AttributeError: module 'nibabel' has no attribute 'spatialimages'

1

Hi ,
I want to plot a 3D .nii fmri data with nilearn, but this error occures:

AttributeError: module ‘nibabel’ has no attribute ‘spatialimages’

my fmri data is prepossessed with afni .

2

Hum, that’s strange. I wonder if you do not have a very old version of nibabel. What’s your nibabel version? You can find this out with:

import nibabel
nibabel.__version__
1 Like
3

@Mansooreh

Would you mind trying this: converting using https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dAFNItoNIFTI.html and then try to plot with Nilearn.

If it works then may be we should handle AFNI images by converting them.

4

the version is : ‘2.0.2’

5

I cannot reproduce, even with nibabel 2.0.2.

Can you post the full traceback.

6

File “”, line 18, in
display = plotting.plot_glass_brain(result_img)#,cmap=‘cool’,colorbar=True,plot_abs=True)

File “C:\Users\Mansooreh\Anaconda3\lib\site-packages\nilearn\plotting\img_plotting.py”, line 1130, in plot_glass_brain
stat_map_img = _utils.check_niimg_3d(stat_map_img, dtype=‘auto’)

File “C:\Users\Mansooreh\Anaconda3\lib\site-packages\nilearn_utils\niimg_conversions.py”, line 322, in check_niimg_3d
return check_niimg(niimg, ensure_ndim=3, dtype=dtype)

File “C:\Users\Mansooreh\Anaconda3\lib\site-packages\nilearn_utils\niimg_conversions.py”, line 271, in check_niimg
niimg = load_niimg(niimg, dtype=dtype)

File “C:\Users\Mansooreh\Anaconda3\lib\site-packages\nilearn_utils\niimg.py”, line 111, in load_niimg
elif not isinstance(niimg, nibabel.spatialimages.SpatialImage):

AttributeError: module ‘nibabel’ has no attribute ‘spatialimages’

7

I’ve tried reproducing this in an anaconda environment (Python: 3.5, nibabel: 2.0.2), and had no troubles finding nibabel.spatialimages.SpatialImage:

Python 3.5.6 |Anaconda, Inc.| (default, Aug 26 2018, 16:30:03) 
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import nibabel
>>> nibabel.spatialimages.SpatialImage
<class 'nibabel.spatialimages.SpatialImage'>

Perhaps there’s an issue with your install. Could you try conda update nibabel?

1 Like
8

The problem is solved with updating nibabel !!!
Thank you very much for your help.

1 Like
9

Thank you for your help. The problem is solved with updating nibabel.