[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/ants/main.nf

@@ -6,10 +6,10 @@ process REGISTRATION_ANTS {
     container "scilus/scilus:2.2.2"
 
     input:
-        tuple val(meta), path(fixed_image), path(moving_image), path(fixed_mask), path(moving_mask) //** optional, input = [] **//
+        tuple val(meta), path(fixed_image), path(moving_image)
 
     output:
-        tuple val(meta), path("*_warped.nii.gz")                            , emit: image_warped
+        tuple val(meta), path("*_warped.nii.gz")                           , emit: image_warped
         tuple val(meta), path("*_forward1_affine.mat")                     , emit: forward_affine, optional: true
         tuple val(meta), path("*_forward0_warp.nii.gz")                    , emit: forward_warp, optional: true
         tuple val(meta), path("*_backward1_warp.nii.gz")                   , emit: backward_warp, optional: true
@@ -18,8 +18,8 @@ process REGISTRATION_ANTS {
         tuple val(meta), path("*_backward*.{nii.gz,mat}", arity: '1..2')   , emit: backward_image_transform
         tuple val(meta), path("*_backward*.{nii.gz,mat}", arity: '1..2')   , emit: forward_tractogram_transform
         tuple val(meta), path("*_forward*.{nii.gz,mat}", arity: '1..2')    , emit: backward_tractogram_transform
-        tuple val(meta), path("*_registration_ants_mqc.gif")                , emit: mqc, optional: true
-        path "versions.yml"                                                 , emit: versions
+        tuple val(meta), path("*_registration_ants_mqc.gif")               , emit: mqc, optional: true
+        path "versions.yml"                                                , emit: versions
 
     when:
         task.ext.when == null || task.ext.when
@@ -36,10 +36,6 @@ process REGISTRATION_ANTS {
     def nthreads = task.ext.single_thread ? 1 : task.cpus
     args += " -n $nthreads"
 
-    if ( fixed_mask || moving_mask ) {
-        args += " -x \"${fixed_mask ?: 'NULL'},${moving_mask ?: 'NULL'}\""
-    }
-
     if ( task.ext.initial_transform ) args += " -i [$fixed_image,$moving_image,${initialization_types[task.ext.initial_transform]}]"
     if ( task.ext.histogram_bins ) args += " -r $task.ext.histogram_bins"
     if ( task.ext.spline_distance ) args += " -s $task.ext.spline_distance"

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

@@ -145,20 +145,6 @@ input:
         mandatory: true
         ontologies:
           - edam: http://edamontology.org/format_4001 # NIFTI format
-    - fixed_mask:
-        type: file
-        description: Mask(s) for the fixed image space
-        pattern: "*.{nii,nii.gz}"
-        mandatory: false
-        ontologies:
-          - edam: http://edamontology.org/format_4001 # NIFTI format
-    - moving_mask:
-        type: file
-        description: Mask(s) for the moving image space
-        pattern: "*.{nii,nii.gz}"
-        mandatory: false
-        ontologies:
-          - edam: http://edamontology.org/format_4001 # NIFTI format
 output:
   image_warped:
     - - meta:

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

@@ -46,16 +46,8 @@ nextflow_process {
                         file("\${test_data_directory}/t1.nii.gz")
                     ]
                 }
-                ch_T1w_mask = ch_split_test_data.T1w.map{
-                    test_data_directory -> [
-                        [ id:'test' ],
-                        file("\${test_data_directory}/T1w_mask.nii.gz")
-                    ]
-                }
                 input[0] = ch_T1w
                     .join(ch_moving)
-                    .join(ch_T1w_mask)
-                    .map{ meta, T1w, t1, T1w_mask -> [meta, T1w, t1, T1w_mask, []] }
                 """
             }
         }
@@ -89,16 +81,8 @@ nextflow_process {
                         file("\${test_data_directory}/t1.nii.gz")
                     ]
                 }
-                ch_T1w_mask = ch_split_test_data.T1w.map{
-                    test_data_directory -> [
-                        [ id:'test' ],
-                        file("\${test_data_directory}/T1w_mask.nii.gz")
-                    ]
-                }
                 input[0] = ch_T1w
                     .join(ch_moving)
-                    .join(ch_T1w_mask)
-                    .map{ meta, T1w, t1, T1w_mask -> [meta, T1w, t1, T1w_mask, []] }
                 """
             }
         }
@@ -132,16 +116,8 @@ nextflow_process {
                         file("\${test_data_directory}/t1.nii.gz")
                     ]
                 }
-                ch_T1w_mask = ch_split_test_data.T1w.map{
-                    test_data_directory -> [
-                        [ id:'test' ],
-                        file("\${test_data_directory}/T1w_mask.nii.gz")
-                    ]
-                }
                 input[0] = ch_T1w
                     .join(ch_moving)
-                    .join(ch_T1w_mask)
-                    .map{ meta, T1w, t1, T1w_mask -> [meta, T1w, t1, T1w_mask, []] }
                 """
             }
         }
@@ -176,16 +152,8 @@ nextflow_process {
                         file("\${test_data_directory}/t1.nii.gz")
                     ]
                 }
-                ch_T1w_mask = ch_split_test_data.T1w.map{
-                    test_data_directory -> [
-                        [ id:'test' ],
-                        file("\${test_data_directory}/T1w_mask.nii.gz")
-                    ]
-                }
                 input[0] = ch_T1w
                     .join(ch_moving)
-                    .join(ch_T1w_mask)
-                    .map{ meta, T1w, t1, T1w_mask -> [meta, T1w, t1, T1w_mask, []] }
                 """
             }
         }