Merge pull request #6 from anroy1/synthseg2

[New module] Module Synthseg

.github/workflows/run_checks_suite.yml

@@ -137,6 +137,8 @@ jobs:
           - runner: scilus-nf-neuro-runners
           - runner: scilus-nf-neuro-bigmem-runners
             path: modules/nf-neuro/registration/easyreg
+          - runner: scilus-nf-neuro-bigmem-runners
+            path: modules/nf-neuro/segmentation/synthseg
         exclude:
           - path: subworkflows/nf-neuro/load_test_data
     uses: ./.github/workflows/test_component.yml

modules/nf-neuro/segmentation/synthseg/environment.yml

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

modules/nf-neuro/segmentation/synthseg/main.nf

@@ -0,0 +1,113 @@
+process SEGMENTATION_SYNTHSEG {
+    tag "$meta.id"
+    label 'process_single'
+    label 'process_high'
+
+    container "freesurfer/freesurfer:7.4.1"
+
+    input:
+    tuple val(meta), path(image), path(lesion) /* optional, input = [] */, path(fs_license) /* optional, input = [] */
+
+    output:
+    tuple val(meta), path("*__seg.nii.gz")                    , emit: seg
+    tuple val(meta), path("*__mask_wm.nii.gz")                , emit: wm_mask
+    tuple val(meta), path("*__mask_gm.nii.gz")                , emit: gm_mask
+    tuple val(meta), path("*__mask_csf.nii.gz")               , emit: csf_mask
+    tuple val(meta), path("*__gm_parc.nii.gz")                , emit: gm_parc, optional: true
+    tuple val(meta), path("*__resampled_image.nii.gz")        , emit: resample, optional: true
+    tuple val(meta), path("*__volume.csv")                    , emit: volume, optional: true
+    tuple val(meta), path("*__qc_score.csv")                  , emit: qc_score, optional: true
+    path "versions.yml"                                       , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def gpu = task.ext.gpu ? "" : "--cpu"
+    def gm_parc = task.ext.gm_parc ? "--parc" : ""
+    def robust = task.ext.robust ? "--robust" : ""
+    def fast = task.ext.fast ? "--fast" : ""
+    def ct = task.ext.ct ? "--ct" : ""
+    def output_resample = task.ext.output_resample ? "--resample ${prefix}__resampled_image.nii.gz": ""
+    def output_volume = task.ext.output_volume ?  "--vol ${prefix}__volume.csv" : ""
+    def output_qc_score = task.ext.output_qc_score ?  "--qc ${prefix}__qc_score.csv" : ""
+    def crop = task.ext.crop ? "--crop " + task.ext.crop: ""
+
+    """
+    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
+    export OMP_NUM_THREADS=1
+    export OPENBLAS_NUM_THREADS=1
+
+    cp $fs_license \$FREESURFER_HOME/license.txt
+
+    mri_synthseg --i $image --o seg.nii.gz --threads $task.cpus $gpu $robust $fast $ct $output_resample $output_volume $output_qc_score $crop
+
+    cp seg.nii.gz ${prefix}__seg.nii.gz
+
+    if [[ -n "$gm_parc" ]];
+    then
+        # Cortical grey matter parcellation
+        mri_synthseg --i $image --o ${prefix}__gm_parc.nii.gz --threads $task.cpus $gpu $gm_parc $robust $fast $crop
+        mri_convert -i ${prefix}__gm_parc.nii.gz --out_data_type uchar -o ${prefix}__gm_parc.nii.gz
+    fi
+
+    # WM Mask
+    mri_binarize --i seg.nii.gz \
+        --match 2 7 10 12 13 16 28 41 46 49 51 52 60 \
+        --o ${prefix}__mask_wm.nii.gz
+
+    # GM Mask
+    mri_binarize --i seg.nii.gz \
+        --match 3 8 11 17 18 26 42 47 50 52 53 54 58 \
+        --o ${prefix}__mask_gm.nii.gz
+
+    # CSF Mask
+    mri_binarize --i seg.nii.gz \
+        --match 4 5 14 15 24 43 44 \
+        --o ${prefix}__mask_csf.nii.gz
+
+    if [[ -f "$lesion" ]];
+    then
+        mri_binarize --i ${prefix}__mask_wm.nii.gz --merge $lesion --min 0.5 --o ${prefix}__mask_wm.nii.gz
+    fi
+
+    mri_convert -i ${prefix}__mask_wm.nii.gz --out_data_type uchar -o ${prefix}__mask_wm.nii.gz
+    mri_convert -i ${prefix}__mask_gm.nii.gz --out_data_type uchar -o ${prefix}__mask_gm.nii.gz
+    mri_convert -i ${prefix}__mask_csf.nii.gz --out_data_type uchar -o ${prefix}__mask_csf.nii.gz
+
+    rm \$FREESURFER_HOME/license.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        Freesurfer: 7.4.1
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    mri_synthseg -h
+    mri_binarize -h
+    mri_convert -h
+
+    touch ${prefix}__seg.nii.gz
+    touch ${prefix}__mask_wm.nii.gz
+    touch ${prefix}__mask_gm.nii.gz
+    touch ${prefix}__mask_csf.nii.gz
+    touch ${prefix}__gm_parc.nii.gz
+    touch ${prefix}__resampled_image.nii.gz
+    touch ${prefix}__volume.csv
+    touch ${prefix}__qc_score.csv
+
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        Freesurfer: 7.4.1
+    END_VERSIONS
+    """
+}

