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#45 - MRtrix module - betcrop/betantsbet #71

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#45 - MRtrix module - betcrop/betantsbet #71

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75b6551
change mrtrix to scilpy
Manonedde Dec 12, 2024
f9983b5
remove mrtrix version
Manonedde Dec 12, 2024
3c10466
remove mrtrix help
Manonedde Dec 12, 2024
1ce4ae4
update snaptest
Manonedde Dec 12, 2024
f0ac51c
remove mrtrix from metadata
Manonedde Dec 12, 2024
52c120b
Merge branch 'main' into fix_mrtrix_betantsbet
arnaudbore Dec 18, 2024
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6 changes: 2 additions & 4 deletions modules/nf-neuro/betcrop/antsbet/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -34,12 +34,12 @@ process BETCROP_ANTSBET {
-e $template -m $tissues_probabilities ${args.join(' ')}
scil_volume_math.py convert bet/BrainExtractionMask.nii.gz \
${prefix}__t1_bet_mask.nii.gz --data_type uint8
mrcalc $t1 ${prefix}__t1_bet_mask.nii.gz -mult ${prefix}__t1_bet.nii.gz -nthreads $task.cpus
scil_volume_math.py multiplication $t1 ${prefix}__t1_bet_mask.nii.gz \
${prefix}__t1_bet.nii.gz --data_type float32

cat <<-END_VERSIONS > versions.yml
"${task.process}":
scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p')
ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9]+\\+\\).*/\\1/')
END_VERSIONS
"""
Expand All @@ -51,15 +51,13 @@ process BETCROP_ANTSBET {
"""
antsBrainExtraction.sh -h
scil_volume_math.py -h
mrcalc -h

touch ${prefix}__t1_bet.nii.gz
touch ${prefix}__t1_bet_mask.nii.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p')
ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9]+\\+\\).*/\\1/')
END_VERSIONS
"""
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3 changes: 0 additions & 3 deletions modules/nf-neuro/betcrop/antsbet/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,9 +10,6 @@ tools:
- "scilpy":
description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
homepage: "https://github.com/scilus/scilpy.git"
- "MRtrix3":
description: "Toolbox for image processing, analysis and visualisation of dMRI."
homepage: "https://mrtrix.readthedocs.io/en/latest/"
- "ants":
description: "Advanced Normalization Tools."
homepage: "https://github.com/ANTsX/ANTs"
Expand Down
12 changes: 6 additions & 6 deletions modules/nf-neuro/betcrop/antsbet/tests/main.nf.test.snap
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Expand Up @@ -7,7 +7,7 @@
{
"id": "test"
},
"test__t1_bet.nii.gz:md5,bd666c4ce559eab93690131f8b2a9101"
"test__t1_bet.nii.gz:md5,4fc936b6eeb1396e2537c2ec401d89ff"
]
],
"1": [
Expand All @@ -19,7 +19,7 @@
]
],
"2": [
"versions.yml:md5,9fde1445bc10857db69e440781e58cb7"
"versions.yml:md5,bb378e913d4002d0b644d3277892ae20"
],
"mask": [
[
Expand All @@ -34,18 +34,18 @@
{
"id": "test"
},
"test__t1_bet.nii.gz:md5,bd666c4ce559eab93690131f8b2a9101"
"test__t1_bet.nii.gz:md5,4fc936b6eeb1396e2537c2ec401d89ff"
]
],
"versions": [
"versions.yml:md5,9fde1445bc10857db69e440781e58cb7"
"versions.yml:md5,bb378e913d4002d0b644d3277892ae20"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nextflow": "24.10.0"
},
"timestamp": "2024-10-30T17:42:18.337235926"
"timestamp": "2024-12-12T15:46:45.836683711"
}
}
8 changes: 4 additions & 4 deletions subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -43,18 +43,18 @@
"test_cropped.nii.gz",
"test_t1_cropped.nii.gz",
[
"versions.yml:md5,19aaa24cf046e49a4ad4ce5d507ea8aa",
"versions.yml:md5,37229cd5cee6f6788fbc9083d6618c61",
"versions.yml:md5,657fbb224f260392e573b8511c4b798d",
"versions.yml:md5,b979132991d8f72a3585465533bd5730",
"versions.yml:md5,bdd934b4b8456060c36d6d97e4f30740",
"versions.yml:md5,da278daafbe3afa8454021e2716dd205",
"versions.yml:md5,ea32c30f5320f720b2f5dc32ac2535ea"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.04.3"
"nf-test": "0.9.0",
"nextflow": "24.10.0"
},
"timestamp": "2024-12-04T10:38:12.185789"
"timestamp": "2024-12-12T15:50:29.838128539"
}
}
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