Add parcellation optional output and adjust tests

scilus · Sep 20, 2024 · 40c4957 · 40c4957
1 parent 6f66c08
commit 40c4957
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Showing 6 changed files with 39 additions and 20 deletions.
diff --git a/modules/nf-scil/segmentation/synthseg/main.nf b/modules/nf-scil/segmentation/synthseg/main.nf
@@ -12,6 +12,7 @@ process SEGMENTATION_SYNTHSEG {
     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("*__parc.nii.gz")                   , emit: parc, optional: true
     tuple val(meta), path("*__resampled_image.nii.gz")        , emit: resample, optional: true
     tuple val(meta), path("*__vol.csv")                       , emit: vol, optional: true
     tuple val(meta), path("*__qc.csv")                        , emit: qc, optional: true
@@ -41,20 +42,27 @@ process SEGMENTATION_SYNTHSEG {
 
     cp $fs_license \$FREESURFER_HOME/license.txt
 
-    mri_synthseg --i $image --threads $task.cpus --o t1.nii.gz $gpu $parc $robust $fast $ct $output_resample $output_vol $output_qc $crop
+    mri_synthseg --i $image --o seg.nii.gz --threads $task.cpus $gpu $robust $fast $ct $output_resample $output_vol $output_qc $crop
+
+    if [[ $task.parc ]];
+    then
+        # Cortical parcellation
+        mri_synthseg --i $image --o ${prefix}__parc.nii.gz --threads $task.cpus $gpu $parc $robust $fast $crop
+        mri_convert -i ${prefix}__parc.nii.gz --out_data_type uchar -o ${prefix}__parc.nii.gz
+    fi
 
     # WM Mask
-    mri_binarize --i t1.nii.gz \
+    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 t1.nii.gz \
+    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 t1.nii.gz \
+    mri_binarize --i seg.nii.gz \
                 --match 4 5 14 15 24 43 44 \
                 --o ${prefix}__mask_csf.nii.gz
 
@@ -66,6 +74,7 @@ process SEGMENTATION_SYNTHSEG {
     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
+    mri_convert -i ${prefix}__parc.nii.gz --out_data_type uchar ${prefix}__parc.nii.gz
 
     rm \$FREESURFER_HOME/license.txt
 
@@ -87,6 +96,7 @@ process SEGMENTATION_SYNTHSEG {
     touch ${prefix}__mask_wm.nii.gz
     touch ${prefix}__mask_gm.nii.gz
     touch ${prefix}__mask_csf.nii.gz
+    touch ${prefix}__parc.nii.gz
     touch ${prefix}__resampled_image.nii.gz
     touch ${prefix}__vol.csv
     touch ${prefix}__qc.csv

diff --git a/modules/nf-scil/segmentation/synthseg/meta.yml b/modules/nf-scil/segmentation/synthseg/meta.yml
@@ -53,6 +53,11 @@ output:
       description: Nifti CSF mask volume.
       pattern: "*.{nii,nii.gz}"
 
+  - parc:
+      type: file
+      description: Nifti cortical parcellation volume.
+      pattern: "*.{nii,nii.gz}"
+
   - vol:
       type: file
       description: (optional) Output CSV file with volumes for all structures and subjects.

diff --git a/modules/nf-scil/segmentation/synthseg/tests/main.nf.test b/modules/nf-scil/segmentation/synthseg/tests/main.nf.test
@@ -102,6 +102,7 @@ nextflow_process {
                     niftiMD5SUM(process.out.wm_mask.get(0).get(1)),
                     niftiMD5SUM(process.out.gm_mask.get(0).get(1)),
                     niftiMD5SUM(process.out.csf_mask.get(0).get(1)),
+                    niftiMD5SUM(process.out.parc.get(0).get(1)),
                     process.out.resample,
                     process.out.vol,
                     process.out.qc,

diff --git a/modules/nf-scil/segmentation/synthseg/tests/main.nf.test.snap b/modules/nf-scil/segmentation/synthseg/tests/main.nf.test.snap
@@ -1,9 +1,10 @@
 {
     "segmentation - synthseg - options": {
         "content": [
-            "test__mask_wm.nii.gz:md5:header,a0430ca63ccc3bb2b925694cb7568388,data,a7ad690eb017c4146332b0bdeb135aa8",
-            "test__mask_gm.nii.gz:md5:header,a0430ca63ccc3bb2b925694cb7568388,data,370281fcda8be302cd72060e761121d2",
-            "test__mask_csf.nii.gz:md5:header,a0430ca63ccc3bb2b925694cb7568388,data,3d227c46c2d58cf80284a6f48d13d792",
+            "test__mask_wm.nii.gz:md5:header,a0430ca63ccc3bb2b925694cb7568388,data,95946cf22f6adf539b65c72b49eb3b32",
+            "test__mask_gm.nii.gz:md5:header,a0430ca63ccc3bb2b925694cb7568388,data,a54f8c03a17a16d9271534c387434720",
+            "test__mask_csf.nii.gz:md5:header,a0430ca63ccc3bb2b925694cb7568388,data,3895c471bc8b06446a8adbba9fe235f7",
+            "test__parc.nii.gz:md5:header,a0430ca63ccc3bb2b925694cb7568388,data,cb9a481316ae64dceb229879bd0c6619",
             [
 
