[Neuroimaging] Bug in reading freesurfer annotation in nibabel?

[Gael Varoquaux]

Thanks for the info, Satra, it's probably a problem with the file. We are
investigating.

G

On Tue, Feb 21, 2017 at 08:11:39AM -0500, Satrajit Ghosh wrote:
> hi gael,

> seems like a corrupted file. with the same routine i read an annot a2005s, and
> two different a2009s from recent data.

> the annot files store indexed values aligned with the surfaces (e.g., lh.pial,
> lh.white) and in addition can store a color table. the annot value itself is an
> rgb that's bit combined into an integer.

> details here: https://surfer.nmr.mgh.harvard.edu/fswiki/
> LabelsClutsAnnotationFiles#Annotationfile

> cheers,

> satra

> On Tue, Feb 21, 2017 at 7:57 AM, Gael Varoquaux <gael.varoquaux at normalesup.org>
> wrote:

>     Hi,

>     I am trying to load the freesurfer Destrieux atlas annotation file:
>     right.aparc.a2009s.annot
>     and I get the following error:

>     In [2]: import nibabel as nb

>     In [3]:
>     nb.freesurfer.read_annot('/home/varoquau/nilearn_data/destrieux_surface/
>     left.aparc.a2009s.annot')
>     ---------------------------------------------------------------------------
>     IndexError                                Traceback (most recent call
>     last)
>     <ipython-input-3-610fc2be58c1> in <module>()
>     ----> 1
>     nb.freesurfer.read_annot('/home/varoquau/nilearn_data/destrieux_surface/
>     left.aparc.a2009s.annot')

>     /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.

>     Cheers,

>     Gaël
-- 
    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