Merge pull request #1 from frheault/code_transfert_alpha

Not tested but LGTM and since it's a first PR let's go give it a try !

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2020 Sherbrooke Connectivity Imaging Lab
+Copyright (c) 2019 Sherbrooke Connectivity Imaging Lab
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1 +1,32 @@
-# rbx-flow
+# RecobundlesX pipeline
+===================
+
+Run the RecobundlesX pipeline.
+
+If you use this pipeline, please cite:
+
+```
+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
+
+Kurtzer GM, Sochat V, Bauer MW Singularity: Scientific containers for
+mobility of compute. PLoS ONE 12(5): e0177459 (2017)
+https://doi.org/10.1371/journal.pone.0177459
+
+P. Di Tommaso, et al. Nextflow enables reproducible computational workflows.
+Nature Biotechnology 35, 316–319 (2017) https://doi.org/10.1038/nbt.3820
+```
+
+Requirements
+------------
+
+- [Nextflow](https://www.nextflow.io)
+- [scilpy](https://github.com/scilus/scilpy)
+- [ants](https://github.com/ANTsX/ANTs)
+
+Usage
+-----
+
+See *USAGE* or run `nextflow run main.nf --help`
+

USAGE

@@ -0,0 +1,40 @@
+Pipeline for RecobundlesX tractography
+======================================
+
+USAGE
+
+nextflow run main.nf --root ... [OPTIONAL_ARGUMENTS]
+
+DESCRIPTION
+
+--root=/path/to/[root]              Root folder containing multiple subjects
+
+                                    [root]
+                                    ├── S1
+                                    │   ├── *anat.nii.gz
+                                    │   └── *tracking.trk
+                                    └── S2
+                                        └── *
+
+--atlas_config                      Path to json config file
+--atlas_anat                        Path to reference anatomy of the atlas
+--atlas_directory                   Path of the folder containing all atlases
+
+NOTES
+
+OPTIONAL ARGUMENTS (current value)
+--atlas_centroids                       Folder containing centroids (trk) for future tractometry (Must have the same filename as in the atlas_config)
+
+--multi_parameters                      Number of executions for the multi-parameters ($multi_parameters)
+--minimal_vote_ratio                    Percentage of the vote to obtain in order to be considered valid ($minimal_vote_ratio)
+--wb_clustering_thr                     List of distance (mm) for QBx whole brain clustreing ($wb_clustering_thr)
+--seeds                                 List of random seeds values for the rng ($seeds)
+--outlier_alpha                         Remove spurious streamlines based on shape ($outlier_alpha)
+
+--register_processes                    Number of processes for registration task ($register_processes).
+--rbx_processes                         Number of processes for bundle recognition task ($rbx_processes).
+
+Use '-C config_file.config' to specify a non-default configuration file.
+The '-C config_file.config' must be inserted after the nextflow call
+like 'nextflow -C config_file.config run ...'.
+

