Working synb0 wrapper in scilpy #734

frheault · 2023-08-15T17:41:18Z

Quick description

Please include a summary of the changes and the related issue(s) or improvement(s).
Please also include relevant motivation and context. List any dependencies that are required for this change if needed.

By providing a skull strip t1w and b0, this generate a perfect b0 without distortion which can be fed to topup (saying it has infinite bandwitdh) to trick topup into fixing the diffusion without a rev_b0.

Useful when no rev_b0 is available. Could help to simplify Tractoflow?

https://pubmed.ncbi.nlm.nih.gov/31075422/

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Type of change

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Bug fix (non-breaking change which fixes an issue)
New feature (non-breaking change which adds functionality)
Breaking change (fix or feature that would cause existing functionality to not work as expected)
This change requires a documentation update

Provide data, screenshots, command line to test (if relevant)

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Checklist

My code follows the style guidelines of this project (run autopep8)
I added relevant citations to scripts, modules and functions docstrings and descriptions
I have performed a self-review of my code
I have commented my code, particularly in hard-to-understand areas
I have made corresponding changes to the documentation
My changes generate no new warnings
I moved all functions from the script file (except the argparser and main) to scilpy modules
I have added tests that prove my fix is effective or that my feature works
New and existing unit tests pass locally with my changes

arnaudbore · 2023-08-15T18:42:55Z

Build passed ! Good Job 🍻 !

arnaudbore · 2023-08-15T19:30:24Z

Build Failed 💥
https://jenkins.scil.usherbrooke.ca/job/scilpy/job/PR-734/2/

arnaudbore · 2023-08-16T16:29:48Z

Build Failed 💥
https://jenkins.scil.usherbrooke.ca/job/scilpy/job/PR-734/3/

frheault · 2023-08-17T12:30:50Z

The test requires tensorflow, should I just delete the test or we turn it off?

AlexVCaron · 2023-08-17T15:59:31Z

Could the test run conditionally to having Tensorflow installed ? https://stackoverflow.com/questions/36377625/how-to-conditionally-skip-a-test-in-python

Maybe the import error is too early and would prevent this to work ...

arnaudbore · 2023-08-17T20:21:53Z

Build passed ! Good Job 🍻 !

arnaudbore · 2023-09-27T19:54:01Z

Build passed ! Good Job 🍻 !

arnaudbore

Need some testing before moving forward. Overall synthesize_b0 works well but still needs to be tested with topup.

scripts/scil_prepare_topup_command.py

scilpy/utils/image.py

pep8speaks · 2023-10-23T14:04:20Z

Hello @frheault, Thank you for updating !

In the file scilpy/image/volume_operations.py:

Line 211:80: E501 line too long (80 > 79 characters)
Line 233:80: E501 line too long (80 > 79 characters)

Comment last updated at 2024-02-21 21:13:53 UTC

arnaudbore · 2023-10-23T18:43:00Z

Build passed ! Good Job 🍻 !

arnaudbore · 2023-10-23T19:35:32Z

Build passed ! Good Job 🍻 !

…synb0_integration

arnaudbore · 2023-11-02T19:13:44Z

Build Failed 💥
https://jenkins.scil.usherbrooke.ca/job/scilpy/job/PR-734/9/

arnaudbore · 2023-11-02T19:15:18Z

Build Failed 💥
https://jenkins.scil.usherbrooke.ca/job/scilpy/job/PR-734/10/

mdesco

A few minor comments. Hard for me to test on my mac. Don't want to fight with tensorflow...

scripts/scil_synthesize_b0.py

mdesco

Once the minor comments are done. All good

scripts/scil_synthesize_b0.py

arnaudbore · 2023-12-04T19:42:33Z

Build passed ! Good Job 🍻 !

arnaudbore · 2023-12-14T16:15:11Z

Build passed ! Good Job 🍻 !

arnaudbore · 2023-12-18T20:44:17Z

Build passed ! Good Job 🍻 !

smeisler · 2023-12-21T15:34:32Z

Thanks for your work on this, I have started testing it out.

It doesn't seem like the synb0 template fetcher function is defined in the PR, but I presume the template was the file in /data/mni_icbm152_t1_tal_nlin_asym_09c_masked_2_5.nii.gz? If so, the template looked strange after I visualized it when I downloaded it from GitHub:

The resulting b0 map also looked odd, but likely due to trying to register to that odd template image:

smeisler · 2023-12-21T15:38:53Z

The template here looks better: https://github.com/MASILab/Synb0-DISCO/blob/master/atlases/mni_icbm152_t1_tal_nlin_asym_09c_mask_2_5.nii.gz

smeisler · 2023-12-21T15:42:45Z

Fixing the template did the trick!

frheault · 2023-12-22T15:01:07Z

The template here looks better: https://github.com/MASILab/Synb0-DISCO/blob/master/atlases/mni_icbm152_t1_tal_nlin_asym_09c_mask_2_5.nii.gz

I will fix the function and make sure the data inside the repo is reuploaded correctly, thank you !

arnaudbore · 2024-01-12T21:00:47Z

Build passed ! Good Job 🍻 !

arnaudbore · 2024-01-15T14:56:35Z

Build passed ! Good Job 🍻 !

codecov · 2024-02-20T14:15:57Z

Codecov Report

Attention: 85 lines in your changes are missing coverage. Please review.

