> On 3 Nov 2015, at 12:21, Aaron <[log in to unmask]> wrote:
>
> Just to reply to my own question, I mostly got it working. Using the current version of FSL in the default location fixed the errors (apparently the path warnings are not critical). I have an older version (5.0.6) in a non-standard location which the scripts didn't seem to like.
>
The first path is within the FSL release package, so check you have FSLDIR set correctly (and exported) before trying hcp_fix. The second path is a FMRIB internal path and I can find no reference to it in the fix 1.06 sources or indeed the compiled code.
Without being able to find the FSL distro the mc files wouldn't be produced and thus you would see the segmentation fault.
> Octave still doesn't work, it fails at fix_3_clean.m, line 30, column 9.
>
Is this the line that gives the segmentation fault or is there another error message?
> The compiled scripts work, only i noticed in the log that TR is not correctly set. This is set in hcp_fix (fslval $fmri pixdim4). Somewhere in the pipeline scripts the value gets changed - I checked, it's not in the dicom to nifti conversion. Other folks might want to double check this is correct.
>
> Cheers.
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