From 9812ade69c3f37a582fde7cfbefeb28f9a97f64c Mon Sep 17 00:00:00 2001
From: EliseCos <elise.cosenza@u-bordeaux.fr>
Date: Tue, 25 Nov 2025 20:52:38 +0100
Subject: [PATCH 1/2] add ouputs fodf .config

---
 nextflow.config | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/nextflow.config b/nextflow.config
index 887283e..a032ea1 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -29,7 +29,9 @@ params {
 
     // FODF || QBALL
     use_fodf_for_tracking = false
+    run_fodf_metrics = true
     sh_order = 6
+    min_fodf_value = 1000
     
     // Tracking
     run_tracking = true
@@ -403,6 +405,45 @@ process {
         ext.max_dti_shell_value = params.max_dti_shell_value
     }
 
+withName: "RECONST_FODF" {
+        ext.sh_order = 6
+        ext.sh_basis = "descoteaux07"
+        ext.fa_threshold = 0.1
+        ext.md_threshold = 0.003
+        ext.relative_threshold = 0.1
+        ext.absolute_peaks = true
+        ext.peaks = true
+        ext.peak_values = true
+        ext.peak_indices = true
+        ext.afd_max = true
+        ext.afd_total = true
+        ext.afd_sum = true
+        ext.nufo = true
+        ext.b0_thr_extract_b0 = params.b0_threshold
+        ext.min_fodf_shell_value = params.min_fodf_value
+        publishDir = [ 
+            path: { "${params.outdir}/${meta.id}/dwi/"},
+            saveAs: {
+                filename ->
+                if ( filename.contains("fodf.nii.gz") ) { "${meta.id}_model-csd_param-fodf_dwimap.nii.gz" }
+                else if ( filename.contains("wm.nii.gz") ) { "${meta.id}_model-csd_param-wm_dwimap.nii.gz" }
+                else if ( filename.contains("gm.nii.gz") ) { "${meta.id}_model-csd_param-gm_dwimap.nii.gz" }
+                else if ( filename.contains("csf.nii.gz") ) { "${meta.id}_model-csd_param-csf_dwimap.nii.gz" }
+                else if ( filename.contains("vf.nii.gz") ) { "${meta.id}_model-csd_param-vf_dwimap.nii.gz" }
+                else if ( filename.contains("vf_rgb.nii.gz") ) { "${meta.id}_model-csd_param-rgb_dwimap.nii.gz" }
+                else if ( filename.contains("afd_total.nii.gz") ) { "${meta.id}_model-csd_param-afdtot_dwimap.nii.gz" }
+                else if ( filename.contains("afd_sum.nii.gz") ) { "${meta.id}_model-csd_param-afdsum_dwimap.nii.gz" }
+                else if ( filename.contains("afd_max.nii.gz") ) { "${meta.id}_model-csd_param-afdmax_dwimap.nii.gz" }
+                else if ( filename.contains("nufo.nii.gz") ) { "${meta.id}_model-csf_csd_param-nufo_dwimap.nii.gz" }
+                else if ( filename.contains("evecs_v1.nii.gz") ) { "${meta.id}_model-csd_param-v1_dwimap.nii.gz" }
+                else if ( filename.contains("evecs_v2.nii.gz") ) { "${meta.id}_model-csd_param-v2_dwimap.nii.gz" }
+                else if ( filename.contains("evecs_v3.nii.gz") ) { "${meta.id}_model-csd_param-v3_dwimap.nii.gz" }
+                else if ( filename.contains("versions.yml") ) { null }
+                else { params.lean_output ? null : filename }
+            }
+        ]
+    }
+
     withName: "RECONST_QBALL" {
         ext.sh_order = params.sh_order
         ext.qball = true

From 9e857fceb44de600c6a00dfadaf989effd4808a8 Mon Sep 17 00:00:00 2001
From: EliseCos <elise.cosenza@u-bordeaux.fr>
Date: Wed, 26 Nov 2025 11:52:53 +0100
Subject: [PATCH 2/2] remove command run fodf

---
 nextflow.config | 1 -
 1 file changed, 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index a032ea1..7ae23de 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -29,7 +29,6 @@ params {
 
     // FODF || QBALL
     use_fodf_for_tracking = false
-    run_fodf_metrics = true
     sh_order = 6
     min_fodf_value = 1000