[ENH][WIP] Fix registration + use mask apply in tractoflow

modules/nf-neuro/image/applymask/main.nf

@@ -16,12 +16,14 @@ process IMAGE_APPLYMASK {
 
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def suffix = task.ext.first_suffix ? task.ext.first_suffix + "_masked"  : "masked"
     def nthreads_mrtrix = task.ext.single_thread ? "-nthreads 0" : "-nthreads ${task.cpus}"
+    def data_type = task.ext.data_type ? "-datatype ${task.ext.data_type}" : " -datatype float32"
 
     """
     export OMP_NUM_THREADS=${task.ext.single_thread ? 1 : task.cpus}
 
-    mrcalc $image $mask -mult ${prefix}_masked.nii.gz -force -quiet ${nthreads_mrtrix}
+    mrcalc $image $mask -mult ${prefix}_${suffix}.nii.gz -force -quiet ${nthreads_mrtrix} ${data_type}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -31,9 +33,9 @@ process IMAGE_APPLYMASK {
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
-
+    def suffix = task.ext.first_suffix ? task.ext.first_suffix + "_masked"  : "masked"
     """
-    touch ${prefix}_masked.nii.gz
+    touch ${prefix}_${suffix}.nii.gz
 
     mrcalc -h
 

modules/nf-neuro/image/applymask/meta.yml

@@ -32,10 +32,20 @@ input:
         ontologies:
           - edam: http://edamontology.org/format_3989 # GZIP format
 args:
+  - first_suffix:
+      type: string
+      description: Suffix for the output image file. This will be used as the first part of the suffix, followed by "_masked".
+      default: ""
   - single_thread:
       type: boolean
       description: If true, the command will be run in single-threaded mode. By default, the command will use multiple threads based on the number of CPUs allocated to the task.
       default: false
+  - data_type:
+      type: string
+      description: |
+        Data type for the output image. Use the following format:
+        uint8, int16, int32, int64, float16, float32 or float64.
+      default: "float32"
 output:
   image:
     - - meta:

modules/nf-neuro/registration/anattodwi/main.nf

@@ -5,7 +5,7 @@ process REGISTRATION_ANATTODWI {
     container "scilus/scilus:2.2.2"
 
     input:
-        tuple val(meta), path(fixed_reference), path(moving_anat), path(metric)
+        tuple val(meta), path(fixed_reference), path(moving_anat), path(metric), path(fixed_mask), path(moving_mask)
 
     output:
         tuple val(meta), path("*_warped.nii.gz")                            , emit: anat_warped
@@ -26,7 +26,9 @@ process REGISTRATION_ANATTODWI {
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
     def run_qc = task.ext.run_qc as Boolean || false
+    def args = task.ext.args ?: ''
 
+    if ( task.ext.masking_strategy == "both" || task.ext.masking_strategy == "internal" ) args += " -x $fixed_mask?:NULL,$moving_mask?:NULL"
     """
     export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=${task.ext.single_thread ? 1 : task.cpus}
     export OMP_NUM_THREADS=${task.ext.single_thread ? 1 : task.cpus}
@@ -49,7 +51,8 @@ process REGISTRATION_ANATTODWI {
         --metric MI[$fixed_reference,$moving_anat,1,32]\
         --metric CC[$metric,$moving_anat,1,4]\
         --convergence [50x25x10,1e-6,10] --shrink-factors 4x2x1\
-        --smoothing-sigmas 3x2x1
+        --smoothing-sigmas 3x2x1\
+        $args
 
     moving_base=\$(basename "${moving_anat}")
     ext=\${moving_base#*.}

modules/nf-neuro/registration/anattodwi/meta.yml

@@ -43,6 +43,10 @@ args:
       type: integer
       description: Random seed for ANTs registration. Setting a fixed seed can help with reproducibility of results.
       default: 1234
+  - masking_strategy:
+      type: string
+      description: Masking strategy to use for registration. Options are 'none', 'apriori', 'both'.
+      default: "none"
 input:
   - - meta:
         type: map
@@ -70,6 +74,20 @@ input:
         mandatory: true
         ontologies:
           - edam: http://edamontology.org/format_4001 # NIFTI format
+    - fixed_mask:
+        type: file
+        description: Fixed image mask
+        pattern: "*.{nii,nii.gz}"
+        mandatory: false
+        ontologies:
+          - edam: http://edamontology.org/format_4001 # NIFTI format
+    - moving_mask:
+        type: file
+        description: Moving image mask
+        pattern: "*.{nii,nii.gz}"
+        mandatory: false
+        ontologies:
+          - edam: http://edamontology.org/format_4001 # NIFTI format
 output:
   anat_warped:
     - - meta:

modules/nf-neuro/registration/anattodwi/tests/main.nf.test

@@ -56,6 +56,59 @@ nextflow_process {
                 input[0] = ch_b0
                     .join(ch_t1w)
                     .join(ch_fa)
+                    .map{ meta, fixed, moving, fixed_metric -> [meta, fixed, moving, fixed_metric, [], []] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("registration - anattodwi - fixed mask") {
+        config "./nextflow.config"
+        when {
+            process {
+                """
+                ch_split_test_data = LOAD_DATA.out.test_data_directory
+                    .branch{
+                        t1w: it.simpleName == "T1w"
+                        b0: it.simpleName == "b0"
+                        dti: it.simpleName == "dti"
+                    }
+                ch_t1w = ch_split_test_data.t1w.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        file("\${test_data_directory}/T1w.nii.gz")
+                    ]
+                }
+                ch_b0 = ch_split_test_data.b0.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        file("\${test_data_directory}/b0.nii.gz")
+                    ]
+                }
+                ch_fa = ch_split_test_data.dti.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        file("\${test_data_directory}/fa.nii.gz")
+                    ]
+                }
+                ch_fixed_mask = ch_split_test_data.t1w.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        file("\${test_data_directory}/T1w_mask.nii.gz")
+                    ]
+                }
+                input[0] = ch_b0
+                    .join(ch_t1w)
+                    .join(ch_fa)
+                    .join(ch_fixed_mask)
+                    .map{ meta, fixed, moving, fixed_metric, fixed_mask -> [meta, fixed, moving, fixed_metric, fixed_mask, []] }
                 """
             }
         }
@@ -101,6 +154,7 @@ nextflow_process {
                 input[0] = ch_b0
                     .join(ch_t1w)
                     .join(ch_fa)
+                    .map{ meta, fixed, moving, fixed_metric -> [meta, fixed, moving, fixed_metric, [], []] }
                 """
             }
         }