Hi Adam - improving the use of transforms in the NIFTI header is
something we're working on for the new release (it won't be 100%
usage but we're getting there....) - it might be helpful if you could
upload your data with a description of the issues and we can test it
on our in-house versions?
Please upload the files in a single compressed tarfile to
http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
and then email me the upload ID.
Cheers, Steve.
On 2 Aug 2007, at 05:32, Adam Aron wrote:
> Hi,
>
> I have a problem with the orientation of images for FSL.
>
> I'm obliged to use a pre-existing script (for field map correction)
> to convert raw dicom images to
> NIFTI images for my FSL analysis. The script calls both afni and
> fsl commands along the way.
>
> When using afni I can see that the resulting NIFTI structural and
> functional images are nicely lined
> up and correctly oriented.
>
> But fslview shows both of the images upside down and back to front,
> in different ways, and while I
> can run registration and analysis, the results are also inverted
> and flipped.
>
> Apparently the problem relates to the way that the script program
> is putting Cartesian co-
> ordinates in the header.
>
> I can flip the images around using avwswapdim, but I don't think
> this is the correct thing to be
> doing (for example, the script made sure that the axially acquired
> structural image was converted
> into an oblique plane to match the functional - and avwswapdim
> won't respect this).
>
> I'd be much obliged for any help, and could easily provide the images.
>
> Many thanks
> Adam
>
> UC San Diego
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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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