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Fix atlas handling and transform file issues in bundle_seg #80

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Fix atlas handling and transform file issues in bundle_seg #80

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0cd7831
fix external atlas use in bundle_seg
gagnonanthony Dec 12, 2024
b7bf57e
fetch only affine mat for recognize bundle and validate file exist be…
gagnonanthony Dec 13, 2024
ee14337
split transform files into 2 differents named outputs for easier hand…
gagnonanthony Dec 16, 2024
1b6fbc6
update version in synthreg + revert memory limit
gagnonanthony Dec 17, 2024
8d206a8
snapshot tests
AlexVCaron Dec 18, 2024
760c0cd
Merge branch 'main' into fix/atlasbundleseg
AlexVCaron Dec 18, 2024
c36b6f9
Merge branch 'main' into fix/atlasbundleseg
AlexVCaron Dec 19, 2024
fea69e2
Merge branch 'main' into fix/atlasbundleseg
AlexVCaron Dec 19, 2024
633a940
Merge branch 'main' into fix/atlasbundleseg
AlexVCaron Dec 19, 2024
660f744
Merge branch 'main' into fix/atlasbundleseg
AlexVCaron Dec 19, 2024
eef5804
Merge branch 'main' into fix/atlasbundleseg
AlexVCaron Dec 19, 2024
1feba93
Merge branch 'main' into fix/atlasbundleseg
AlexVCaron Dec 19, 2024
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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"
}
}
10 changes: 6 additions & 4 deletions modules/nf-neuro/registration/ants/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -12,8 +12,10 @@ process REGISTRATION_ANTS {

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
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:
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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