modules/nf-neuro/segmentation/synthseg/meta.yml

@@ -0,0 +1,87 @@
+name: "segmentation_synthseg"
+description: Perform Brain Tissues Segmentation using Freesurfer synthseg on a T1 image. Optionally, a binary mask of lesion can be add to correct the white matter mask. Note that tests using synthseg are non-reproductible.
+keywords:
+  - Segmentation
+  - Freesurfer
+  - Tissues
+  - Synthetic
+  - AI
+  - CNN
+tools:
+  - "Freesurfer":
+      description: "An open source neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images."
+      homepage: "https://surfer.nmr.mgh.harvard.edu/"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - image:
+      type: file
+      description: Nifti T1 volume to segment into tissue maps.
+      pattern: "*.{nii,nii.gz}"
+
+  - lesion:
+      type: file
+      description: Nifti lesion volume to correct the white matter with a lesion mask. The lesion mask must be a binary mask.
+      pattern: "*.{nii,nii.gz}"
+
+  - fs_license:
+      type: file
+      description: The path to your FreeSurfer license. To get one, go to https://surfer.nmr.mgh.harvard.edu/registration.html. Optional. If you have already set your license as prescribed by Freesurfer (copied to a .license file in your $FREESURFER_HOME), this is not required.
+      pattern: "*.txt"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - wm_mask:
+      type: file
+      description: Nifti WM mask volume.
+      pattern: "*.{nii,nii.gz}"
+
+  - gm_mask:
+      type: file
+      description: Nifti GM mask volume.
+      pattern: "*.{nii,nii.gz}"
+
+  - csf_mask:
+      type: file
+      description: Nifti CSF mask volume.
+      pattern: "*.{nii,nii.gz}"
+
+  - gm_parc:
+      type: file
+      description: (optional) Nifti cortical parcellation volume.
+      pattern: "*.{nii,nii.gz}"
+
+  - volume:
+      type: file
+      description: (optional) Output CSV file with volumes for all structures and subjects.
+      pattern: "*.csv"
+
+  - qc_score:
+      type: file
+      description: (optional) Output CSV file with qc scores for all subjects.
+      pattern: "*.csv"
+
+  - resample:
+      type: file
+      description: (optional) in order to return segmentations at 1mm resolution, the input images are internally resampled (except if they already are at 1mm). Use this optional flag to save the resampled images. This must be the same type as --i.
+      pattern: "*.{nii,nii.gz}"
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@anroy1"
+maintainers:
+  - "@anroy1"

