Merge pull request #7 from anroy1/synthregistration

[New module] Freesurfer synthregistration

.github/workflows/run_checks_suite.yml

@@ -139,6 +139,8 @@ jobs:
             path: modules/nf-neuro/registration/easyreg
           - runner: scilus-nf-neuro-bigmem-runners
             path: modules/nf-neuro/segmentation/synthseg
+          - runner: scilus-nf-neuro-bigmem-runners
+            path: modules/nf-neuro/registration/synthregistration
         exclude:
           - path: subworkflows/nf-neuro/load_test_data
     uses: ./.github/workflows/test_component.yml

modules/nf-neuro/registration/synthregistration/environment.yml

@@ -0,0 +1,3 @@
+channels: []
+dependencies: []
+name: registration_synthregistration

modules/nf-neuro/registration/synthregistration/main.nf

@@ -0,0 +1,63 @@
+process REGISTRATION_SYNTHREGISTRATION {
+    tag "$meta.id"
+    label 'process_single'
+
+    container "freesurfer/synthmorph:3"
+    containerOptions "--entrypoint ''"
+
+    input:
+    tuple val(meta), path(moving), path(fixed)
+
+    output:
+    tuple val(meta), path("*__output_warped.nii.gz"), emit: warped_image
+    tuple val(meta), path("*__affine_warp.lta"), emit: affine_transform
+    tuple val(meta), path("*__deform_warp.nii.gz"), emit: deform_transform
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def affine = task.ext.affine ? "-m " + task.ext.affine : "-m affine"
+    def warp = task.ext.warp ? "-m " + task.ext.warp : "-m deform"
+    def header = task.ext.header ? "-H" : ""
+    def gpu = task.ext.gpu ? "-g" : ""
+    def lambda = task.ext.lambda ? "-r " + task.ext.lambda : ""
+    def steps = task.ext.steps ? "-n " + task.ext.steps : ""
+    def extent = task.ext.extent ? "-e " + task.ext.extent : ""
+    def weight = task.ext.weight ? "-w " + task.ext.weight : ""
+
+    """
+    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
+    export OMP_NUM_THREADS=1
+    export OPENBLAS_NUM_THREADS=1
+
+    mri_synthmorph -j $task.cpus ${affine} -t ${prefix}__affine_warp.lta $moving $fixed
+    mri_synthmorph -j $task.cpus ${warp} ${gpu} ${lambda} ${steps} ${extent} ${weight} -i ${prefix}__affine_warp.lta  -t ${prefix}__deform_warp.nii.gz -o ${prefix}__output_warped.nii.gz $moving $fixed
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        Freesurfer: 7.4
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    mri_synthmorph -h
+
+    touch ${prefix}__output_warped.nii.gz
+    touch ${prefix}__affine_warp.lta
+    touch ${prefix}__deform_warp.nii.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        Freesurfer: 7.4
+    END_VERSIONS
+    """
+}

modules/nf-neuro/registration/synthregistration/meta.yml

@@ -0,0 +1,61 @@
+---
+name: "registration_synthregistration"
+description: Perform registration using SynthMorph from Freesurfer. Outputs transforms in Freesurfer format .lta for affine and .nii.gz (synthmorph also supports .mgz) for deform, both in RAS orientation. Conversion to other formats is done using lta_convert and mri_warp_convert respectively, which support a wide range of conversion formats and orientations, such as ANTs ans FSL. To convert the output of this module, use the registration/convert module successively to it. Note that tests using synthmorph are non-reproductible.
+keywords:
+  - Registration
+  - Brain imaging
+  - MRI
+  - Synthetic
+  - AI
+  - CNN
+tools:
+  - "Freesurfer":
+      description: "Freesurfer Synthmorph"
+      homepage: "https://martinos.org/malte/synthmorph/"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - moving:
+      type: file
+      description: Nifti volume moving for registration
+      pattern: "*.{nii,nii.gz}"
+
+  - fixed:
+      type: file
+      description: Nifti volume fixed for registration
+      pattern: "*.{nii,nii.gz}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - affine_transform:
+      type: file
+      description: Affine transform for initialization
+      pattern: "*.{lta}"
+
+  - deform_transform:
+      type: file
+      description: Deform transformation
+      pattern: "*.{nii.gz}"
+
+  - warped_image:
+      type: file
+      description: Warped image
+      pattern: "*.{nii,.nii.gz}"
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@anroy1"

modules/nf-neuro/registration/synthregistration/tests/main.nf.test

@@ -0,0 +1,56 @@
+nextflow_process {
+
+    name "Test Process REGISTRATION_SYNTHREGISTRATION"
+    script "../main.nf"
+    process "REGISTRATION_SYNTHREGISTRATION"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "registration"
+    tag "registration/synthregistration"
+
+    tag "subworkflows"
+    tag "subworkflows/load_test_data"
+
+    // ** Assertion only uses file name since there is a discrepancy when tests are ran remotly. ** //
+    // ** Synthmorph is an AI model and freesurfer does not control for randomness in computation yet, both in terms of seeding and operation ordering.** //
+
+    setup {
+            run("LOAD_TEST_DATA", alias: "LOAD_DATA") {
+                script "../../../../../subworkflows/nf-neuro/load_test_data/main.nf"
+                process {
+                    """
+                    input[0] = Channel.from( [ "processing.zip" ] )
+                    input[1] = "test.load-test-data"
+                    """
+                }
+            }
+        }
+
+    test("registration - synthregistration") {
+        config "./nextflow.config"
+        when {
+            process {
+                """
+                input[0] = LOAD_DATA.out.test_data_directory
+                    .map{ test_data_directory -> [
+                    [ id:'test', single_end:false ],
+                    file("\${test_data_directory}/mni_masked_2x2x2.nii.gz"),
+                    file("\${test_data_directory}/b0_mean.nii.gz")
+                ]}
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.warped_image.get(0).get(1)).name,
+                    file(process.out.affine_transform.get(0).get(1)).name,
+                    file(process.out.deform_transform.get(0).get(1)).name,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+}

modules/nf-neuro/registration/synthregistration/tests/main.nf.test.snap

@@ -0,0 +1,17 @@
+{
+    "registration - synthregistration": {
+        "content": [
+            "test__output_warped.nii.gz",
+            "test__affine_warp.lta",
+            "test__deform_warp.nii.gz",
+            [
+                "versions.yml:md5,49fb9c85da9f696926d1ab46ef0968fb"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-01T22:36:18.972035"
+    }
+}

modules/nf-neuro/registration/synthregistration/tests/nextflow.config

@@ -0,0 +1,10 @@
+process {
+    memory = "20G"
+    withName: "REGISTRATION_SYNTHREGISTRATION" {
+        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+        ext.affine = "affine"
+        ext.warp = "deform"
+        ext.lambda = 0.9
+        ext.steps = 9
+    }
+}

modules/nf-neuro/registration/synthregistration/tests/tags.yml

@@ -0,0 +1,2 @@
+registration/synthregistration:
+  - "modules/nf-neuro/registration/synthregistration/**"