Comparison is base (89ac8ce) 68.50% compared to head (bc117fb) 68.25%.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #734      +/-   ##
==========================================
- Coverage   68.50%   68.25%   -0.25%     
==========================================
  Files         387      388       +1     
  Lines       20867    20950      +83     
  Branches     3214     3216       +2     
==========================================
+ Hits        14294    14300       +6     
- Misses       5285     5363      +78     
+ Partials     1288     1287       -1

Components	Coverage Δ
Scripts	`70.92% <1.38%> (-0.36%)`	⬇️
Library	`63.64% <26.31%> (-0.07%)`	⬇️

arnaudbore

A couple of comments, almost GTG

scripts/scil_volume_b0_synthesis.py

scripts/tests/test_synthesize_b0.py

scilpy/image/volume_operations.py

frheault added 2 commits August 15, 2023 13:38

Working synb0

e6f31fc

Fix affine and added tests

ae3e84e

arnaudbore self-requested a review August 15, 2023 18:42

frheault added 2 commits August 16, 2023 10:07

Working as synb0 github

7a67dce

Fine registration

8e42ecc

skip test if not TF

0adca04

Merge branch 'master' of github.com:scilus/scilpy into synb0_integration

ecb96bb

arnaudbore reviewed Oct 20, 2023

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scilpy/utils/image.py Outdated Show resolved Hide resolved

Fix Arnaud last comments

47e1053

Merge with master

5e68c83

arnaudbore self-requested a review October 23, 2023 18:42

Add warning

d0a991a

frheault added the enhancement label Oct 23, 2023

frheault added 4 commits November 2, 2023 14:26

merge

1878ef7

merge

0ec6723

Move back fetcher

9986857

Merge branch 'test_volume_math_2' of github.com:frheault/scilpy into …

41caa25

…synb0_integration

Merge branch 'master' of github.com:scilus/scilpy into synb0_integration

3e9b2c9

mdesco reviewed Nov 17, 2023

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mdesco approved these changes Nov 17, 2023

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arnaudbore reviewed Nov 17, 2023

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frheault added 2 commits December 4, 2023 14:00

Merge branch 'master' of github.com:scilus/scilpy into synb0_integration

4b577fc

Fix max comment

ed8be3c

arnaudbore self-requested a review December 4, 2023 19:42

frheault added 4 commits December 14, 2023 09:57

Merge branch 'master' of github.com:scilus/scilpy into synb0_integration

7b84414

Merge with masther

05e61cd

Fix conflict

9c34008

Add back the missing file

21e503f

Merge branch 'master' of github.com:scilus/scilpy into synb0_integration

c9eba44

frheault added 2 commits January 15, 2024 09:17

Merge branch 'master' of github.com:scilus/scilpy into synb0_integration

00b0d5a

Add back fetcher

5080ab2

Fix conflict

da0cf1e

Merge branch 'master' of github.com:scilus/scilpy into synb0_integration

03c4c2c

arnaudbore requested changes Feb 21, 2024

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scripts/tests/test_synthesize_b0.py Outdated Show resolved Hide resolved

scilpy/image/volume_operations.py Outdated Show resolved Hide resolved

frheault added 2 commits February 21, 2024 15:00

Arnaud comments

81b5d27

Use proper filename for script

bc117fb

arnaudbore merged commit 594fbb7 into scilus:master Feb 22, 2024
2 checks passed

frheault deleted the synb0_integration branch February 28, 2024 21:04

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Working synb0 wrapper in scilpy #734

Working synb0 wrapper in scilpy #734

frheault commented Aug 15, 2023 •

edited by arnaudbore

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Working synb0 wrapper in scilpy #734

Working synb0 wrapper in scilpy #734

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frheault commented Aug 15, 2023 • edited by arnaudbore Loading

Quick description

Type of change

Provide data, screenshots, command line to test (if relevant)

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arnaudbore commented Aug 15, 2023

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arnaudbore commented Aug 16, 2023

frheault commented Aug 17, 2023

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Comment last updated at 2024-02-21 21:13:53 UTC

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