[Improvement] add synthseg option to anatomical_segmentation

modules/nf-scil/segmentation/fastseg/main.nf

@@ -7,7 +7,7 @@ process SEGMENTATION_FASTSEG {
         'scilus/scilus:2.0.2' }"
 
     input:
-        tuple val(meta), path(image), path(lesion)
+        tuple val(meta), path(image), path(lesion) /* optional, input = [] */
 
     output:
         tuple val(meta), path("*mask_wm.nii.gz")                , emit: wm_mask

subworkflows/nf-scil/anatomical_segmentation/main.nf

@@ -1,6 +1,9 @@
 // ** Importing modules from nf-scil ** //
 include { SEGMENTATION_FASTSEG       } from '../../../modules/nf-scil/segmentation/fastseg/main'
 include { SEGMENTATION_FREESURFERSEG } from '../../../modules/nf-scil/segmentation/freesurferseg/main'
+include { SEGMENTATION_SYNTHSEG      } from '../../../modules/nf-scil/segmentation/synthseg/main'
+
+params.run_synthseg = params.run_synthseg ?: false
 
 workflow ANATOMICAL_SEGMENTATION {
 
@@ -15,6 +18,10 @@ workflow ANATOMICAL_SEGMENTATION {
 
         ch_versions = Channel.empty()
 
+        if ( ch_image && ch_freesurferseg ) {
+            error('Both input channels cannot be passed simultaneously')
+        }
+
         if ( ch_freesurferseg ) {
             // ** Freesurfer segmentation ** //
             SEGMENTATION_FREESURFERSEG ( ch_freesurferseg )
@@ -28,18 +35,35 @@ workflow ANATOMICAL_SEGMENTATION {
             gm_map = Channel.empty()
             csf_map = Channel.empty()
         }
+
         else {
-            // ** FSL fast segmentation ** //
-            SEGMENTATION_FASTSEG ( ch_image )
-            ch_versions = ch_versions.mix(SEGMENTATION_FASTSEG.out.versions.first())
+            if ( params.run_synthseg ) {
+                // ** Freesurfer synthseg segmentation ** //
+                SEGMENTATION_SYNTHSEG ( ch_image )
+                ch_versions = ch_versions.mix(SEGMENTATION_SYNTHSEG.out.versions.first())
 
-            // ** Setting outputs ** //
-            wm_mask = SEGMENTATION_FASTSEG.out.wm_mask
-            gm_mask = SEGMENTATION_FASTSEG.out.gm_mask
-            csf_mask = SEGMENTATION_FASTSEG.out.csf_mask
-            wm_map = SEGMENTATION_FASTSEG.out.wm_map
-            gm_map = SEGMENTATION_FASTSEG.out.gm_map
-            csf_map = SEGMENTATION_FASTSEG.out.csf_map
+                // ** Setting outputs ** //
+                wm_mask = SEGMENTATION_SYNTHSEG.out.wm_mask
+                gm_mask = SEGMENTATION_SYNTHSEG.out.gm_mask
+                csf_mask = SEGMENTATION_SYNTHSEG.out.csf_mask
+                wm_map = Channel.empty()
+                gm_map = Channel.empty()
+                csf_map = Channel.empty()
+            }
+
+            else {
+                // ** FSL fast segmentation ** //
+                SEGMENTATION_FASTSEG ( ch_image )
+                ch_versions = ch_versions.mix(SEGMENTATION_FASTSEG.out.versions.first())
+
+                // ** Setting outputs ** //
+                wm_mask = SEGMENTATION_FASTSEG.out.wm_mask
+                gm_mask = SEGMENTATION_FASTSEG.out.gm_mask
+                csf_mask = SEGMENTATION_FASTSEG.out.csf_mask
+                wm_map = SEGMENTATION_FASTSEG.out.wm_map
+                gm_map = SEGMENTATION_FASTSEG.out.gm_map
+                csf_map = SEGMENTATION_FASTSEG.out.csf_map
+            }
         }
 
     emit:

