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Fix atlas handling and transform file issues in bundle_seg #80

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merged 10 commits into from
Jan 15, 2025
Merged

Fix atlas handling and transform file issues in bundle_seg #80

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793a515
fix external atlas use in bundle_seg
gagnonanthony Dec 12, 2024
7d971e9
fetch only affine mat for recognize bundle and validate file exist be…
gagnonanthony Dec 13, 2024
c43c5ce
split transform files into 2 differents named outputs for easier hand…
gagnonanthony Dec 16, 2024
5612cb5
update version in synthreg + revert memory limit
gagnonanthony Dec 17, 2024
5e6995e
snapshot tests
AlexVCaron Dec 18, 2024
5633f82
more memory for bundleseg
AlexVCaron Jan 13, 2025
0bf1801
ask 40Gb in subworkflow as well
AlexVCaron Jan 13, 2025
00c4871
fix md5sum for version file + Alex's comments
gagnonanthony Jan 15, 2025
a89f99e
make it more pretty
gagnonanthony Jan 15, 2025
0998703
revert snap for synthreg module and update the subworkflow snap
gagnonanthony Jan 15, 2025
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5 changes: 3 additions & 2 deletions modules/nf-neuro/registration/anattodwi/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -10,8 +10,9 @@ process REGISTRATION_ANATTODWI {
tuple val(meta), path(t1), path(b0), path(metric)

output:
tuple val(meta), path("*0GenericAffine.mat"), path("*1InverseWarp.nii.gz") , emit: transfo_trk
tuple val(meta), path("*1Warp.nii.gz"), path("*0GenericAffine.mat") , emit: transfo_image
tuple val(meta), path("*0GenericAffine.mat") , emit: affine
tuple val(meta), path("*1Warp.nii.gz") , emit: warp
tuple val(meta), path("*1InverseWarp.nii.gz") , emit: inverse_warp
tuple val(meta), path("*t1_warped.nii.gz") , emit: t1_warped
path "versions.yml" , emit: versions

Expand Down
42 changes: 28 additions & 14 deletions modules/nf-neuro/registration/anattodwi/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -8,8 +8,7 @@
"id": "test",
"single_end": false
},
"test__output0GenericAffine.mat:md5,6eef07f9004fb96e57ae0404ffef174c",
"test__output1InverseWarp.nii.gz:md5,28694d2b41f5209ab8f1acbb219014fe"
"test__output0GenericAffine.mat:md5,6eef07f9004fb96e57ae0404ffef174c"
]
],
"1": [
Expand All @@ -18,8 +17,7 @@
"id": "test",
"single_end": false
},
"test__output1Warp.nii.gz:md5,e0995852e251bee5521572a4495a0bd6",
"test__output0GenericAffine.mat:md5,6eef07f9004fb96e57ae0404ffef174c"
"test__output1Warp.nii.gz:md5,e0995852e251bee5521572a4495a0bd6"
]
],
"2": [
Expand All @@ -28,13 +26,10 @@
"id": "test",
"single_end": false
},
"test__t1_warped.nii.gz:md5,9c34f424900adea263e39ed1f37a793f"
"test__output1InverseWarp.nii.gz:md5,28694d2b41f5209ab8f1acbb219014fe"
]
],
"3": [
"versions.yml:md5,3b94092e010fc0f6bf505074a393ddcc"
],
"t1_warped": [
[
{
"id": "test",
Expand All @@ -43,35 +38,54 @@
"test__t1_warped.nii.gz:md5,9c34f424900adea263e39ed1f37a793f"
]
],
"transfo_image": [
"4": [
"versions.yml:md5,3b94092e010fc0f6bf505074a393ddcc"
],
"affine": [
[
{
"id": "test",
"single_end": false
},
"test__output1Warp.nii.gz:md5,e0995852e251bee5521572a4495a0bd6",
"test__output0GenericAffine.mat:md5,6eef07f9004fb96e57ae0404ffef174c"
]
],
"transfo_trk": [
"inverse_warp": [
[
{
"id": "test",
"single_end": false
},
"test__output0GenericAffine.mat:md5,6eef07f9004fb96e57ae0404ffef174c",
"test__output1InverseWarp.nii.gz:md5,28694d2b41f5209ab8f1acbb219014fe"
]
],
"t1_warped": [
[
{
"id": "test",
"single_end": false
},
"test__t1_warped.nii.gz:md5,9c34f424900adea263e39ed1f37a793f"
]
],
"versions": [
"versions.yml:md5,3b94092e010fc0f6bf505074a393ddcc"
],
"warp": [
[
{
"id": "test",
"single_end": false
},
"test__output1Warp.nii.gz:md5,e0995852e251bee5521572a4495a0bd6"
]
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nextflow": "24.10.2"
},
"timestamp": "2024-11-22T17:16:41.404087811"
"timestamp": "2024-12-16T17:41:00.965919497"
}
}
14 changes: 8 additions & 6 deletions modules/nf-neuro/registration/ants/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -11,10 +11,12 @@ process REGISTRATION_ANTS {
tuple val(meta), path(fixedimage), path(movingimage), path(mask) //** optional, input = [] **//

output:
tuple val(meta), path("*_warped.nii.gz") , emit: image
tuple val(meta), path("*__output{0Warp.nii.gz,1GenericAffine.mat}") , emit: transfo_image
tuple val(meta), path("*__output{0,1}Inverse{Warp.nii.gz,Affine.mat}") , emit: transfo_trk
path "versions.yml" , emit: versions
tuple val(meta), path("*_warped.nii.gz") , emit: image
tuple val(meta), path("*__output0Warp.nii.gz") , emit: warp, optional:true
tuple val(meta), path("*__output1GenericAffine.mat") , emit: affine
tuple val(meta), path("*__output1InverseWarp.nii.gz") , emit: inverse_warp, optional: true
tuple val(meta), path("*__output0InverseAffine.mat") , emit: inverse_affine
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when
Expand Down Expand Up @@ -62,7 +64,7 @@ process REGISTRATION_ANTS {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
ants: antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/'
ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/')
END_VERSIONS
"""

Expand All @@ -82,7 +84,7 @@ process REGISTRATION_ANTS {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
ants: antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/'
ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/')
END_VERSIONS
"""
}
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