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import matplotlib induce an error in matlab. For instance when using sct_apply_transfo:
```
File "/Users/taduv_admin/codes/spinalcordtoolbox/bin/sct_apply_transfo", line 24, in
from sct_crop_image i…
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### Summary
ecc_pipeline change intensity range for non B0 scans
### Actual behavior
I have a raw diffusion image with B0 scan intensities around 1000 and other scans around 200.
After the ecc_p…
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Upon installation, i get the following error:
~~~
[jcohen@cedar5 sct]$ SCT_INSTALL_TYPE=in-place add_to_path=no change_default_path=yes ./install_sct
Welcome to the SCT installer!
SCT versio…
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```
Running Sphinx v1.6.5
making output directory...
loading translations [en]... done
loading pickled environment... not yet created
loading intersphinx inventory from https://docs.python.org/ob…
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I'm closing an old issue #597 and providing a new list of files that returns errors and warnings with `flake8`.
Below is the output of
```
for f in `find . -name "*.py" ! -name "test_auto*"`; do …
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### Summary
The ecc pipeline should only change the output through the generated flirt matrices and the modulation of the volumes to account for the scaling and shearing of the volumes. (this may be …
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### Summary
I am able to run the FSL head motion correction pipeline, however, I am wondering how I can specify the output directory
### Actual behavior
Here is a minimal example:
```
from ni…
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### Description
In some systems, the "rm -rf tmp.XX" line crashes even though writing permission is enabled.
The error message is: `rm: cannot remove 'tmp.170921145753': Directory not empty`. Thi…
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I am using workflows.dmri.fsl.artifacts all_fmb_pipeline for dti preprocessing. The output is vol0000_warp_maths_thresh_merged.nii.gz for all subjects. I prefer a more unique name for each subject and…
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### Description
output same as input
compute_dti cannot be run successfully
[dmri_crop_moco.nii.gz](https://github.com/neuropoly/spinalcordtoolbox/files/1452378/dmri_crop_moco.nii.gz)
[bvecs…