Ahh, I made an assumption that the warning was only nifti related, and I
guess it really applies to both analyze and nifti files. Sorry for the
bother, this looks to be unrelated to FSL itself.
On Wed, 19 Dec 2007 08:11:38 +0000, Steve Smith <[log in to unmask]> wrote:
>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
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