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Merge pull request #1 from arnaudbore/first_release
First release
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‎USAGE‎

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register_flow pipeline
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=====================
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Register t1, metrics and tractograms to template space.
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We suggest to use https://github.com/scilus/combine_flows to create input.
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USAGE
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nextflow run main.nf [OPTIONAL_ARGUMENTS] --input --template
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DESCRIPTION
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--input=/path/to/[root] Root folder containing multiple subjects
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[root]
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├── S1
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│ │── *t1.nii.gz (orig space)
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| └── metrics (optional)
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| │ └── *.nii.gz
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| └── tractograms (optional)
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| └── *.trks
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└── S2
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└── *
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--template=/path/to/template_t1.nii.gz Path to a nifti T1 template used for registration.
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It has to be named template_t1.nii.gz
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OPTIONAL ARGUMENTS (current value)
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--linear_registration If set, it will use linear registration instead of non linear registration ($linear_registration).
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--quick_registration If set, it will use antsRegistrationSyNQuick.sh instead of antsRegistrationSyN.sh for registration ($quick_registration).
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--output_dir Specify a new output directory to avoid overwriting results (when dealing with multiple input labels) ($output_dir).
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--processes_register Number of processes for registration task ($processes_register).
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--processes The number of parallel processes to launch ($cpu_count).
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Only affects the local scheduler.
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AVAILABLE PROFILES (using -profile option (e.g. -profile fully_reproducible))
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macos When this profile is used, TractoFlow will modify a parameter (scratch) for MacOS users.
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fully_reproducible When this profile is used, all the parameters will be set to have 100% reproducible results.
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NOTES
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To set the number of parallel processes to launch, please use:
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'nextflow run -qs {nb_processes}'.
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The intermediate working directory is, by default, set to './work'.
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To change it, use the '-w WORK_DIR' argument.
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The default config file is connectoflow/nextflow.config.
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Use '-C config_file.config' to specify a non-default configuration file.
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The '-C config_file.config' must be inserted after the nextflow call
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like 'nextflow -C config_file.config run ...'.

