Merge pull request #11 from gagnonanthony/fix/dtishells

FIX: Add required parameters for DTI and fODF shells at runtime.
scilus · Jan 10, 2025 · d2deb2e · d2deb2e
2 parents c4ce1b5 + 8b8e8ab
commit d2deb2e
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Showing 11 changed files with 120 additions and 7 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased] - [2025-01-08]
 
+### `Added`
+
+- Required --dti_shells and --fodf_shells parameters.
+
 ### `Changed`
 
 - Fastsurfer and freesurfer outputs are now in their own dedicated output folder.

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/docs/usage.md b/docs/usage.md
@@ -122,10 +122,10 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p
 The typical command for running the pipeline is as follows:
 
 ```bash
-nextflow run scilus/nf-pediatric -r main --input ./samplesheet.csv --outdir ./results -profile docker
+nextflow run scilus/nf-pediatric -r main --input ./samplesheet.csv --outdir ./results --dti_shells "0 1000" --fodf_shells "0 1000" -profile docker
 ```
 
-This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
+This will launch the pipeline with the `docker` configuration profile. There is only 4 parameters that need to be supplied at runtime: `--input`: for the path to your samplesheet, `--oudir`: path to the output directory, `--dti_shells`: if the tracking profile is selected, you need to identify which shell to use for DTI fitting (0 and 1000 were selected in the previous example), and `--fodf_shells`: if the tracking profile is selected, specify your shells as for the DTI parameter. See below for more information about profiles.
 
 Note that the pipeline will create the following files in your working directory:
 

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
@@ -419,14 +419,20 @@
                     "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 +483,14 @@
                     "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",
@@ -543,6 +549,12 @@
                     "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/tests/chained.nf.test b/tests/chained.nf.test
@@ -53,6 +53,9 @@ nextflow_pipeline {
                 params.connectomics = true
                 params.tracking = true
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
             }
         }
 
@@ -85,6 +88,9 @@ nextflow_pipeline {
                 params.tracking = true
                 params.freesurfer = true
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
                 params.use_fastsurfer = true
                 params.fs_license = "https://www.dropbox.com/scl/fi/0s8lp6lydyd0rxawxb4jm/license.txt?rlkey=hz54oc0d4sor69avqphtrjvgn&st=9e0yij97&dl=0"
             }
@@ -122,6 +128,9 @@ nextflow_pipeline {
                 params.connectomics = true
                 params.tracking = true
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
             }
         }
 
@@ -164,6 +173,9 @@ nextflow_pipeline {
                 params.local_min_len                    = 15
                 params.local_fa_seeding_mask_threshold  = 0.10
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
             }
         }
 

diff --git a/tests/multisubjects.nf.test b/tests/multisubjects.nf.test
@@ -14,6 +14,9 @@ nextflow_pipeline {
                 params.outdir = "$outputDir"
                 params.use_fastsurfer = true
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
                 params.connectomics = true
                 params.tracking = true
                 params.freesurfer = true
@@ -55,6 +58,9 @@ nextflow_pipeline {
                 params.tracking = true
                 params.infant = true
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
                 // ** Infant specific parameters ** //
                 params.dwi_run_synthstrip               = true
                 params.dwi_normalize_fa_mask_threshold  = 0.10

diff --git a/tests/tracking.nf.test b/tests/tracking.nf.test
@@ -13,6 +13,9 @@ nextflow_pipeline {
                 params.input = "$projectDir/tests/data/samplesheet_testtracking.csv"
                 params.outdir = "$outputDir"
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
                 params.tracking = true
 
             }
@@ -43,6 +46,9 @@ nextflow_pipeline {
                 params.input = "$projectDir/tests/data/samplesheet_testtracking.csv"
                 params.outdir = "$outputDir"
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
                 params.tracking = true
                 params.skip_dwi_preprocessing = true
 
@@ -76,6 +82,9 @@ nextflow_pipeline {
 
                 params.tracking = true
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
             }
         }
 
@@ -85,6 +94,48 @@ nextflow_pipeline {
         }
     }
 
+    test("Tracking profile no dti shells - should fail") {
+
+        when {
+            params {
+
+                params.input = "$projectDir/tests/data/samplesheet_testtracking_norev.csv"
+                params.outdir = "$outputDir"
+
+                params.tracking = true
+
+                params.fodf_shells = "0 1000"
+
+            }
+        }
+
+        then {
+            assert workflow.failed
+            assert workflow.stdout.contains("Please provide the DTI shells using --dti_shells parameter")
+        }
+    }
+
+    test("Tracking profile no fodf shells - should fail") {
+
+        when {
+            params {
+
+                params.input = "$projectDir/tests/data/samplesheet_testtracking_norev.csv"
+                params.outdir = "$outputDir"
+
+                params.tracking = true
+
+                params.dti_shells = "0 1000"
+
+            }
+        }
+
+        then {
+            assert workflow.failed
+            assert workflow.stdout.contains("Please provide the FODF shells using --fodf_shells parameter")
+        }
+    }
+
     test("Tracking profile no dwi - should fail") {
 
         when {
@@ -93,6 +144,9 @@ nextflow_pipeline {
                 params.input = "$projectDir/tests/data/samplesheet_testtracking_nodwi.csv"
                 params.outdir = "$outputDir"
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
                 params.tracking = true
 
             }
@@ -126,6 +180,9 @@ nextflow_pipeline {
                 params.local_fa_seeding_mask_threshold  = 0.10
                 params.run_local_tracking               = true
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
             }
         }
 
@@ -167,6 +224,9 @@ nextflow_pipeline {
                 params.local_min_len                    = 15
                 params.local_fa_seeding_mask_threshold  = 0.10
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
             }
         }
 
@@ -187,6 +247,9 @@ nextflow_pipeline {
                 params.tracking = true
                 params.infant = true
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
                 // ** Infant specific parameters ** //
                 params.dwi_run_synthstrip               = true
                 params.dwi_normalize_fa_mask_threshold  = 0.10
@@ -217,6 +280,9 @@ nextflow_pipeline {
                 params.tracking = true
                 params.infant = true
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
                 // ** Infant specific parameters ** //
                 params.dwi_run_synthstrip               = true
                 params.dwi_normalize_fa_mask_threshold  = 0.10

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 {
@@ -152,6 +152,9 @@ workflow PEDIATRIC {
     //
     if ( params.tracking ) {
 
+        if ( !params.dti_shells ) { error "Please provide the DTI shells using --dti_shells parameter" }
+        if ( !params.fodf_shells ) { error "Please provide the FODF shells using --fodf_shells parameter" }
+
         /* Load topup config if provided */
         if ( params.dwi_susceptibility_config_file ) {
             if ( file(params.dwi_susceptibility_config_file).exists() ) {