[Neuroimaging] Bug in reading freesurfer annotation in nibabel?

Gael Varoquaux gael.varoquaux at normalesup.org
Tue Feb 21 07:57:28 EST 2017


I am trying to load the freesurfer Destrieux atlas annotation file:
and I get the following error:

In [2]: import nibabel as nb

In [3]:
IndexError                                Traceback (most recent call
<ipython-input-3-610fc2be58c1> in <module>()
----> 1

/home/varoquau/dev/nibabel/nibabel/freesurfer/io.pyc in
read_annot(filepath, orig_ids)
    320     with open(filepath, "rb") as fobj:
    321         dt = ">i4"
--> 322         vnum = np.fromfile(fobj, dt, 1)[0]
    323         data = np.fromfile(fobj, dt, vnum * 2).reshape(vnum, 2)
    324         labels = data[:, 1]

IndexError: index 0 is out of bounds for axis 0 with size 0

Same failure for the right annotation (with nibabel 2.1 or master).

Am I doing something wrong (eg file corrupted) or are people having the
same problem? This is a naive question: I know nothing about surfaces.



    Gael Varoquaux
    Researcher, INRIA Parietal
    NeuroSpin/CEA Saclay , Bat 145, 91191 Gif-sur-Yvette France
    Phone:  ++ 33-1-69-08-79-68
    http://gael-varoquaux.info            http://twitter.com/GaelVaroquaux

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