main.nf

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+#!/usr/bin/env nextflow
+
+if(params.help) {
+    usage = file("$baseDir/USAGE")
+    cpu_count = Runtime.runtime.availableProcessors()
+
+    bindings = ["atlas_config":"$params.atlas_config",
+                "atlas_directory":"$params.atlas_directory",
+                "atlas_centroids":"$params.atlas_centroids",
+                "multi_parameters":"$params.multi_parameters",
+                "minimal_vote_ratio":"$params.minimal_vote_ratio",
+                "wb_clustering_thr":"$params.wb_clustering_thr",
+                "seeds":"$params.seeds",
+                "outlier_alpha":"$params.outlier_alpha",
+                "register_processes":"$params.register_processes",
+                "rbx_processes":"$params.rbx_processes"]
+
+    engine = new groovy.text.SimpleTemplateEngine()
+    template = engine.createTemplate(usage.text).make(bindings)
+    print template.toString()
+    return
+}
+
+log.info "SCIL RecobundlesX pipeline"
+log.info "=========================="
+log.info ""
+log.info "Start time: $workflow.start"
+log.info ""
+
+log.debug "[Command-line]"
+log.debug "$workflow.commandLine"
+log.debug ""
+
+log.info "[Git Info]"
+log.info "$workflow.repository - $workflow.revision [$workflow.commitId]"
+log.info ""
+
+log.info "Options"
+log.info "======="
+log.info ""
+log.info "[Atlas]"
+log.info "Atlas Config: $params.atlas_config"
+log.info "Atlas Anat: $params.atlas_anat"
+log.info "Atlas Directory: $params.atlas_directory"
+log.info "Atlas Centroids: $params.atlas_centroids"
+log.info ""
+log.info "[Recobundles options]"
+log.info "Multi-Parameters Executions: $params.multi_parameters"
+log.info "Minimal Vote Percentage: $params.minimal_vote_ratio"
+log.info "Whole Brain Clustering Threshold: $params.wb_clustering_thr"
+log.info "Random Seeds: $params.seeds"
+log.info "Outlier Removal Alpha: $params.outlier_alpha"
+log.info ""
+log.info ""
+
+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}",
+                        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)
+
+workflow.onComplete {
+    log.info "Pipeline completed at: $workflow.complete"
+    log.info "Execution status: ${ workflow.success ? 'OK' : 'failed' }"
+    log.info "Execution duration: $workflow.duration"
+}
+
+anat_for_registration
+    .combine(atlas_anat)
+    .set{anats_for_registration}
+process Register_Anat {
+    cpus params.register_processes
+    input:
+    set sid, file(native_anat), file(atlas) from anats_for_registration
+
+    output:
+    set sid, "${sid}__output0GenericAffine.txt" into transformation_for_recognition, transformation_for_centroids
+    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 ${sid}__output0GenericAffine.txt --hm --ras
+    """ 
+}
+
+
+anat_for_reference
+    .join(transformation_for_centroids, by: 0)
+    .set{anat_and_transformation}
+process Transform_Centroids {
+    input:
+    set sid, file(anat), file(transfo) from anat_and_transformation
+    each file(centroid) from atlas_centroids
+    output:
+    file "${sid}__${centroid.baseName}.trk"
+    script:
+    """
+    scil_apply_transform_to_tractogram.py ${centroid} ${anat} ${transfo} ${sid}__${centroid.baseName}.trk --inverse --remove_invalid
+    """ 
+}
+
+tractogram_for_recognition
+    .combine(transformation_for_recognition, by: 0)
+    .combine(atlas_config)
+    .combine(atlas_directory)
+    .set{tractogram_and_transformation}
+process Recognize_Bundles {
+    cpus params.rbx_processes
+    input:
+    set sid, file(tractogram), 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:
+    """
+    mkdir tmp/
+    scil_recognize_multi_bundles.py ${tractogram} ${config} ${directory}/*/ ${transfo} --inverse --output 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 $params.rbx_processes
+    mv tmp/* ./
+    """ 
+}
+
+bundles_for_cleaning
+    .transpose()
+    .set{all_bundles_for_cleaning}
+process Clean_Bundles {
+    input:
+    set sid, file(bundle) from all_bundles_for_cleaning
+    output:
+    file "${sid}__*_cleaned.trk"
+    script:
+    bname = bundle.name.take(bundle.name.lastIndexOf('.'))
+    """
+    scil_outlier_rejection.py ${bundle} "${sid}__${bname}_cleaned.trk" --alpha $params.outlier_alpha
+    """ 
+}

nextflow.config

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+process {
+    publishDir = {"./results_rbx/$sid/$task.process"}
+    scratch = true
+    stageInMode = 'copy'
+    stageOutMode = 'rsync'
+    tag = { "$sid" }
+    afterScript = 'sleep 1'
+}
+
+params {
+    help=false
+    root=false
+    atlas_centroids=false
+    atlas_directory=false
+    atlas_anat=false
+    atlas_config=false
+
+    //**Recobundle segmentation**//
+        multi_parameters=18
+        minimal_vote_ratio=0.5
+        wb_clustering_thr="15 12"
+        seeds="0"
+        outlier_alpha=0.5
+
+    //**Number of processes per tasks**//
+        register_processes=4
+        rbx_processes=4
+}
+
+singularity.autoMounts = true
+
+profiles {
+    fully_reproducible {
+        params.register_processes=1
+        params.rbx_processes=1
+    }
+
+    macos {
+            process.scratch="/tmp"
+    }
+}