You need to re-download FSL.
There are a number of bug-fixes including a fix to this file that
will make bedpostx run at a more sensible speed.
cheers
t
On 5 Mar 2008, at 22:39, Eric Hwang wrote:
> Hi Tim,
>
> Thanks for the quick response. Here is the output:
> #!/bin/sh
>
> #$ -cwd
> #$ -q long.q
> #$ -S /bin/sh
> #$ -V
> #$ -N bedpostx
> #$ -m a
> #$ -o $1.bedpostX/logs -e $1.bedpostX/logs
>
> subjdir=$1
> nfibres=$2
> fudge=$3
> bi=$4
> slice=$5
>
> slicezp=`${FSLDIR}/bin/zeropad $slice 4`
>
> ${FSLDIR}/bin/xfibres\
> --data=$subjdir/data_slice_$slicezp\
> --mask=$subjdir/nodif_brain_mask_slice_$slicezp\
> -b $subjdir/bvals -r $subjdir/bvecs\
> --forcedir --logdir=$subjdir.bedpostX/diff_slices/data_slice_
> $slicezp\
> --fudge=$fudge --nj=5000 --bi=$bi --se=100 --upe=24 --nfibres=
> $nfibres >
> $subjd ir.bedpostX/logs/log$slicezp && echo Done
>
> If this helps, I am running FSL 4.0.0. (original zipped filename:
> fsl-4.0.0-centos4_64.tar.gz).
>
> Thanks,
> Eric
>
>
>> Hi Eric - I would think this is not normal unless you happened to
>> download FSL very soon after FSL4 was released, when there was an
>> error in one of the scripts.
>>
>> can you run the following
>>
>> cat $FSLDIR/bin/bedpostx_single_slice.sh
>>
>> and email the output
>>
>> T
>>
>>
>> On 5 Mar 2008, at 18:55, Eric Hwang wrote:
>>
>>> Hi all,
>>>
>>> I'm new to this so let me know if this is posted in the wrong
>>> place. I am
>>> currently trying to red FDT's bedpostx on a 51 direction DTI data
>>> set. It
>>> has taken almost an entire week to even get through half the
>>> slices. Is this
>>> normal or have I done something wrong?
>>>
>>> Thanks,
>>> Eric Hwang
>>>
>>
>
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