subworkflows/nf-scil/anatomical_segmentation/meta.yml

@@ -7,6 +7,8 @@ description: |
       and CSF masks/maps.
   2)  Channel with FreeSurfer's parcellations files will result in using Scilpy's tools to produce
       WM, GM, and CSF masks (probability maps are not produced with this option).
+  3)  Given the synthseg related parameter in entry, will use synthseg instead of FSL FAST, producing
+      WM, GM and CSF masks.
   Typical next steps after this subworkflow would be to combine the resulting masks/maps with fODF
   data to perform TRACKING.
 keywords:
@@ -17,6 +19,7 @@ keywords:
 components:
   - segmentation/fastseg
   - segmentation/freesurferseg
+  - segmentation/synthseg
 input:
   - ch_image:
       type: file
@@ -33,6 +36,12 @@ input:
         parcellations into masks.
         Structure: [ val(meta), path(aparc_aseg), path(wm_parc) ]
       pattern: "*.mgz"
+  - ch_lesion:
+      type: file
+      description: |
+        The optional input channel containing a Nifti lesion volume to correct the white matter with a lesion mask. The lesion mask must be a binary masks.
+        Structure: [ val(meta), path(image) ]
+      pattern: "*.{nii,nii.gz}"
 output:
   - wm_mask:
       type: file
@@ -59,21 +68,21 @@ output:
       type: file
       description: |
         Channel containing WM probability maps. Will be only outputted if FSL's fast segmentation
-        is used and not with FreeSurfer's parcellation files.
+        is used and not with Synthseg and FreeSurfer's parcellation files.
         Structure: [ val(meta), path(wm_maps) ]
       pattern: "*.{nii,nii.gz}"
   - gm_maps:
       type: file
       description: |
         Channel containing GM probability maps. Will be only outputted if FSL's fast segmentation
-        is used and not with FreeSurfer's parcellation files.
+        is used and not with Synthseg and FreeSurfer's parcellation files.
         Structure: [ val(meta), path(gm_maps) ]
       pattern: "*.{nii,nii.gz}"
   - csf_maps:
       type: file
       description: |
         Channel containing CSF probability maps. Will be only outputted if FSL's fast segmentation
-        is used and not with FreeSurfer's parcellation files.
+        is used and not with Synthseg and FreeSurfer's parcellation files.
         Structure: [ val(meta), path(csf_maps) ]
       pattern: "*.{nii,nii.gz}"
   - versions:

subworkflows/nf-scil/anatomical_segmentation/tests/main.nf.test

@@ -3,7 +3,6 @@ nextflow_workflow {
     name "Test Subworkflow ANATOMICAL_SEGMENTATION"
     script "../main.nf"
     workflow "ANATOMICAL_SEGMENTATION"
-    config "./nextflow.config"
 
     tag "subworkflows"
     tag "subworkflows_nfcore"
@@ -12,6 +11,7 @@ nextflow_workflow {
     tag "segmentation"
     tag "segmentation/fastseg"
     tag "segmentation/freesurferseg"
+    tag "segmentation/synthseg"
 
     tag "load_test_data"
 
@@ -28,16 +28,16 @@ nextflow_workflow {
         }
 
     test("anatomical_segmentation - fslfast") {
-
+        config "./nextflow.config"
         when {
             workflow {
                 """
                 ch_split_test_data = LOAD_DATA.out.test_data_directory
                     .branch{
-                        t1w: it.simpleName == "T1w"
+                        T1w: it.simpleName == "T1w"
                         freesurfer: it.simpleName == "freesurfer_nifti"
                     }
-                input[0] = ch_split_test_data.t1w.map{
+                input[0] = ch_split_test_data.T1w.map{
                     test_data_directory -> [
                         [ id:'test' ],
                         file("\${test_data_directory}/T1w.nii.gz", checkIfExists: true),
@@ -51,19 +51,27 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success},
-                { assert snapshot(workflow.out).match()}
+                { assert snapshot(
+                    niftiMD5SUM(workflow.out.wm_mask.get(0).get(1)),
+                    niftiMD5SUM(workflow.out.gm_mask.get(0).get(1)),
+                    niftiMD5SUM(workflow.out.csf_mask.get(0).get(1)),
+                    niftiMD5SUM(workflow.out.wm_map.get(0).get(1)),
+                    niftiMD5SUM(workflow.out.gm_map.get(0).get(1)),
+                    niftiMD5SUM(workflow.out.csf_map.get(0).get(1)),
+                    workflow.out.versions
+                ).match()}
             )
         }
     }
 
     test("anatomical_segmentation - freesurferseg") {
-
+        config "./nextflow.config"
         when {
             workflow {
                 """
                 ch_split_test_data = LOAD_DATA.out.test_data_directory
                     .branch{
-                        t1w: it.simpleName == "T1w"
+                        T1w: it.simpleName == "T1w"
                         freesurfer: it.simpleName == "freesurfer_nifti"
                     }
                 input[0] = []
@@ -81,7 +89,46 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(workflow.out).match() }
+                { assert snapshot(
+                    niftiMD5SUM(workflow.out.wm_mask.get(0).get(1)),
+                    niftiMD5SUM(workflow.out.gm_mask.get(0).get(1)),
+                    niftiMD5SUM(workflow.out.csf_mask.get(0).get(1)),
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("anatomical_segmentation - synthseg") {
+        config "./nextflow_synthseg.config"
+        when {
+            workflow {
+                """
+                ch_split_test_data = LOAD_DATA.out.test_data_directory
+                    .branch{
+                        T1w: it.simpleName == "T1w"
+                        freesurfer: it.simpleName == "freesurfer_nifti"
+                    }
+                input[0] = ch_split_test_data.T1w.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ], // meta map
+                        file("\${test_data_directory}/anat/anat_image.nii.gz", checkIfExists: true),
+                        []
+                    ]}
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    niftiMD5SUM(workflow.out.wm_mask.get(0).get(1)),
+                    niftiMD5SUM(workflow.out.gm_mask.get(0).get(1)),
+                    niftiMD5SUM(workflow.out.csf_mask.get(0).get(1)),
+                    workflow.out.versions
+                ).match()}
             )
         }
     }

subworkflows/nf-scil/anatomical_segmentation/tests/nextflow_synthseg.config

@@ -0,0 +1,9 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
+
+params {
+    run_synthseg = true
+}