Hi - sounds like the NIFTI files aren't valid - have you tried:
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0710&L=FSL&P=R37968&I=-3&X=6C96442BC5CB061A97&Y=steve%40fmrib.ox.ac.uk
Cheers.
On 19 Feb 2008, at 22:20, Emily Stoneham wrote:
> Hello again!
>
> I saw that some other people had similar issues, but it looks like
> the assumption is that this
> means nothing (can ignore it), but because I am sort of learning as
> I go, I would like to tell you
> what I did and see if maybe the warning is because I didn't handle
> the data correctly (which I
> suspect).
>
> I used MRIConvert to get all the files converted to 3D format.
> In each run, there are 290 image files that I had to fix because the
> sagittals were all upside down.
> No sweat there.
>
> I went to FEAT, mostly because I wanted to do motion correction
> (can't figure out how to separate
> this from FEAT, as I am a UNIX idiot), and when I realized I needed
> 4 D, I went back and
> reconverted the files to 4D in MRIConvert. Since I knew the
> sagittals would be flipped, I did a
> fslswapdim on the 4D file (seems to have worked).
>
> I used that swapped file in the FEAT Data where it says 'Select 4D
> data' (seemed a no brainer that
> that was the file they wanted). Because there are 290 images taken
> in the run, I put 290 in total
> volumes (first question- is that incorrect?).
>
> FEAT is Running, but it is giving me rows and rows of this warning:
>
> Prestats
> Total original volumes = 290
> Deleting 3 volume(s) - BE WARNED for future analysis!
>
> /Users/MLE/fsl/bin/fslroi
> /Users/MLE/Desktop/
> KALBFLEISCH_5295_36_1_7_ep2d_pace_moco_3DFilter_20080107_swapped
> prefiltered_func_data 3 287
> ++ WARNING:
> nifti_read_buffer(/Users/MLE/Desktop/
> KALBFLEISCH_5295_36_1_7_ep2d_pace_moco_3DFilter_200
> 80107_swapped.nii.gz):
> data bytes needed = 393216
> data bytes input = 336047
> number missing = 57169 (set to 0)
> ++ WARNING:
> nifti_read_buffer(/Users/MLE/Desktop/
> KALBFLEISCH_5295_36_1_7_ep2d_pace_moco_3DFilter_200
> 80107_swapped.nii.gz):
> data bytes needed = 393216
> data bytes input = 0
> number missing = 393216 (set to 0)
>
> Is there something in this warning that will tell me what I need to
> correct to get it right?
>
> Let me know if you want the full details of what I actually entered
> into FEAT to make it work.
>
> Regards,
> Emily
>
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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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