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WIP - Update scilpy & tractometry #2

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merged 14 commits into from
Oct 21, 2020
Merged

WIP - Update scilpy & tractometry #2

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9a8c56b
Fix argument and remove useless txt
frheault Jul 1, 2020
2a3f7ad
Compatibility with tractometry-flow
frheault Jul 2, 2020
17b0a08
Consistent with tractometry
frheault Jul 2, 2020
6f8bcdf
New process IC
frheault Sep 11, 2020
34ba356
Fixed IC
frheault Sep 17, 2020
8fa6ac4
Change anat to fa in usage
frheault Sep 17, 2020
196f4f1
Fuse invalid with reco
frheault Sep 19, 2020
fbd133b
more robust input
frheault Sep 23, 2020
68828e7
Remove tractogram before move
frheault Sep 23, 2020
3b54986
Guillaume comments
frheault Oct 2, 2020
2124a93
Memory limit
frheault Oct 5, 2020
d361c09
Change RAM
frheault Oct 8, 2020
3c8aa15
Remove IC
frheault Oct 13, 2020
1260bc5
Resolve Max comments
frheault Oct 18, 2020
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11 changes: 5 additions & 6 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ log.info "Input: $params.root"
root = file(params.root)
/* Watch out, files are ordered alphabetically in channel */
in_data = Channel
.fromFilePairs("$root/**/{*tracking.trk,*anat.nii.gz}",
.fromFilePairs("$root/**/{*tracking.trk,*fa.nii.gz}",
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size: 2,
maxDepth:2,
flat: true) {it.parent.name}
Expand All @@ -67,7 +67,7 @@ root = file(params.root)
atlas_directory = Channel.fromPath("$params.atlas_directory")

if (params.atlas_centroids) {
atlas_centroids = Channel.fromPath("$params.atlas_centroids/*.trk")
atlas_centroids = Channel.fromPath("$params.atlas_centroids/*_centroid.trk")
}
else {
atlas_centroids = Channel.empty()
Expand Down Expand Up @@ -95,12 +95,11 @@ process Register_Anat {
set sid, file(native_anat), file(atlas) from anats_for_registration

output:
set sid, "${sid}__output0GenericAffine.txt" into transformation_for_recognition, transformation_for_centroids
set sid, "${sid}__output0GenericAffine.mat" into transformation_for_recognition, transformation_for_centroids
file "${sid}__outputWarped.nii.gz"
script:
"""
antsRegistrationSyNQuick.sh -d 3 -f ${native_anat} -m ${atlas} -n ${params.register_processes} -o ${sid}__output -t a
ConvertTransformFile 3 ${sid}__output0GenericAffine.mat ${sid}__output0GenericAffine.txt --hm --ras
"""
}

Expand All @@ -116,7 +115,7 @@ process Transform_Centroids {
file "${sid}__${centroid.baseName}.trk"
script:
"""
scil_apply_transform_to_tractogram.py ${centroid} ${anat} ${transfo} ${sid}__${centroid.baseName}.trk --inverse --remove_invalid
scil_apply_transform_to_tractogram.py ${centroid} ${anat} ${transfo} ${sid}__${centroid.baseName}.trk --inverse --cut_invalid
"""
}

Expand All @@ -136,7 +135,7 @@ process Recognize_Bundles {
script:
"""
mkdir tmp/
scil_recognize_multi_bundles.py ${tractogram} ${config} ${directory}/*/ ${transfo} --inverse --output tmp/ \
scil_recognize_multi_bundles.py ${tractogram} ${config} ${directory}/*/ ${transfo} --inverse --out_dir tmp/ \
--log_level DEBUG --multi_parameters $params.multi_parameters --minimal_vote_ratio $params.minimal_vote_ratio \
--tractogram_clustering_thr $params.wb_clustering_thr --seeds $params.seeds --processes $params.rbx_processes
mv tmp/* ./
Expand Down