             ],
@@ -12,15 +13,15 @@
                     {
                         "id": "test"
                     },
-                    "test__vol.csv:md5,d0a69e3e2fbd7184dfcdf8bc2c35d673"
+                    "test__vol.csv:md5,c5c29a038e4f43abcce1845bc429952c"
                 ]
             ],
             [
                 [
                     {
                         "id": "test"
                     },
-                    "test__qc.csv:md5,4627c87c018fe1e5f2b0803e78aff306"
+                    "test__qc.csv:md5,333de3d7b60916596f0460c808b598f5"
                 ]
             ],
             [
@@ -31,13 +32,13 @@
             "nf-test": "0.9.0-rc1",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-17T17:33:59.710663"
+        "timestamp": "2024-09-20T14:42:35.40267"
     },
     "segmentation - synthseg - basic": {
         "content": [
-            "test__mask_wm.nii.gz:md5:header,a0430ca63ccc3bb2b925694cb7568388,data,10191bbea81929574adf7cf9b9122a07",
-            "test__mask_gm.nii.gz:md5:header,a0430ca63ccc3bb2b925694cb7568388,data,eb6e177ec5ede4102fec41163d0c612a",
-            "test__mask_csf.nii.gz:md5:header,a0430ca63ccc3bb2b925694cb7568388,data,27060f0edda8db50469061177e085d76",
+            "test__mask_wm.nii.gz:md5:header,a0430ca63ccc3bb2b925694cb7568388,data,1b5a4d63ae2b56d9d6936313b5225b55",
+            "test__mask_gm.nii.gz:md5:header,a0430ca63ccc3bb2b925694cb7568388,data,c093a4b4c8c5804342b7ea8eea6164fb",
+            "test__mask_csf.nii.gz:md5:header,a0430ca63ccc3bb2b925694cb7568388,data,c9abaab9c5e047fadf928a6520929d5e",
             [
                 "versions.yml:md5,b65418e9ce2ab1cce590b1f659e18c1d"
             ]
@@ -46,13 +47,13 @@
             "nf-test": "0.9.0-rc1",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-17T17:33:11.109853"
+        "timestamp": "2024-09-20T14:40:33.985446"
     },
     "segmentation - synthseg - lesion": {
         "content": [
             "test__mask_wm.nii.gz:md5:header,a0430ca63ccc3bb2b925694cb7568388,data,6d99d71cff4a2f9d147c45b1ee36dce0",
-            "test__mask_gm.nii.gz:md5:header,a0430ca63ccc3bb2b925694cb7568388,data,eb6e177ec5ede4102fec41163d0c612a",
-            "test__mask_csf.nii.gz:md5:header,a0430ca63ccc3bb2b925694cb7568388,data,27060f0edda8db50469061177e085d76",
+            "test__mask_gm.nii.gz:md5:header,a0430ca63ccc3bb2b925694cb7568388,data,c093a4b4c8c5804342b7ea8eea6164fb",
+            "test__mask_csf.nii.gz:md5:header,a0430ca63ccc3bb2b925694cb7568388,data,c9abaab9c5e047fadf928a6520929d5e",
             [
                 "versions.yml:md5,b65418e9ce2ab1cce590b1f659e18c1d"
             ]
@@ -61,6 +62,6 @@
             "nf-test": "0.9.0-rc1",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-17T17:36:18.384824"
+        "timestamp": "2024-09-20T14:44:24.290916"
     }
 }
diff --git a/modules/nf-scil/segmentation/synthseg/tests/nextflow_basic.config b/modules/nf-scil/segmentation/synthseg/tests/nextflow_basic.config
@@ -1,4 +1,5 @@
 process {
-    memory = '14G'
+    memory = "8G"
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    ext.fast = true
 }
diff --git a/modules/nf-scil/segmentation/synthseg/tests/nextflow_options.config b/modules/nf-scil/segmentation/synthseg/tests/nextflow_options.config
@@ -1,9 +1,10 @@
 process {
+    memory = "8G"
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
     ext.robust = true
-    ext.fast = true
     ext.output_resample = true
     ext.output_vol = true
     ext.output_qc = true
-    ext.crop = 64
+    ext.crop = 150
+    ext.parc = true
 }