Hi Kevin,
Your file Allfocicoords_ALE_C05_1k.nii might be formatted as a nifti extension. This has been seen in another recent post on the FSL list.
can you upload the file so I can debug?
upload link: https://oxfile.ox.ac.uk/oxfile/work/extBox?id=690991047F8A89D9F1
Cheers,
Taylor Hanayik
Taylor Hanayik PhD
FMRIB, John Radcliffe Hospital
University of Oxford
[log in to unmask]
> On Feb 25, 2019, at 1:33 PM, Kevin Ridley <[log in to unmask]> wrote:
>
> To whom it may concern,
>
> I have an error message of:
> Image Exception : #22 :: Failed to read volume Allfocicoords_ALE_C05_1k.nii
> Error : Error: short read, file may be truncated
> Failed to read volume Allfocicoords_ALE_C05_1k.nii
> Error : Error: short read, file may be truncated
>
> I have inputed: kevins-MacBook-Air:desktop kevinridley$ flirt -in Allfocicoords_ALE_C05_1k.nii -ref Q1AV_brain.nii.gz -out Allfocicoords_ALE_C05_1k.nii.gz -init Colin1Q1AVbrain.mat -applyxfm
>
> All files are on the desktop and in the terminal it is set to ds desktop.
> Any clues as to what has gone wrong?
>
> Yours sincerely,
>
> Kevin Ridley
>
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