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[Module] Antsbet #69

Merged
merged 14 commits into from
Mar 18, 2024
Merged

[Module] Antsbet #69

merged 14 commits into from
Mar 18, 2024

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ThoumyreStanislas
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add module bet t1 with antsbrainextraction.sh
test passed correctly

@AlexVCaron AlexVCaron linked an issue Feb 22, 2024 that may be closed by this pull request
@AlexVCaron AlexVCaron mentioned this pull request Feb 22, 2024
@AlexVCaron AlexVCaron removed a link to an issue Feb 27, 2024
@ThoumyreStanislas
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The tests failed because I added new data and tried with a local direction for the data and the test passed. I then changed the directory to nf-scil and the test failed because the data was missing from nf-scil.

@AlexVCaron AlexVCaron changed the title [WIP} add module Antsbet [Module][WIP] Antsbet Mar 8, 2024
@AlexVCaron AlexVCaron added this to the nf-scil modules v1.0 milestone Mar 9, 2024
@AlexVCaron AlexVCaron self-requested a review March 9, 2024 04:20
@AlexVCaron
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Can you share me the missing test data ? Either in an archive or directly here as links. I'll add them so they are available for your test case using the Scilpy_Fetcher

@AlexVCaron
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The test package is online, the name : antsbet.zip !

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Some really minor comments. I'll review further once tests are running 😉

modules/nf-scil/betcrop/antsbet/main.nf Outdated Show resolved Hide resolved
modules/nf-scil/betcrop/antsbet/main.nf Outdated Show resolved Hide resolved
modules/nf-scil/betcrop/antsbet/meta.yml Outdated Show resolved Hide resolved
@AlexVCaron
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The archive is up-to-date on the main branch ! I placed two variations of the T1image :

  • t1.nii.gz which is really close to the template (not the best test case)
  • t1_unaligned.nii.gz which I virtually moved away further (two rotations and a translation, better as a test)

Can you try recreating the test yml files with the unaligned image, see if it passes ?

@AlexVCaron AlexVCaron merged commit 796278e into scilus:main Mar 18, 2024
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@AlexVCaron AlexVCaron changed the title [Module][WIP] Antsbet [Module] Antsbet Mar 18, 2024
@ThoumyreStanislas ThoumyreStanislas deleted the ants_bet_crop branch June 13, 2024 18:53
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2 participants