added required parameters specifying dti and fodf shells for more rep…

…roducibility
scilus · Jan 9, 2025 · 7340fce · 7340fce
1 parent c4ce1b5
commit 7340fce
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Showing 6 changed files with 29 additions and 5 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -356,6 +356,8 @@ process {
     withName: 'NF_PEDIATRIC:PEDIATRIC:PREPROC_DWI:NORMALIZE_DWI' {
         ext.fa_mask_threshold = params.dwi_normalize_fa_mask_threshold
         ext.dwi_shell_tolerance = params.dwi_normalize_shell_tolerance
+        ext.dti_shells = params.dti_shells
+        ext.max_dti_shell_value = params.dti_max_shell_value
         publishDir = [
             path: { "${params.outdir}/${meta.id}/dwi/"},
             mode: params.publish_dir_mode,
@@ -458,6 +460,7 @@ process {
         ext.dwi_shell_tolerance = params.dti_shell_tolerance
         ext.max_dti_shell_value = params.dti_max_shell_value
         ext.b0_thr_extract_b0 = params.dti_b0_threshold
+        ext.dti_shells = params.dti_shells
 
         // ** DTI metrics to output ** //
         ext.ad = true
@@ -502,6 +505,8 @@ process {
         ext.dwi_shell_tolerance = params.frf_dwi_shell_tolerance
         ext.max_dti_shell_value = params.frf_max_dti_shell_value
         ext.min_fodf_shell_value = params.frf_min_fodf_shell_value
+        ext.fodf_shells = params.fodf_shells
+        ext.dti_shells = params.dti_shells
         ext.b0_thr_extract_b0 = params.frf_b0_threshold
         ext.set_method = params.frf_set_method
         ext.set_frf = params.frf_set_frf
@@ -522,6 +527,7 @@ process {
     withName: 'NF_PEDIATRIC:PEDIATRIC:RECONST_FODF' {
         ext.dwi_shell_tolerance = params.fodf_shell_tolerance
         ext.min_fodf_shell_value = params.fodf_min_fodf_shell_value
+        ext.fodf_shells = params.fodf_shells
         ext.b0_thr_extract_b0 = params.fodf_b0_threshold
         ext.sh_order = params.fodf_sh_order
         ext.sh_basis = params.fodf_sh_basis

diff --git a/nextflow.config b/nextflow.config
@@ -103,6 +103,7 @@ params {
     dti_shell_tolerance                     = 50
     dti_max_shell_value                     = 1500
     dti_b0_threshold                        = 20
+    dti_shells                              = null
 
     // FRF
     frf_fa                                  = 0.7
@@ -121,6 +122,7 @@ params {
     // FODF Metrics
     fodf_shell_tolerance                    = 50
     fodf_min_fodf_shell_value               = 100
+    fodf_shells                             = null
     fodf_b0_threshold                       = 20
     fodf_sh_order                           = 8
     fodf_sh_basis                           = "descoteaux07"

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -406,6 +406,7 @@
             "fa_icon": "fas fa-brain",
             "description": "Options for DTI processing.",
             "help_text": "These options are used to configure the DTI processing steps in the pipeline. You can use these options to customise the behaviour of the DTI processing steps.",
+            "required": ["dti_shells"],
             "properties": {
                 "dti_shell_tolerance": {
                     "type": "integer",
@@ -419,14 +420,20 @@
                     "description": "Maximum shell value used in the DTI processing step.",
                     "fa_icon": "fas fa-brain",
                     "default": 1500,
-                    "hidden": false
+                    "hidden": true
                 },
                 "dti_b0_threshold": {
                     "type": "integer",
                     "description": "B0 threshold used in the DTI processing step.",
                     "fa_icon": "fas fa-brain",
                     "default": 20,
                     "hidden": true
+                },
+                "dti_shells": {
+                    "type": "string",
+                    "description": "Shells used in the DTI processing step.",
+                    "fa_icon": "fas fa-brain",
+                    "hidden": false
                 }
             }
         },
@@ -477,14 +484,14 @@
                     "description": "Maximum DTI shell value used.",
                     "fa_icon": "fas fa-brain",
                     "default": 1500,
-                    "hidden": false
+                    "hidden": true
                 },
                 "frf_min_fodf_shell_value": {
                     "type": "integer",
                     "description": "Minimum FODF shell value used.",
                     "fa_icon": "fas fa-brain",
                     "default": 100,
-                    "hidden": false
+                    "hidden": true
                 },
                 "frf_b0_threshold": {
                     "type": "integer",
@@ -530,6 +537,7 @@
             "fa_icon": "fas fa-brain",
             "description": "Options for FODF processing.",
             "help_text": "These options are used to configure the FODF processing steps in the pipeline. You can use these options to customise the behaviour of the FODF processing steps.",
+            "required": ["fodf_shells"],
             "properties": {
                 "fodf_shell_tolerance": {
                     "type": "integer",
@@ -543,6 +551,12 @@
                     "description": "Minimum FODF shell value used.",
                     "fa_icon": "fas fa-brain",
                     "default": 100,
+                    "hidden": true
+                },
+                "fodf_shells": {
+                    "type": "string",
+                    "description": "Shells used in the FODF processing step.",
+                    "fa_icon": "fas fa-brain",
                     "hidden": false
                 },
                 "fodf_b0_threshold": {

diff --git a/subworkflows/nf-neuro/preproc_t1/main.nf b/subworkflows/nf-neuro/preproc_t1/main.nf
@@ -92,6 +92,7 @@ workflow PREPROC_T1 {
             ch_bet = IMAGE_RESAMPLE.out.image
                 .join(ch_template)
                 .join(ch_probability_map)
+                .map{ it + [[], []] }
 
             BETCROP_ANTSBET ( ch_bet )
             ch_versions = ch_versions.mix(BETCROP_ANTSBET.out.versions.first())

diff --git a/subworkflows/nf-neuro/preproc_t1/preproc_t1.diff b/subworkflows/nf-neuro/preproc_t1/preproc_t1.diff
@@ -3,7 +3,7 @@ Changes in component 'nf-neuro/preproc_t1'
 Changes in 'preproc_t1/main.nf':
 --- subworkflows/nf-neuro/preproc_t1/main.nf
 +++ subworkflows/nf-neuro/preproc_t1/main.nf
-@@ -88,9 +88,10 @@
+@@ -88,9 +88,11 @@
              // The template and probability maps are mandatory if running antsBET. Since the
              // error message from nextflow when they are absent is either non-informative or
              // missing, we use ifEmpty to provide a more informative one.
@@ -13,6 +13,7 @@ Changes in 'preproc_t1/main.nf':
 -                .join(ch_probability_map.ifEmpty{ error("ANTS BET needs a tissue probability map") })
 +                .join(ch_template)
 +                .join(ch_probability_map)
++                .map{ it + [[], []] }
 
              BETCROP_ANTSBET ( ch_bet )
              ch_versions = ch_versions.mix(BETCROP_ANTSBET.out.versions.first())

diff --git a/workflows/pediatric.nf b/workflows/pediatric.nf
@@ -126,7 +126,7 @@ workflow PEDIATRIC {
 
         ch_template = Channel.fromPath(params.t1_bet_template, checkIfExists: true)
         ch_probability_map = Channel.fromPath(params.t1_bet_template_probability_map, checkIfExists: true)
-            .map{ it + [[], []] }
+
         if ( params.t1_synthstrip_weights ) {
             ch_t1_weights = Channel.fromPath(params.t1_synthstrip_weights, checkIfExists: false)
         } else {