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Merged
arnaudbore merged 3 commits into from
Sep 24, 2025
Merged

update containers - module registration #195

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f8f4324
update containers registration
arnaudbore Sep 22, 2025
b244910
merge main and fix conflict
arnaudbore Sep 23, 2025
e087f32
merge main and answer comments
arnaudbore Sep 24, 2025
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22 changes: 16 additions & 6 deletions modules/nf-neuro/registration/anattodwi/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -2,9 +2,7 @@ process REGISTRATION_ANATTODWI {
tag "$meta.id"
label 'process_single'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif':
'scilus/scilus:19c87b72bcbc683fb827097dda7f917940fda123' }"
container "scilus/scilus:2.2.0"

input:
tuple val(meta), path(t1), path(b0), path(metric)
Expand Down Expand Up @@ -73,11 +71,11 @@ process REGISTRATION_ANATTODWI {
# Iterate over images.
for image in t1_warped b0;
do
scil_viz_volume_screenshot.py *\${image}.nii.gz \${image}_coronal.png \
scil_viz_volume_screenshot *\${image}.nii.gz \${image}_coronal.png \
--slices \$coronal_mid --axis coronal \$viz_params
scil_viz_volume_screenshot.py *\${image}.nii.gz \${image}_sagittal.png \
scil_viz_volume_screenshot *\${image}.nii.gz \${image}_sagittal.png \
--slices \$sagittal_mid --axis sagittal \$viz_params
scil_viz_volume_screenshot.py *\${image}.nii.gz \${image}_axial.png \
scil_viz_volume_screenshot *\${image}.nii.gz \${image}_axial.png \
--slices \$axial_mid --axis axial \$viz_params

if [ \$image != b0 ];
Expand Down Expand Up @@ -107,6 +105,7 @@ process REGISTRATION_ANATTODWI {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9.a-zA-Z-]+).*/\\1/')
mrtrix: \$(mrinfo -version 2>&1 | grep "== mrinfo" | sed -E 's/== mrinfo ([0-9.]+).*/\\1/')
imagemagick: \$(convert -version | sed -n 's/.*ImageMagick \\([0-9]\\{1,\\}\\.[0-9]\\{1,\\}\\.[0-9]\\{1,\\}\\).*/\\1/p')
Expand All @@ -117,7 +116,17 @@ process REGISTRATION_ANATTODWI {
def prefix = task.ext.prefix ?: "${meta.id}"

"""
set +e
function handle_code () {
local code=\$?
ignore=( 1 )
[[ " \${ignore[@]} " =~ " \$code " ]] || exit \$code
}
trap 'handle_code' ERR

