From c1ed83ff3ea2e191989374f8e580aa655a5ec7e4 Mon Sep 17 00:00:00 2001
From: EliseCos <elise.cosenza@u-bordeaux.fr>
Date: Fri, 17 Apr 2026 17:36:57 +0200
Subject: [PATCH 01/15] [WIP] creation module BET for invivo

---
 assets/Docker/brain_extraction.py       | 30 +++++++++++++++++
 modules/local/mouse/bet/environment.yml |  3 ++
 modules/local/mouse/bet/main.nf         | 42 +++++++++++++++++++++++
 modules/local/mouse/bet/meta.yml        | 45 +++++++++++++++++++++++++
 4 files changed, 120 insertions(+)
 create mode 100644 assets/Docker/brain_extraction.py
 create mode 100644 modules/local/mouse/bet/environment.yml
 create mode 100644 modules/local/mouse/bet/main.nf
 create mode 100755 modules/local/mouse/bet/meta.yml

diff --git a/assets/Docker/brain_extraction.py b/assets/Docker/brain_extraction.py
new file mode 100644
index 0000000..5be1f5e
--- /dev/null
+++ b/assets/Docker/brain_extraction.py
@@ -0,0 +1,30 @@
+#! /usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+Extract the brain mask from an anatomical image using ants and antspynet.
+"""
+
+import argparse
+import os
+
+import ants
+import antspynet
+import argparse
+from antspynet import mouse_brain_extraction
+
+parser = argparse.ArgumentParser(description="")
+parser.add_argument('input_anat', type=str, help="Path to the anatomical image.")
+parser.add_argument('output_mask', type=str, help="Path to the output mask file.")
+
+args = parser.parse_args()
+
+filename_input=args.input_anat
+filename_output=args.output_mask
+
+mri_image = ants.image_read(filename_input)
+
+output = mouse_brain_extraction(mri_image,modality="t2")
+ants.image_write(output,filename_output)
+
+
diff --git a/modules/local/mouse/bet/environment.yml b/modules/local/mouse/bet/environment.yml
new file mode 100644
index 0000000..054a77f
--- /dev/null
+++ b/modules/local/mouse/bet/environment.yml
@@ -0,0 +1,3 @@
+channels: []
+dependencies: []
+name: "mouse_bet"  
diff --git a/modules/local/mouse/bet/main.nf b/modules/local/mouse/bet/main.nf
new file mode 100644
index 0000000..218a13e
--- /dev/null
+++ b/modules/local/mouse/bet/main.nf
@@ -0,0 +1,42 @@
+process MOUSE_BET {
+    label 'process_high'
+
+    container "scilus/scilpy:dev"
+
+    input:
+        tuple val(meta), path(anat)
+    output:
+        tuple val(meta), path("*__mask.nii.gz")      , emit: mask
+        path "versions.yml"                          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+
+    """
+    
+    brain_extraction.py $anat ${prefix}__mask.nii.gz
+    fslmaths ${prefix}__mask.nii.gz -bin ${prefix}__mask.nii.gz
+    scil_volume_math convert ${prefix}__mask.nii.gz ${prefix}__mask.nii.gz -f --data_type int8
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    fslmaths
+    scil_volume_math -h
+
+    touch all__stats.json
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+    END_VERSIONS
+    """
+}
\ No newline at end of file
diff --git a/modules/local/mouse/bet/meta.yml b/modules/local/mouse/bet/meta.yml
new file mode 100755
index 0000000..b5358d4
--- /dev/null
+++ b/modules/local/mouse/bet/meta.yml
@@ -0,0 +1,45 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/scilus/nf-neuro/main/modules/meta-schema.json
+name: "preproc_singleeddy"
+description: Apply Eddy (and Topup if already run)
+keywords:
+  - BET
+  - T1
+  - eddy
+tools:
+  - "scilpy":
+      description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
+      homepage: "https://github.com/scilus/scilpy.git"
+  - "FSL":
+      description: "FSL Toolbox and Scilpy Toolbox"
+      homepage: "https://fsl.fmrib.ox.ac.uk/fsl/fslwiki"
+input:
+  # Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - anat:
+      type: file
+      description: Anat Nifti image
+      pattern: "*.{nii,nii.gz}"
+
+
+output:
+  #Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - mask:
+      type: file
+      description: mask brain-extracted
+      pattern: "*__mask.{nii,nii.gz}"
+
+
+authors:
+  - "@EliseCos"
\ No newline at end of file

From 3e121385cfaf55d96f81663737eb759723466f69 Mon Sep 17 00:00:00 2001
From: EliseCos <elise.cosenza@u-bordeaux.fr>
Date: Fri, 17 Apr 2026 20:07:41 +0200
Subject: [PATCH 02/15] [WIP] add .config + docker

