Merge pull request #2 from frheault/update_scilpy

WIP - Update scilpy & tractometry
scilus · Oct 21, 2020 · 0b68bad · 0b68bad
2 parents bb81603 + 1260bc5
commit 0b68bad
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diff --git a/README.md b/README.md
@@ -2,10 +2,15 @@
 ===================
 
 Run the RecobundlesX pipeline.
+To access the example atlases:
+https://zenodo.org/record/4104300#.X4xdG51KhdU
 
 If you use this pipeline, please cite:
 
 ```
+Rheault, Francois. Analyse et reconstruction de faisceaux de la matière blanche.
+page 137-170, (2020), https://savoirs.usherbrooke.ca/handle/11143/17255
+
 Garyfallidis, Eleftherios, et al. Recognition of white matter bundles using
 local and global streamline-based registration and clustering.
 NeuroImage 170 (2018) https://doi.org/10.1016/j.neuroimage.2017.07.015

diff --git a/USAGE b/USAGE
@@ -3,15 +3,15 @@ Pipeline for RecobundlesX tractography
 
 USAGE
 
-nextflow run main.nf --root ... [OPTIONAL_ARGUMENTS]
+nextflow run main.nf --input ... [OPTIONAL_ARGUMENTS]
 
 DESCRIPTION
 
---root=/path/to/[root]              Root folder containing multiple subjects
+--input=/path/to/[root]              Root folder containing multiple subjects
 
                                     [root]
                                     ├── S1
-                                    │   ├── *anat.nii.gz
+                                    │   ├── *fa.nii.gz
                                     │   └── *tracking.trk
                                     └── S2
                                         └── *

diff --git a/main.nf b/main.nf
@@ -53,32 +53,36 @@ log.info "Outlier Removal Alpha: $params.outlier_alpha"
 log.info ""
 log.info ""
 
-log.info "Input: $params.root"
-root = file(params.root)
+log.info "Input: $params.input"
+root = file(params.input)
 /* Watch out, files are ordered alphabetically in channel */
-    in_data = Channel
-        .fromFilePairs("$root/**/{*tracking.trk,*anat.nii.gz}",
-                        size: 2,
-                        maxDepth:2,
-                        flat: true) {it.parent.name}
-
-    atlas_anat = Channel.fromPath("$params.atlas_anat")
-    atlas_config = Channel.fromPath("$params.atlas_config")
-    atlas_directory = Channel.fromPath("$params.atlas_directory")
-
-    if (params.atlas_centroids) {
-        atlas_centroids = Channel.fromPath("$params.atlas_centroids/*.trk")
-    }
-    else {
-        atlas_centroids = Channel.empty()
-    }
-
-(anat_for_registration, anat_for_reference, tractogram_for_recognition) = in_data
-    .map{sid, anat, tractogram -> 
-        [tuple(sid, anat),
-        tuple(sid, anat),
-        tuple(sid, tractogram)]}
-    .separate(3)
+Channel
+    .fromPath("$root/**/*tracking*.trk",
+                    maxDepth:1)
+    .map{[it.parent.name, it]}
+    .set{tractogram_for_recognition}
+
+Channel
+    .fromPath("$root/**/*fa.nii.gz",
+                    maxDepth:1)
+    .map{[it.parent.name, it]}
+    .into{anat_for_registration;anat_for_reference_centroids;anat_for_reference_bundles}
+
+if (!(params.atlas_anat) || !(params.atlas_config) || !(params.atlas_directory)) {
+    error "You must specify all 3 atlas related input. --atlas_anat, " +
+    "--atlas_config and --atlas_directory all are mandatory."
+}
+
+atlas_anat = Channel.fromPath("$params.atlas_anat")
+atlas_config = Channel.fromPath("$params.atlas_config")
+atlas_directory = Channel.fromPath("$params.atlas_directory")
+
+if (params.atlas_centroids) {
+    atlas_centroids = Channel.fromPath("$params.atlas_centroids/*_centroid.trk")
+}
+else {
+    atlas_centroids = Channel.empty()
+}
 
 workflow.onComplete {
     log.info "Pipeline completed at: $workflow.complete"
@@ -91,21 +95,22 @@ anat_for_registration
     .set{anats_for_registration}
 process Register_Anat {
     cpus params.register_processes
+    memory '2 GB'
+
     input:
     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
     """ 
 }
 
 
-anat_for_reference
+anat_for_reference_centroids
     .join(transformation_for_centroids, by: 0)
     .set{anat_and_transformation}
 process Transform_Centroids {
@@ -116,29 +121,35 @@ 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
     """ 
 }
 
+
 tractogram_for_recognition
-    .combine(transformation_for_recognition, by: 0)
+    .join(anat_for_reference_bundles)
+    .join(transformation_for_recognition)
     .combine(atlas_config)
     .combine(atlas_directory)
     .set{tractogram_and_transformation}
 process Recognize_Bundles {
     cpus params.rbx_processes
+    memory params.rbx_memory_limit
+
     input:
-    set sid, file(tractogram), file(transfo), file(config), file(directory) from tractogram_and_transformation
+    set sid, file(tractogram), file(refenrence), file(transfo), file(config), file(directory) from tractogram_and_transformation
     output:
     set sid, "*.trk" into bundles_for_cleaning
     file "results.json"
     file "logfile.txt"
     script:
     """
+    scil_remove_invalid_streamlines.py ${tractogram} tractogram_ic.trk --reference ${refenrence} --remove_single_point --remove_overlapping_points
     mkdir tmp/
-    scil_recognize_multi_bundles.py ${tractogram} ${config} ${directory}/*/ ${transfo} --inverse --output tmp/ \
+    scil_recognize_multi_bundles.py tractogram_ic.trk ${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
+    rm tractogram_ic.trk
     mv tmp/* ./
     """ 
 }

diff --git a/nextflow.config b/nextflow.config
@@ -25,11 +25,16 @@ params {
     //**Number of processes per tasks**//
         register_processes=4
         rbx_processes=4
+        params.rbx_memory_limit='8 GB'
 }
 
 singularity.autoMounts = true
 
 profiles {
+    large_dataset {
+        params.rbx_memory_limit='16 GB'
+    }
+
     fully_reproducible {
         params.register_processes=1
         params.rbx_processes=1