Merge pull request #71 from Manonedde/fix_mrtrix_betantsbet

#45 - MRtrix module - betcrop/betantsbet
scilus · Jan 15, 2025 · 5c2bc5c · 5c2bc5c
2 parents d36ec09 + b8949dd
commit 5c2bc5c
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Showing 5 changed files with 16 additions and 19 deletions.
diff --git a/modules/nf-neuro/betcrop/antsbet/main.nf b/modules/nf-neuro/betcrop/antsbet/main.nf
@@ -34,12 +34,12 @@ process BETCROP_ANTSBET {
         -e $template -m $tissues_probabilities ${args.join(' ')}
     scil_volume_math.py convert bet/BrainExtractionMask.nii.gz \
         ${prefix}__t1_bet_mask.nii.gz --data_type uint8
-    mrcalc $t1 ${prefix}__t1_bet_mask.nii.gz -mult ${prefix}__t1_bet.nii.gz -nthreads $task.cpus
+    scil_volume_math.py multiplication $t1 ${prefix}__t1_bet_mask.nii.gz \
+        ${prefix}__t1_bet.nii.gz --data_type float32
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
-        mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p')
         ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9]+\\+\\).*/\\1/')
     END_VERSIONS
     """
@@ -48,13 +48,13 @@ process BETCROP_ANTSBET {
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
+
     touch ${prefix}__t1_bet.nii.gz
     touch ${prefix}__t1_bet_mask.nii.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
-        mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p')
         ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9]+\\+\\).*/\\1/')
     END_VERSIONS
 
@@ -67,6 +67,6 @@ process BETCROP_ANTSBET {
 
     antsBrainExtraction.sh
     scil_volume_math.py -h
-    mrcalc -h
+
     """
 }
diff --git a/modules/nf-neuro/betcrop/antsbet/meta.yml b/modules/nf-neuro/betcrop/antsbet/meta.yml
@@ -10,9 +10,6 @@ tools:
   - "scilpy":
       description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
       homepage: "https://github.com/scilus/scilpy.git"
-  - "MRtrix3":
-      description: "Toolbox for image processing, analysis and visualisation of dMRI."
-      homepage: "https://mrtrix.readthedocs.io/en/latest/"
   - "ants":
       description: "Advanced Normalization Tools."
       homepage: "https://github.com/ANTsX/ANTs"

diff --git a/modules/nf-neuro/betcrop/antsbet/tests/main.nf.test b/modules/nf-neuro/betcrop/antsbet/tests/main.nf.test
@@ -70,7 +70,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    niftiMD5SUM(process.out.t1.get(0).get(1)),
+                    niftiMD5SUM(process.out.t1.get(0).get(1), 1),
                     niftiMD5SUM(process.out.mask.get(0).get(1)),
                     process.out.versions
                 ).match() }

diff --git a/modules/nf-neuro/betcrop/antsbet/tests/main.nf.test.snap b/modules/nf-neuro/betcrop/antsbet/tests/main.nf.test.snap
@@ -1,28 +1,28 @@
 {
     "betcrop - antsbet": {
         "content": [
-            "test__t1_bet.nii.gz:md5:header,72167012fa8893d3c3531d5d1245b84a,data,e31b24e1dadf5b067211544fca1f3f01",
+            "test__t1_bet.nii.gz:md5:header,e7cfbd06624321d70cbd667a77315ba3,data,381da559c1f38a2526f58b741eb0f7fc",
             "test__t1_bet_mask.nii.gz:md5:header,f7389fe98c9a7e3a87c90b7ca05ea14a,data,1572808125554e50ff73fbe0e28037a9",
             [
-                "versions.yml:md5,9fde1445bc10857db69e440781e58cb7"
+                "versions.yml:md5,bb378e913d4002d0b644d3277892ae20"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-17T20:31:09.4739"
+        "timestamp": "2025-01-15T16:55:54.33351491"
     },
     "betcrop - antsbet - stub-run": {
         "content": [
             [
-                "versions.yml:md5,9fde1445bc10857db69e440781e58cb7"
+                "versions.yml:md5,bb378e913d4002d0b644d3277892ae20"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-12T10:20:29.72452"
+        "timestamp": "2025-01-14T20:42:47.191136661"
     }
 }
diff --git a/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap b/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap
@@ -297,18 +297,18 @@
             "test_cropped.nii.gz",
             "test_t1_cropped.nii.gz",
             [
-                "versions.yml:md5,19aaa24cf046e49a4ad4ce5d507ea8aa",
                 "versions.yml:md5,37229cd5cee6f6788fbc9083d6618c61",
                 "versions.yml:md5,657fbb224f260392e573b8511c4b798d",
                 "versions.yml:md5,b979132991d8f72a3585465533bd5730",
                 "versions.yml:md5,bdd934b4b8456060c36d6d97e4f30740",
+                "versions.yml:md5,da278daafbe3afa8454021e2716dd205",
                 "versions.yml:md5,ea32c30f5320f720b2f5dc32ac2535ea"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-12-04T10:38:12.185789"
+        "timestamp": "2024-12-12T15:50:29.838128539"
     }
 }