Indeed - I think you would save yourself a lot of time by fixing the
input files to be valid NIFTI!
But yes, if you have set FSLOUTPUTTYPE to ANALYZE then I believe that
no NIFTI files should be generated at any stage.
Cheers.
On 18 Dec 2007, at 23:29, Shawn Yeh wrote:
> Hi, been reading the archive looking for clues to the WARNING: posn
> not header size messages in my
> log reports.
>
> One question: does FSL 4.0 use nii.gz formats for intermediate
> files generated during FEAT?
>
> I ask this because I attempted to do a FEAT report comparison using
> ANALYZE format (hdr/img) in
> FSL 4.0 with that of an older FSL 3.x report. I set the
> FSLOUTPUTTYPE to ANALYZE, which I thought
> should sidestep any nifti related warnings(such as posn not header
> size). However, I still
> encountered them in the report log. Some investigation has led me
> to believe that the warnings
> come from differently localized gzip/gunzip, as the same nifti files
> will report the warning (when
> using utils such as fslhd or fslinfo) when compressed (nii.gz), but
> seem normal when uncompressed
> (nii). Unless there are other changes when compressing a file to
> nii.gz, they ought be be identical, so
> my conclusion was that the fslutils are using a different build of
> gzip/gunzip than the ones on our
> machines.
>
> Of course, the likelihood is great that our conversion tool (UCLA)
> is the main culprit, but in the interim, I'd like to know of
> possible temporary solutions.
>
> Thanks in advance.
>
---------------------------------------------------------------------------
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
---------------------------------------------------------------------------
|