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neurolibre / brainiak-tutorials

Tutorials that cover topics from basics to advanced fMRI analysis
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10-isc: nilearn plotting error #6

Open manojneuro opened 5 years ago

manojneuro commented 5 years ago

We get a plotting error when running 10-isc.

Steps to replicate:

  1. In the notebook set upper_limit_n_subjs = 5
  2. Execute cells.
  3. Error occurs in Section 2.3, in the cell before Exercise 3. 
    surf_map = plotting.plot_surf_stat_map(
fsaverage.infl_left, texture, 
hemi='left', view=view, 
title= title_text, 
threshold=threshold, cmap='RdYlBu_r', 
colorbar=True,
bg_map=fsaverage.sulc_left)
    Error: NotImplementedError: It is not currently possible to manually set the aspect on 3D axes
ltetrel commented 5 years ago

What version of nilearn are you using on google collab ?

ltetrel commented 5 years ago

We are now using 0.5.2 version. So it seems to be an issue with nilearn . A depreciationWarning coming after this release : https://nilearn.github.io/whats_new.html#id42 @manojneuro Can you confirm that the notebooks are running on google collab with nilearn 0.5.2 ?

pbellec commented 5 years ago

@manojneuro any update?

manojneuro commented 5 years ago

@ltetrel on Colab the notebooks are running on 0.5.2. There seemed to have been an issue with this plotting function in nilearn in 0.5.1, that is fixed in 0.5.2. Could you double check if you have 0.5.2 installed?

manojneuro commented 5 years ago

@ltetrel An update on this issue. It seems to be a problem with matplotlib 3.1, see here: https://github.com/nipy/mindboggle/issues/177

They recommend either waiting for the next nilearn release, or going back to an older version of matplotlib. I tested with matplotlib==3.0.3 and it works on Colab.

ltetrel commented 5 years ago

Interresting, maybe we should wait for the new nilearn release then

manojneuro commented 5 years ago

I'm not sure when the release will be out, we can always upgrade once the release is out.