Fix Alex's comments

scilus · Sep 26, 2024 · cc7c8af · cc7c8af
1 parent 294f6cb
commit cc7c8af
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Showing 6 changed files with 24 additions and 26 deletions.
diff --git a/modules/nf-neuro/registration/synthregistration/environment.yml b/modules/nf-neuro/registration/synthregistration/environment.yml
@@ -1,7 +1,3 @@
----
-name: "registration_synthregistration"
-channels:
-  - Docker
-  - Apptainer
-dependencies:
-  - "Freesurfer:synthmorph"
+channels: []
+dependencies: []
+name: registration_synthregistration
diff --git a/modules/nf-neuro/registration/synthregistration/main.nf b/modules/nf-neuro/registration/synthregistration/main.nf
@@ -10,8 +10,8 @@ process REGISTRATION_SYNTHREGISTRATION {
 
     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
-    tuple val (meta), path("*__init_warp.lta"), emit: init_transform
     path "versions.yml"           , emit: versions
 
     when:
@@ -21,7 +21,7 @@ process REGISTRATION_SYNTHREGISTRATION {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
-    def init = task.ext.init ? "-m " + task.ext.init : "-m affine"
+    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" : ""
@@ -35,8 +35,8 @@ process REGISTRATION_SYNTHREGISTRATION {
     export OMP_NUM_THREADS=1
     export OPENBLAS_NUM_THREADS=1
 
-    mri_synthmorph -j $task.cpus ${init} -t ${prefix}__init_warp.lta $moving $fixed
-    mri_synthmorph -j $task.cpus ${warp} ${gpu} ${lambda} ${steps} ${extent} ${weight} -i ${prefix}__init_warp.lta  -t ${prefix}__deform_warp.nii.gz -o ${prefix}__output_warped.nii.gz $moving $fixed
+    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}":
@@ -52,8 +52,8 @@ process REGISTRATION_SYNTHREGISTRATION {
     mri_synthmorph -h
 
     touch ${prefix}__output_warped.nii.gz
+    touch ${prefix}__affine_warp.lta
     touch ${prefix}__deform_warp.nii.gz
-    touch ${prefix}__init_warp.lta
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-neuro/registration/synthregistration/meta.yml b/modules/nf-neuro/registration/synthregistration/meta.yml
@@ -1,10 +1,13 @@
 ---
 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, which can be converted for ANTs with respectively lta_convert and mri_warp_convert, which support a wide range of conversion formats and orientations. Conversion can be processed using the registration/convert module which can be used successively to this one.
+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.
 keywords:
-  - registration
+  - Registration
   - Brain imaging
   - MRI
+  - Synthetic
+  - AI
+  - CNN
 tools:
   - "Freesurfer":
       description: "Freesurfer Synthmorph"
@@ -34,7 +37,7 @@ output:
         Groovy Map containing sample information
         e.g. `[ id:'test', single_end:false ]`
 
-  - init_transform:
+  - affine_transform:
       type: file
       description: Affine transform for initialization
       pattern: "*.{lta}"

diff --git a/modules/nf-neuro/registration/synthregistration/tests/main.nf.test b/modules/nf-neuro/registration/synthregistration/tests/main.nf.test
@@ -17,7 +17,7 @@ nextflow_process {
                 script "../../../../../subworkflows/nf-neuro/load_test_data/main.nf"
                 process {
                     """
-                    input[0] = Channel.from( [ "freesurfer.zip" ] )
+                    input[0] = Channel.from( [ "processing.zip" ] )
                     input[1] = "test.load-test-data"
                     """
                 }
@@ -32,8 +32,8 @@ nextflow_process {
                 input[0] = LOAD_DATA.out.test_data_directory
                     .map{ test_data_directory -> [
                     [ id:'test', single_end:false ],
-                    file("\${test_data_directory}/t1.nii.gz"),
-                    file("\${test_data_directory}/fa.nii.gz")
+                    file("\${test_data_directory}/mni_masked_2x2x2.nii.gz"),
+                    file("\${test_data_directory}/b0_mean.nii.gz")
                 ]}
                 """
             }
@@ -43,8 +43,8 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     niftiMD5SUM(process.out.warped_image.get(0).get(1)),
+                    process.out.affine_transform,
                     niftiMD5SUM(process.out.deform_transform.get(0).get(1)),
-                    process.out.init_transform,
                     process.out.versions
                 ).match() }
             )

diff --git a/modules/nf-neuro/registration/synthregistration/tests/main.nf.test.snap b/modules/nf-neuro/registration/synthregistration/tests/main.nf.test.snap
@@ -1,17 +1,17 @@
 {
     "registration - synthregistration": {
         "content": [
-            "test__output_warped.nii.gz:md5:header,a1c8a7cfd88d5b632700819988507e8b,data,2526d950d4d6786c40faf5285e2f08af",
-            "test__deform_warp.nii.gz:md5:header,4a9989cf78e087331c587e0d656ee96f,data,3dcaa6acc0ee1a933d8792d9c2fc740d",
+            "test__output_warped.nii.gz:md5:header,616ccfd9e4dd6202483736565cca4946,data,81a995f1f9c8ff28b60206767528f078",
             [
                 [
                     {
                         "id": "test",
                         "single_end": false
                     },
-                    "test__init_warp.lta:md5,eb15bf7f338f1d5bd71227c40b6dbc68"
+                    "test__affine_warp.lta:md5,86e977bba905112ce22d18fe265321f4"
                 ]
             ],
+            "test__deform_warp.nii.gz:md5:header,513f2229597974a5b77a761d52d2c671,data,694f8b2b18234277cb8eebd60ab18c16",
             [
                 "versions.yml:md5,49fb9c85da9f696926d1ab46ef0968fb"
             ]
@@ -20,6 +20,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-24T17:03:44.420784"
+        "timestamp": "2024-09-25T01:17:49.969972"
     }
 }
diff --git a/modules/nf-neuro/registration/synthregistration/tests/nextflow.config b/modules/nf-neuro/registration/synthregistration/tests/nextflow.config
@@ -1,10 +1,9 @@
 process {
+    memory = "14G"
     withName: "REGISTRATION_SYNTHREGISTRATION" {
         publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-        memory = 20
-        ext.init = "affine"
+        ext.affine = "affine"
         ext.warp = "deform"
-        ext.threads = 1
         ext.lambda = 0.9
         ext.steps = 9
     }