder
> #PBS -e /home/nsanchez/Desktop/error_files/error.$PBS_JOBID
> #PBS -o /home/nsanchez/Desktop/output_files/output.$PBS_JOBID
>
> # we don't have a Sun Grid Environment cluster (SGE), so don't use it
> SGE_ROOT=""
> export SGE_ROOT
>
> FSLDIR=/opt/fsl # directory where the fsl program is located. This should not change.
> EXAMPLEDIR=/home/nsanchez/Desktop # directory where the script and data folder are located
> DATADIR=$EXAMPLEDIR/NT_DTI # directory where data is stored
> RESULTSDIR=$EXAMPLEDIR/resultsNT # directory where results will be stored
> EXECUTEDIR=$RESULTSDIR/NT_DTI # directory that data is copied to, which will be analyzed - last folder should be the same as the data directory
>
> rm -rf $RESULTSDIR # remove previous results if necessary
> mkdir $RESULTSDIR # make directory to store results from this analysis
>
> echo "Starting FDT (bedpost) at $(date)"
>
> # Copy data directory into the results directory. Results directory will be split into a data dir and a .bedpostx dir, which contains the results of the analysis.
> cp -r $DATADIR $RESULTSDIR
>
> # run bedpostx
> unset FSLMACHINELIST
> bedpostx $EXECUTEDIR -n 2
>
> # finish up
> echo "end time = $(date)"
>
> ################################################################
>
> I uploaded the requested documents
>
> Thanks a lot for your help!
>
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