modules/nf-neuro/segmentation/synthseg/tests/main.nf.test

@@ -0,0 +1,160 @@
+nextflow_process {
+
+    name "Test Process SEGMENTATION_SYNTHSEG"
+    script "../main.nf"
+    process "SEGMENTATION_SYNTHSEG"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "segmentation"
+    tag "segmentation/synthseg"
+
+    tag "subworkflows"
+    tag "subworkflows/load_test_data"
+
+    setup {
+        run("LOAD_TEST_DATA", alias: "LOAD_DATA") {
+            script "../../../../../subworkflows/nf-neuro/load_test_data/main.nf"
+            process {
+                """
+                input[0] = Channel.from( [ "heavy.zip", "freesurfer.zip", "processing.zip" ] )
+                input[1] = "test.load-test-data"
+                """
+            }
+        }
+    }
+
+// ** Assertion only uses file name since there is a discrepancy when tests are ran remotly. ** //
+// ** Synthseg's direct output was emitted as an output to help assess its non-reproductibility ** //
+// ** Synthseg is an AI model and freesurfer does not control for randomness in computation yet, both in terms of seeding and operation ordering.** //
+
+    test("segmentation - synthseg - basic") {
+        config "./nextflow_basic.config"
+        when {
+            process {
+                """
+                ch_split_test_data = LOAD_DATA.out.test_data_directory
+                    .branch{
+                        heavy: it.simpleName == "heavy"
+                        freesurfer: it.simpleName == "freesurfer"
+                    }
+                ch_anat = ch_split_test_data.heavy.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/anat/anat_image.nii.gz"),
+                        []
+                    ]
+                }
+                ch_license = ch_split_test_data.freesurfer.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/license.txt")
+                    ]
+                }
+                input[0] = ch_anat
+                    .join(ch_license)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.wm_mask.get(0).get(1)).name,
+                    file(process.out.gm_mask.get(0).get(1)).name,
+                    file(process.out.csf_mask.get(0).get(1)).name,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("segmentation - synthseg - options") {
+        config "./nextflow_options.config"
+        when {
+            process {
+                """
+                ch_split_test_data = LOAD_DATA.out.test_data_directory
+                    .branch{
+                        processing: it.simpleName == "processing"
+                        freesurfer: it.simpleName == "freesurfer"
+                    }
+                ch_anat = ch_split_test_data.processing.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/mni_masked_2x2x2.nii.gz"),
+                        []
+                    ]
+                }
+                ch_license = ch_split_test_data.freesurfer.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/license.txt")
+                    ]
+                }
+                input[0] = ch_anat
+                    .join(ch_license)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.wm_mask.get(0).get(1)).name,
+                    file(process.out.gm_mask.get(0).get(1)).name,
+                    file(process.out.csf_mask.get(0).get(1)).name,
+                    file(process.out.gm_parc.get(0).get(1)).name,
+                    niftiMD5SUM(process.out.resample.get(0).get(1)),
+                    process.out.volume,
+                    process.out.qc_score,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("segmentation - synthseg - lesion") {
+        config "./nextflow_basic.config"
+        when {
+            process {
+                """
+                ch_split_test_data = LOAD_DATA.out.test_data_directory
+                    .branch{
+                        heavy: it.simpleName == "heavy"
+                        freesurfer: it.simpleName == "freesurfer"
+                    }
+                ch_anat = ch_split_test_data.heavy.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/anat/anat_image.nii.gz"),
+                        file("\${test_data_directory}/anat/anat_mask.nii.gz")
+                    ]
+                }
+                ch_license = ch_split_test_data.freesurfer.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/license.txt")
+                    ]
+                }
+                input[0] = ch_anat
+                    .join(ch_license)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.wm_mask.get(0).get(1)).name,
+                    file(process.out.gm_mask.get(0).get(1)).name,
+                    file(process.out.csf_mask.get(0).get(1)).name,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+}