Hi,
Just to add to this.
The error message you are getting is very serious and cannot be
fixed by correctheader. A large part of your image data is missing!
This is far more than a header issue and indicates that dcm2nii
has failed in this case.
As Steve says, use fslswapdim to reorient your images instead.
All the best,
Mark
On 3 Nov 2008, at 19:06, Steve Smith wrote:
> Hi - I guess dcm2nii isn't an FSL program? Sounds like it's not
> creating legal NIFTI files. You can just reorient images with the
> FSL program fslswapdim
>
> Cheers.
>
>
> On 3 Nov 2008, at 18:42, Laura deSouza wrote:
>
>> Hi All,
>>
>> I had a bunch of .nii format data that I needed reoriented, and I
>> used
>> dcm2nii. The data had run fine through slicesdir when I checked it
>> originally, but post-reorientation I get errors. I'm running
>> through the
>> rest of the analysis anyway, and it seems not to interfere. Here's
>> the error
>> message I get:
>>
>> odys0162
>> ++ WARNING: nifti_read_buffer (odys0162.nii.gz):
>> data bytes needed = 23068672
>> data bytes input = 21756486
>> number missing = 1312186 (set to 0)
>>
>> except that it appears for several of my files. I've seen a
>> solution that
>> says to run correctheader on these files. Would that work in this
>> case?
>>
>> Thanks!
>> Laura
>>
>
>
> ---------------------------------------------------------------------------
> 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)
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