Fix get_3d_peaks when using mask #455
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xyz must be of shape n*3 to be used by wgraph_from_3d_grid, hence the use of the 3D mask array instead of the 1D ravelled mask array in np.where
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Ok ! Bien vu - le mieux serait de simuler les cartes d’activation et de
faire tourner le pipeline
Prends du temps avec ta famille demain!
JB
…On Thu, Aug 22, 2019 at 12:36 PM Alexandre PEREZ ***@***.***> wrote:
Issue
The get_3d_peaks function from nipy.labs.statistical_mapping throws an
error when using it with a mask.
Minimal reproductible example
from nilearn import datasets, masking, imagefrom nipy.labs.statistical_mapping import get_3d_peaks
template = datasets.load_mni152_template()
mask = masking.compute_gray_matter_mask(template)
imgs = datasets.fetch_neurovault_motor_task()
img = image.resample_to_img(imgs.images[0], template)
get_3d_peaks(img, mask=mask)
Error
Traceback (most recent call last):
File "minimal.py", line 10, in <module>
get_3d_peaks(img, mask=mask)
File ".../venv/lib/python3.7/site-packages/nipy/labs/statistical_mapping.py", line 199, in get_3d_peaks
ff = field_from_graph_and_data(wgraph_from_3d_grid(xyz, k=18), data)
File ".../venv/lib/python3.7/site-packages/nipy/algorithms/graph/graph.py", line 527, in wgraph_from_3d_grid
raise ValueError('xyz should have shape n * 3')
ValueError: xyz should have shape n * 3
Versions
nipy==0.4.2
nilearn==0.5.2
Fix
xyz must be of shape n*3 to be used by wgraph_from_3d_grid, hence the use
of the 3D mask array instead of the 1D ravelled mask array in np.where.
------------------------------
You can view, comment on, or merge this pull request online at:
#455
Commit Summary
- Fix get_3d_peaks when using mask
File Changes
- *M* nipy/labs/statistical_mapping.py
<https://github.com/nipy/nipy/pull/455/files#diff-0> (2)
Patch Links:
- https://github.com/nipy/nipy/pull/455.patch
- https://github.com/nipy/nipy/pull/455.diff
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Hi, any news ? |
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I'm very very sorry to be so slow here - but can you think of a test for this fix? I will honestly get to this very quickly, if you do still have interest. |
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No problem! I am not working on this anymore but I can try to have a look in the following weeks. |
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That would be kind. I'm very sorry for the delay. |
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Issue
The
get_3d_peaksfunction fromnipy.labs.statistical_mappingthrows an error when using it with a mask.Minimal reproductible example
Error
Versions
Fix
xyzmust be of shape n*3 to be used bywgraph_from_3d_grid, hence the use of the 3D mask array instead of the 1D ravelled mask array innp.where.