---
 assets/Docker/Dockerfile        |  3 +++
 main.nf                         | 18 +++++++++++++++++-
 modules/local/mouse/bet/main.nf |  4 ++--
 nextflow.config                 |  3 +++
 4 files changed, 25 insertions(+), 3 deletions(-)

diff --git a/assets/Docker/Dockerfile b/assets/Docker/Dockerfile
index 18237a0..c6e7d71 100644
--- a/assets/Docker/Dockerfile
+++ b/assets/Docker/Dockerfile
@@ -28,6 +28,9 @@ RUN chmod 777 /ANO_taxonomy_EC_V4.csv
 COPY mouse_extract_masks.py /usr/local/bin/
 RUN chmod 777 /usr/local/bin/mouse_extract_masks.py
 
+COPY brain_extraction.py /usr/local/bin/
+RUN chmod 777 /usr/local/bin/brain_extraction.py
+
 WORKDIR /
 ADD atlas.tar.gz /
 
diff --git a/main.nf b/main.nf
index e48f43b..cfb6a0f 100644
--- a/main.nf
+++ b/main.nf
@@ -3,6 +3,7 @@ include { DENOISING_MPPCA } from './modules/nf-neuro/denoising/mppca/main.nf'
 include { PREPROC_SINGLEEDDY } from './modules/local/preproc/singleeddy/main.nf'
 include { UTILS_EXTRACTB0 } from './modules/nf-neuro/utils/extractb0/main.nf'
 include { NNUNET } from './subworkflows/local/nnunet/'
+include { MOUSE_BET } from './modules/local/mouse/bet/main.nf'
 include { MOUSE_N4 } from './modules/local/mouse/n4/main.nf'
 include { IMAGE_RESAMPLE as RESAMPLE_DWI} from './modules/nf-neuro/image/resample/main.nf'
 include { IMAGE_RESAMPLE as RESAMPLE_MASK} from './modules/nf-neuro/image/resample/main.nf'
@@ -57,6 +58,10 @@ workflow get_data {
                         .map { mask_file -> def sid = mask_file.parent.name
                         [[id: sid], mask_file] }
         
+        anat_channel = Channel.fromPath("$input/**/*anat.nii.gz")
+                        .map { anat_file -> def sid = anat_file.parent.name
+                        [[id: sid], anat_file] }
+        
         template_channel = Channel.fromPath("$projectDir/assets/reference_rgb_mqc.png")
         
         lut_channel = Channel.of([
@@ -68,6 +73,7 @@ workflow get_data {
     emit:
         dwi   = dwi_channel
         mask  = mask_channel
+        anat = anat_channel
         template_rgb = template_channel
         lut = lut_channel
 }
@@ -105,6 +111,7 @@ workflow {
             log.warn('Using the output from the preqc module is highly experimental. Please be careful.')
             ch_after_preqc = PRE_QC.out.dwi
             bvs_after_preqc = PRE_QC.out.bvs
+            
         }
         else {
             ch_after_preqc = Channel.empty()
@@ -136,7 +143,16 @@ workflow {
     else {
         ch_after_eddy = ch_eddy
     }
-    
+
+    if (params.invivo){
+        MOUSE_BET(data.anat)
+        ch_after_eddy = ch_eddy.join(
+            MOUSE_BET.out.mask)
+    }
+    else {
+        ch_after_eddy = ch_eddy
+    }
+
     UTILS_EXTRACTB0(ch_after_eddy)
     ch_nnunet = ch_after_eddy.join(UTILS_EXTRACTB0.out.b0)
     .join(data.mask, by: 0, remainder: true)
diff --git a/modules/local/mouse/bet/main.nf b/modules/local/mouse/bet/main.nf
index 218a13e..c5ac737 100644
--- a/modules/local/mouse/bet/main.nf
+++ b/modules/local/mouse/bet/main.nf
@@ -13,10 +13,10 @@ process MOUSE_BET {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    
+
     brain_extraction.py $anat ${prefix}__mask.nii.gz
     fslmaths ${prefix}__mask.nii.gz -bin ${prefix}__mask.nii.gz
     scil_volume_math convert ${prefix}__mask.nii.gz ${prefix}__mask.nii.gz -f --data_type int8
diff --git a/nextflow.config b/nextflow.config
index a5f9674..e18dbc3 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -14,6 +14,9 @@ params {
     // Eddy
     run_eddy = true
     processes = 10
+
+    // Invivo
+    invivo = false
     
     // N4
     run_n4 = true

From 75ab998b52c6172a398f350ae9016459fe5e350c Mon Sep 17 00:00:00 2001
From: EliseCos <elise.cosenza@u-bordeaux.fr>
Date: Fri, 24 Apr 2026 17:40:03 +0200
Subject: [PATCH 03/15] [WIP] add new container

---
 modules/local/mouse/bet/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/local/mouse/bet/main.nf b/modules/local/mouse/bet/main.nf
index c5ac737..c1ec46f 100644
--- a/modules/local/mouse/bet/main.nf
+++ b/modules/local/mouse/bet/main.nf
@@ -1,7 +1,7 @@
 process MOUSE_BET {
     label 'process_high'
 
