Hi - the Varian conversion software isn't part of the general FSL
release, it's an Oxford-only thing. I'll copy Stuart into this, who
may be able to help.
Cheers.
On 16 Jan 2008, at 11:03, Patrick Hales wrote:
> Hi
> I am trying to process a basic set of diffusion weighted images (one
> with no applied diffusion
> gradients, and 6 with diff grads applied in non-colinear
> directions). My 'raw data' is coming out of
> a Varian scanner, and I am using:
> load_varian <input_filename> <output_filename> -auto
> to convert the data to nifti format. I then use:
> fslmerge -t <output_filename> <list of input filenames>
> to merge these data into a 4D dataset.
>
> Processing the 4D dataset with DTIfit seems to work ok (ie no error
> messages), however, when I
> try to look at the results in FSL view I can't get any sensible
> info. I have discussed this problem
> with someone at fmrib and they have told me that the diffusion
> tensor calculation will not work if
> the first image (with b=0) doesn't not have a higher intensity than
> the other diffusion weighted
> images. The problem is, when I look at the raw data (before
> converting to nifti), the b=0 image
> does indeed have the highest intensity. However, when I look at a
> plot of the time-series through
> the 4D dataset in fslview, this is not the case. It seems fslmerge
> is putting the files together in the
> wrong order, although I have double checked the 'fslmerge' command I
> am using and all the input
> files are entered correctly.
>
> If anyone can help with this I would be very grateful. Many thanks
> Patrick Hales
>
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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