‎main.nf‎

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#!/usr/bin/env nextflow
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if(params.help) {
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usage = file("$baseDir/USAGE")
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cpu_count = Runtime.runtime.availableProcessors()
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bindings = ["quick_registration":"$params.quick_registration",
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"linear_registration":"$params.linear_registration",
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"output_dir":"$params.output_dir",
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"processes_register":"$params.processes_register",
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"cpu_count":"$cpu_count"]
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engine = new groovy.text.SimpleTemplateEngine()
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template = engine.createTemplate(usage.text).make(bindings)
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print template.toString()
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return
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}
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log.info "Run Registration to template space"
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log.info "============================="
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log.info ""
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log.info ""
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log.info "Start time: $workflow.start"
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log.info ""
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log.debug "[Command-line]"
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log.debug "$workflow.commandLine"
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log.debug ""
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log.info "[Git Info]"
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log.info "$workflow.repository - $workflow.revision [$workflow.commitId]"
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log.info ""
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log.info "[Inputs]"
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log.info "Root: $params.input"
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log.info "Template: $params.template"
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log.info "Output directory: $params.output_dir"
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log.info ""
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log.info "Number of processes per tasks"
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log.info "============================="
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log.info "Template registration: $params.processes_register"
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log.info ""
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root = file(params.input)
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/* Watch out, files are ordered alphabetically in channel */
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Channel
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.fromPath("$root/**/*t1.nii.gz",
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maxDepth:1)
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.map{[it.parent.name, it]}
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.into{in_t1; subjects_for_count}
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in_trks = Channel
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.fromFilePairs("$root/**/tractograms/*.trk",
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size: -1,
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maxDepth:2) {it.parent.parent.name}
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if (!params.template.contains("template_t1.nii.gz")) {
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error "Error ~ Template filename should be named template_t1.nii.gz."}
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Channel.fromPath(file(params.template))
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.into{template_for_registration;template_for_transformation_trks;template_for_transformation_metrics; template_check_name}
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in_metrics = Channel
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.fromFilePairs("$root/**/metrics/*.nii.gz",
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size: -1,
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maxDepth:2) {it.parent.parent.name}
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subjects_for_count.count()
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.subscribe{a -> if (a == 0)
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error "Error ~ No subjects found. Please check the naming convention, your --input path."}
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if (!params.template){
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error "Error ~ Please set the template to use."
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}
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in_t1.combine(template_for_registration).set{anats_for_registration}
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process Register_T1_to_template {
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cpus params.processes_register
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memory '2 GB'
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publishDir = params.registration
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input:
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set sid, file(anat), file(template) from anats_for_registration
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output:
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set sid, "${sid}__output0GenericAffine.mat", "${sid}__output1Warp.nii.gz", "${sid}__output1InverseWarp.nii.gz" into nonlinear_transformation_for_trks, nonlinear_transformation_for_metrics optional true
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set sid, "${sid}__output0GenericAffine.mat" into linear_transformation_for_trks, linear_transformation_for_metrics optional true
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set sid, "${sid}__outputWarped.nii.gz" into t1_to_template
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script:
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"""
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${params.script_registration} -d 3 -m ${anat} -f ${template} -n ${task.cpus} -o "${sid}__output" -t ${params.transfo}
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"""
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}
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process Get_T1_Template_Space{
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cpus 1
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publishDir = params.outdir_t1
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input:
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set sid, file(t1_warped) from t1_to_template
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output:
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file "${sid}__t1_to_template.nii.gz"
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script:
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"""
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mv ${t1_warped} ${sid}__t1_to_template.nii.gz
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"""
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}
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Channel.empty()
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.into{nonlinear_metrics_transformation_for_metrics; linear_metrics_transformation_for_metrics}
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if(params.linear_registration){
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in_metrics
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.transpose()
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.combine(template_for_transformation_metrics)
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.combine(linear_transformation_for_metrics, by: 0)
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.set{linear_metrics_transformation_for_metrics}
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}
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else{
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in_metrics
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.transpose()
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.combine(template_for_transformation_metrics)
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.combine(nonlinear_transformation_for_metrics, by: 0)
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.set{nonlinear_metrics_transformation_for_metrics}
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}
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process Linear_Registration_Metrics_to_template {
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cpus 1
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publishDir = params.registration_metrics
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input:
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set sid, file(metric), file(template), file(transfo) from linear_metrics_transformation_for_metrics
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output:
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file "*_to_template.nii.gz"
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script:
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if (params.linear_registration)
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"""
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if [[ "$metric" == *"nufo"* ]]; then
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antsApplyTransforms -d 3 -i $metric -r $template -t $transfo -o ${metric.getSimpleName()}_to_template.nii.gz -n NearestNeighbor
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else
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antsApplyTransforms -d 3 -i $metric -r $template -t $transfo -o ${metric.getSimpleName()}_to_template.nii.gz
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fi
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"""
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}
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process NonLinear_Registration_Metrics_to_template {
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cpus 1
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publishDir = params.registration_metrics
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input:
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set sid, file(metric), file(template), file(transfo), file(warp), file(inverse_warp) from nonlinear_metrics_transformation_for_metrics
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output:
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file "*_to_template.nii.gz"
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script:
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"""
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antsApplyTransforms -d 3 -i $metric -r $template -t $warp $transfo -o ${metric.getSimpleName()}_to_template.nii.gz
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"""
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}
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Channel.empty()
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.into{linear_trks_transformation_for_trks; nonlinear_trks_transformation_for_trks}
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if(params.linear_registration){
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in_trks
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.transpose()
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.combine(template_for_transformation_trks)
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.combine(linear_transformation_for_trks, by: 0)
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.set{linear_trks_transformation_for_trks}
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}
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else{
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in_trks
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.transpose()
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.combine(template_for_transformation_trks)
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.combine(nonlinear_transformation_for_trks, by: 0)
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.set{nonlinear_trks_transformation_for_trks}
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}
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process Linear_Registration_Tractograms_to_template {
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cpus 1
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publishDir = params.registration_trks
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input:
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set sid, file(tractogram), file(template), file(transfo) from linear_trks_transformation_for_trks
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output:
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file "*_to_template.trk"
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script:
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"""
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scil_apply_transform_to_tractogram.py ${tractogram} ${template} ${transfo} ${tractogram.getSimpleName()}_to_template.trk --inverse
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"""
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}
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process NonLinear_Registration_Tractograms_to_template {
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cpus 1
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publishDir = params.registration_trks
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input:
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set sid, file(tractogram), file(template), file(transfo), file(warp), file(inverse_warp) from nonlinear_trks_transformation_for_trks
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output:
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file "*_to_template.trk"
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script:
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"""
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scil_apply_transform_to_tractogram.py ${tractogram} ${template} ${transfo} ${tractogram.getSimpleName()}_to_template.trk --inverse --inverse --in_deformation ${inverse_warp}
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"""
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}

‎nextflow.config‎

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process {
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tag = {"$sid"}
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publishDir = {"./results_registration/$sid/$task.process"}
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errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' }
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maxRetries = 3
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maxErrors = -1
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scratch = true
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stageInMode = 'copy'
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stageOutMode = 'rsync'
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}
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params {
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help=false
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root=false
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template=false
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output_dir="./results_registration/"
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params.outdir_t1=[path: {"./$params.output_dir/$sid/"}]
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params.registration_metrics=[path: {"./$params.output_dir/$sid/Metrics_into_template_space/"}]
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params.registration_trks=[path: {"./$params.output_dir/$sid/Trks_into_template_space/"}]
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params.registration=[path: {"./$params.output_dir/$sid/Non-Linear_Registration_To_Template/"}]
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// **Transformation** //
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transfo="s"
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script_registration="antsRegistrationSyN.sh"
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linear_registration=false
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quick_registration=false
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// **Number of processes per tasks**//
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processes_register=4
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//**Process control**//
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processes = false
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}
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if(params.linear_registration)
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{
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params.transfo="a"
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params.registration=[path: {"./$params.output_dir/$sid/Linear_Registration_To_Template/"}]
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}
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if(params.quick_registration)
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{
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params.script_registration="antsRegistrationSyNQuick.sh"
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}
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if(params.processes) {
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if(params.processes > Runtime.runtime.availableProcessors()) {
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throw new RuntimeException("Number of processes higher than available CPUs.")
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}
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else if(params.processes < 1) {
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throw new RuntimeException("When set, number of processes must be >= 1 " +
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"and smaller or equal to the number of CPUs.")
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}
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else {
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executor.$local.cpus = params.processes
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}
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}
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singularity.autoMounts = true
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profiles {
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fully_reproducible {
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params.processes_register=1
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}
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macos {
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process.scratch="/tmp"
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}
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}

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