antsRegistration -h
scil_viz_volume_screenshot -h
convert -h

touch ${prefix}__t1_warped.nii.gz
touch ${prefix}__output0GenericAffine.mat
Expand All @@ -127,6 +136,7 @@ process REGISTRATION_ANATTODWI {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9.a-zA-Z-]+).*/\\1/')
mrtrix: \$(mrinfo -version 2>&1 | grep "== mrinfo" | sed -E 's/== mrinfo ([0-9.]+).*/\\1/')
imagemagick: \$(convert -version | sed -n 's/.*ImageMagick \\([0-9]\\{1,\\}\\.[0-9]\\{1,\\}\\.[0-9]\\{1,\\}\\).*/\\1/p')
Expand Down
38 changes: 19 additions & 19 deletions modules/nf-neuro/registration/anattodwi/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
"id": "test",
"single_end": false
},
"test__output0GenericAffine.mat:md5,6eef07f9004fb96e57ae0404ffef174c"
"test__output0GenericAffine.mat:md5,18d03f6c1fd587b00b3bc9363eb8ed4f"
]
],
"1": [
Expand All @@ -17,7 +17,7 @@
"id": "test",
"single_end": false
},
"test__output1Warp.nii.gz:md5,e0995852e251bee5521572a4495a0bd6"
"test__output1Warp.nii.gz:md5,aa42d4dd6f227d986cd99df45425d5c5"
]
],
"2": [
Expand All @@ -26,7 +26,7 @@
"id": "test",
"single_end": false
},
"test__output1InverseWarp.nii.gz:md5,28694d2b41f5209ab8f1acbb219014fe"
"test__output1InverseWarp.nii.gz:md5,6a04d7c100075b4ba7a276a55a4094bd"
]
],
"3": [
Expand All @@ -35,7 +35,7 @@
"id": "test",
"single_end": false
},
"test__t1_warped.nii.gz:md5,9c34f424900adea263e39ed1f37a793f"
"test__t1_warped.nii.gz:md5,39c30c6251cba224989bc74a31540121"
]
],
"4": [
Expand All @@ -44,19 +44,19 @@
"id": "test",
"single_end": false
},
"test_registration_anattodwi_mqc.gif:md5,74a7cf404c443726487683c23bd926c0"
"test_registration_anattodwi_mqc.gif:md5,687252d31b0109f99a174b4e3960e4e6"
]
],
"5": [
"versions.yml:md5,f368bc76bf8d1f1a68caea3597b0c65b"
"versions.yml:md5,77dc5dd2d9f2f2b772043eef8471eb13"
],
"affine": [
[
{
"id": "test",
"single_end": false
},
"test__output0GenericAffine.mat:md5,6eef07f9004fb96e57ae0404ffef174c"
"test__output0GenericAffine.mat:md5,18d03f6c1fd587b00b3bc9363eb8ed4f"
]
],
"inverse_warp": [
Expand All @@ -65,7 +65,7 @@
"id": "test",
"single_end": false
},
"test__output1InverseWarp.nii.gz:md5,28694d2b41f5209ab8f1acbb219014fe"
"test__output1InverseWarp.nii.gz:md5,6a04d7c100075b4ba7a276a55a4094bd"
]
],
"mqc": [
Expand All @@ -74,7 +74,7 @@
"id": "test",
"single_end": false
},
"test_registration_anattodwi_mqc.gif:md5,74a7cf404c443726487683c23bd926c0"
"test_registration_anattodwi_mqc.gif:md5,687252d31b0109f99a174b4e3960e4e6"
]
],
"t1_warped": [
Expand All @@ -83,39 +83,39 @@
"id": "test",
"single_end": false
},
"test__t1_warped.nii.gz:md5,9c34f424900adea263e39ed1f37a793f"
"test__t1_warped.nii.gz:md5,39c30c6251cba224989bc74a31540121"
]
],
"versions": [
"versions.yml:md5,f368bc76bf8d1f1a68caea3597b0c65b"
"versions.yml:md5,77dc5dd2d9f2f2b772043eef8471eb13"
],
"warp": [
[
{
"id": "test",
"single_end": false
},
"test__output1Warp.nii.gz:md5,e0995852e251bee5521572a4495a0bd6"
"test__output1Warp.nii.gz:md5,aa42d4dd6f227d986cd99df45425d5c5"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.3"
"nf-test": "0.9.0",
"nextflow": "25.04.7"
},
"timestamp": "2025-02-20T14:58:42.372471"
"timestamp": "2025-09-22T21:23:44.360834413"
},
"registration - anattodwi -stub-run": {
"content": [
[
"versions.yml:md5,f368bc76bf8d1f1a68caea3597b0c65b"
"versions.yml:md5,77dc5dd2d9f2f2b772043eef8471eb13"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.3"
"nf-test": "0.9.0",
"nextflow": "25.04.7"
},
"timestamp": "2025-02-20T14:58:49.169195"
"timestamp": "2025-09-22T21:24:00.939016823"
}
}
14 changes: 8 additions & 6 deletions modules/nf-neuro/registration/ants/main.nf
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,7 @@ process REGISTRATION_ANTS {
tag "$meta.id"
label 'process_medium'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
"https://scil.usherbrooke.ca/containers/scilus_latest.sif":
"scilus/scilus:19c87b72bcbc683fb827097dda7f917940fda123"}"
container "scilus/scilus:2.2.0"

input:
tuple val(meta), path(fixedimage), path(movingimage), path(mask) /* optional, input = [] */
Expand Down Expand Up @@ -80,11 +78,11 @@ process REGISTRATION_ANTS {
# Iterate over images.
for image in fixedimage warped;
do
scil_viz_volume_screenshot.py *\${image}.nii.gz \${image}_coronal.png \
scil_viz_volume_screenshot *\${image}.nii.gz \${image}_coronal.png \
--slices \$coronal_dim --axis coronal \$viz_params
scil_viz_volume_screenshot.py *\${image}.nii.gz \${image}_sagittal.png \
scil_viz_volume_screenshot *\${image}.nii.gz \${image}_sagittal.png \
--slices \$sagittal_dim --axis sagittal \$viz_params
scil_viz_volume_screenshot.py *\${image}.nii.gz \${image}_axial.png \
scil_viz_volume_screenshot *\${image}.nii.gz \${image}_axial.png \
--slices \$axial_dim --axis axial \$viz_params
if [ \$image != fixedimage ];
then
Expand All @@ -109,6 +107,7 @@ process REGISTRATION_ANTS {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9.a-zA-Z-]+).*/\\1/')
mrtrix: \$(mrinfo -version 2>&1 | grep "== mrinfo" | sed -E 's/== mrinfo ([0-9.]+).*/\\1/')
imagemagick: \$(convert -version | grep "Version:" | sed -E 's/.*ImageMagick ([0-9.-]+).*/\\1/')
Expand All @@ -130,6 +129,8 @@ process REGISTRATION_ANTS {

antsRegistrationSyNQuick.sh -h
antsApplyTransforms -h
convert -h
scil_viz_volume_screenshot -h

touch ${prefix}__t1_warped.nii.gz
touch ${prefix}__output0GenericAffine.mat
Expand All @@ -139,6 +140,7 @@ process REGISTRATION_ANTS {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9.a-zA-Z-]+).*/\\1/')
mrtrix: \$(mrinfo -version 2>&1 | grep "== mrinfo" | sed -E 's/== mrinfo ([0-9.]+).*/\\1/')
imagemagick: \$(convert -version | grep "Version:" | sed -E 's/.*ImageMagick ([0-9.-]+).*/\\1/')
Expand Down
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