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v0.5

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Merge pull request #65 from sct-pipeline/jca/cnr

Add CNR figure for spine-generic data

v0.4

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jcohenadad Julien Cohen-Adad
Now outputting CNR for gm-challenge data

v0.3

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Updated code for simulations (#66)

* Minor PEP8 fixes

* Cropped phantom and changed output default folder

* Added tqdm progress bar

* Fixed generation of cord and GM masks

* Cleanup

* Updated .gitignore

* Refactoring to remove duplication

* Cleanup

* Updated README

* Started refactoring to get rid of old code deps

* Fixed CSV reading code

* Fixed subprocess syntax

* Output results in separate folder

* Also output WM mask

* Introduced WM mask

* Implemented metrics computation

* Cleanup

* Fixed wrong dict usage; updated README

* Cleanup

* Updated TODO

* Fixed xticklabels

* Fixed Matplotlib warning

Warning:
<ipython-input-3-13658aa197ad>:1: UserWarning: FixedFormatter should only be used together with FixedLocator
  ax.set_yticklabels(yticklabels, fontsize=fontsize_axes)

Solution:
https://stackoverflow.com/questions/63723514/userwarning-fixedformatter-should-only-be-used-together-with-fixedlocator

* Fixed TypeError: a bytes-like object is required, not 'str'

Solution:
https://stackoverflow.com/questions/34283178/typeerror-a-bytes-like-object-is-required-not-str-in-python-and-csv

* Output in simu_results/

* Updated .gitignore

* Need to uncache otherwise the nibabel object changes

More info:
https://nipy.org/nibabel/images_and_memory.html

* Removed verbose

* Added progress bar

* Changed output location

* Compute contrast in %

* Fixed creation of WM mask

It was waaay to big

* Eroded GM and WM masks further

To address the accuracy issue when computing metrics

* Cosmetic changes on the figure

* Cleanup

* Fixed centering of xtick

v0.2

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jcohenadad Julien Cohen-Adad
Fixed dtype conversion issue for main processing script

The same fix was already implemented for the spine-generic processing script. Now, when processing the new sub-20210728 dataset, the issue is back, so we need to apply the fix also here.

v0.1

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Updated code to new BIDS-compliant dataset (#56)

* Updated code to new BIDS-compliant dataset

Fixes #55

* Removed debugging mode with set -x