Additionally, although FSL4 is apparently in your path (you are
calling FSL 4 functions),
your FSLDIR is apparently set to an old FSL3 directory -
If you change this to point to the FSL4 installation, I am sure
bedpost_datacheck will tell you your bvecs/bvals are wrong!
Cheers
T
On 21 Aug 2007, at 22:53, Andreas Bartsch wrote:
> Hi,
> you don't seem to have the data & nodif_brain_mask files in the
> directory (which has sort of a strange path, I'd say). Furtermore,
> you must check that your bvals has all values in a single line.
> Cheers-
> Andreas
>
> ________________________________
>
> Von: FSL - FMRIB's Software Library im Auftrag von Roger Moore
> Gesendet: Di 21.08.2007 21:46
> An: [log in to unmask]
> Betreff: Re: [FSL] using dtifit
>
>
> Hi Saad,
>
> Thanks for the reply.
>
> Okay, when I am in the directory which contains
> 'bedpostx_datacheck' and I give directory which contains my input
> files, I get the following:
>
> corona10% pwd
> /vol/vipdata/packages/fsl-4.0.0/bin
> corona10% ./bedpostx_datacheck /vol/vipdata/users/rjm06/itk/linux/bin
> /vol/vipdata/users/rjm06/itk/linux/bin/data
> ./bedpostx_datacheck: line 12: /vol/vipdata/packages/fsl3.3.7/bin/
> fslinfo: No su
> ch file or directory
>
> /vol/vipdata/users/rjm06/itk/linux/bin/nodif_brain_mask
> ./bedpostx_datacheck: line 12: /vol/vipdata/packages/fsl3.3.7/bin/
> fslinfo: No su
> ch file or directory
>
> num lines in /vol/vipdata/users/rjm06/itk/linux/bin/bvals
> 2
> num words in /vol/vipdata/users/rjm06/itk/linux/bin/bvals
> 16
> num lines in /vol/vipdata/users/rjm06/itk/linux/bin/bvecs
> 3
> num words in /vol/vipdata/users/rjm06/itk/linux/bin/bvecs
> 48
> ./bedpostx_datacheck: line 28: /vol/vipdata/packages/fsl3.3.7/bin/
> fslval: No such file or directory
> ./bedpostx_datacheck: line 29: /vol/vipdata/packages/fsl3.3.7/bin/
> fslval: No such file or directory
> ./bedpostx_datacheck: line 30: /vol/vipdata/packages/fsl3.3.7/bin/
> fslval: No such file or directory
> ./bedpostx_datacheck: line 31: /vol/vipdata/packages/fsl3.3.7/bin/
> fslval: No such file or directory
> ./bedpostx_datacheck: line 33: /vol/vipdata/packages/fsl3.3.7/bin/
> fslval: No such file or directory
> ./bedpostx_datacheck: line 34: /vol/vipdata/packages/fsl3.3.7/bin/
> fslval: No such file or directory
> ./bedpostx_datacheck: line 35: /vol/vipdata/packages/fsl3.3.7/bin/
> fslval: No such file or directory
> data dimensions do not match mask dimensions
> ./bedpostx_datacheck: line 51: [: 16: unary operator expected
> ./bedpostx_datacheck: line 54: [: 16: unary operator expected
> corona10%
>
>
> I'm sure the above will mean more to you than it does to
> me....would be great if you could tell me how to remedy the problem.
>
> Thank you,
>
> Roger
>
>
> Saad Jbabdi wrote:
>
> Hi Roger,
>
> What does bedpost_datacheck (or bedpostx_datacheck if you're using
> FSL4.0) give on your dtifit directory?
>
> Saad
>
>
> On 21 Aug 2007, at 17:32, Roger Moore wrote:
>
>
> Hello,
>
> I am trying to use dtifit, but so far unsuccessfully. My command
> line and error message are shown below.
>
> corona10% /vol/vipdata/packages/fsl-4.0.0/bin/dtifit -k
> diffusion.nii.gz -o dtiout -m nodif_brain.nii.gz -r bvecfile -b
> bvalfile -V
> data file diffusion.nii.gz
> mask file nodif_brain.nii.gz
> bvecs bvecfile
> bvals bvalfile
> reading data
> reading mask
> ok
> 0 128 0 128 0 64
> setting up vols
> copying input properties to output volumes
> zeroing output volumes
> ok
> Forming A matrix
> terminate called after throwing an instance of
> 'NEWMAT::IndexException'
> Abort
> corona10%
> It appears to happen in the function form_Amat(r,b)....but I
> don't know why....r (bvecsfile) and b (bvalsfile) are the right
> dimensions (3x16 and 1x16).
>
> If anybody could suggest what the problem might I would be very
> grateful.
>
> Thank you,
>
> Roger
>
>
>
> ---------------------------------------------------------------------
> ------
> Saad Jbabdi,
> Postdoctoral Research Assistant,
> Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222545 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~saad
> ---------------------------------------------------------------------
> ------
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