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

Christopher J Markiewicz effigies at bu.edu
Tue Jul 21 18:36:33 CEST 2015

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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