[Neuroimaging] Wrong fMRI sig.nii shape when loading with nibabel

[Noam Peled]

Thanks, it worked!

On Tue, Jul 21, 2015 at 12:49 PM Christopher J Markiewicz <effigies at bu.edu>
wrote:

> On 07/21/2015 12:27 PM, Noam Peled wrote:
> > Hello all,
> > I'm having an issue with loading fMRI sig.nii files.
> > I've created two overlays using selxavg3-sess, where the only difference
> > between them is the surface parameter in preproc-sess
> > and mkanalysis-sess. In the first I used fsaverage, and in the second
> > the actual subject.
> > Both seems to be ok via fmri_info and tksurfer-sess.
> > The problem is when I'm trying to use nibabel to load them.
> > The fsaverage is getting loaded just fine, whether the other one gets a
> > (-1, 1, 1, 1) shape.
> > Here are the file:
> > sig_fsaverage.nii.gz
> > <https://www.dropbox.com/s/9ojymqrdd51cslh/sig_fsaverage.nii.gz?dl=0>
> > sig_subject.nii.gz
> > <https://www.dropbox.com/s/czysnf8jfsmz753/sig_subject.nii.gz?dl=0>
> > Any ideas?
> >
> > Thanks!
> > Noam Peled
>
> These look to be FreeSurfer nifti surface hack problems. The easiest way
> to get what you want in the short term would be:
>
>     mri_convert sig_fsaverage.{nii.gz,mgz}
>     mri_convert sig_subject.{nii.gz,mgz}
>
> And load the .mgz files.
>
> The problem here is that the Nifti code to deal with these surfaces is
> expecting the shape to be 3 dimensional, not 4.
>
> --
> Christopher J Markiewicz
> Ph.D. Candidate, Quantitative Neuroscience Laboratory
> Boston University
>
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