-    container "scilus/scilpy:dev"
+    container "scilus/antspynet:dev"
 
     input:
         tuple val(meta), path(anat)
@@ -17,7 +17,7 @@ process MOUSE_BET {
 
     """
 
-    brain_extraction.py $anat ${prefix}__mask.nii.gz
+    antsMouseBrainExtraction $anat ${prefix}__mask.nii.gz
     fslmaths ${prefix}__mask.nii.gz -bin ${prefix}__mask.nii.gz
     scil_volume_math convert ${prefix}__mask.nii.gz ${prefix}__mask.nii.gz -f --data_type int8
 

From 9fe23f3cbf3669674ff69bcf77028b9225fc6adb Mon Sep 17 00:00:00 2001
From: EliseCos <elise.cosenza@u-bordeaux.fr>
Date: Mon, 27 Apr 2026 15:03:44 +0200
Subject: [PATCH 04/15] [ENH] update container

---
 modules/local/mouse/bet/main.nf | 3 ---
 nextflow.config                 | 5 +++++
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/modules/local/mouse/bet/main.nf b/modules/local/mouse/bet/main.nf
index c1ec46f..5d679e9 100644
--- a/modules/local/mouse/bet/main.nf
+++ b/modules/local/mouse/bet/main.nf
@@ -16,7 +16,6 @@ process MOUSE_BET {
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-
     antsMouseBrainExtraction $anat ${prefix}__mask.nii.gz
     fslmaths ${prefix}__mask.nii.gz -bin ${prefix}__mask.nii.gz
     scil_volume_math convert ${prefix}__mask.nii.gz ${prefix}__mask.nii.gz -f --data_type int8
@@ -32,8 +31,6 @@ process MOUSE_BET {
     fslmaths
     scil_volume_math -h
 
-    touch all__stats.json
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
diff --git a/nextflow.config b/nextflow.config
index e18dbc3..2780da2 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -267,6 +267,11 @@ process {
         ]
     }
 
+    withName: "MOUSE_BET" {
+        container = 'scilus/antspynet:dev'
+        containerOptions = '--entrypoint ""'
+    }
+
     withName: "UTILS_EXTRACTB0" {
         ext.b0_threshold = params.b0_threshold
     }

From a0c8cb0ea031f4832c0b8eb09e021b696c8b046f Mon Sep 17 00:00:00 2001
From: EliseCos <elise.cosenza@u-bordeaux.fr>
Date: Tue, 28 Apr 2026 20:33:39 +0200
Subject: [PATCH 05/15] [WIP] add subworkflow BET for in vivo

Co-authored-by: Copilot <copilot@github.com>
---
 main.nf                                       |  11 ++--
 .../{bet => brainextraction}/environment.yml  |   0
 .../mouse/{bet => brainextraction}/main.nf    |   5 +-
 .../mouse/{bet => brainextraction}/meta.yml   |   5 +-
 .../local/mouse/convertbet/environment.yml    |   3 ++
 modules/local/mouse/convertbet/main.nf        |  48 ++++++++++++++++++
 modules/local/mouse/convertbet/meta.yml       |  44 ++++++++++++++++
 modules/local/mouse/convertjson/main.nf       |   1 +
 .../local/mouse/preparebet/environment.yml    |   3 ++
 modules/local/mouse/preparebet/main.nf        |  40 +++++++++++++++
 modules/local/mouse/preparebet/meta.yml       |  40 +++++++++++++++
 nextflow.config                               |   3 +-
 subworkflows/.DS_Store                        | Bin 0 -> 6148 bytes
 subworkflows/local/bet/main.nf                |  27 ++++++++++
 14 files changed, 217 insertions(+), 13 deletions(-)
 rename modules/local/mouse/{bet => brainextraction}/environment.yml (100%)
 rename modules/local/mouse/{bet => brainextraction}/main.nf (82%)
 rename modules/local/mouse/{bet => brainextraction}/meta.yml (91%)
 create mode 100644 modules/local/mouse/convertbet/environment.yml
 create mode 100644 modules/local/mouse/convertbet/main.nf
 create mode 100755 modules/local/mouse/convertbet/meta.yml
 create mode 100644 modules/local/mouse/preparebet/environment.yml
 create mode 100644 modules/local/mouse/preparebet/main.nf
 create mode 100755 modules/local/mouse/preparebet/meta.yml
 create mode 100644 subworkflows/.DS_Store
 create mode 100644 subworkflows/local/bet/main.nf

diff --git a/main.nf b/main.nf
index cfb6a0f..587e715 100644
--- a/main.nf
+++ b/main.nf
@@ -3,7 +3,7 @@ include { DENOISING_MPPCA } from './modules/nf-neuro/denoising/mppca/main.nf'
 include { PREPROC_SINGLEEDDY } from './modules/local/preproc/singleeddy/main.nf'
 include { UTILS_EXTRACTB0 } from './modules/nf-neuro/utils/extractb0/main.nf'
 include { NNUNET } from './subworkflows/local/nnunet/'
-include { MOUSE_BET } from './modules/local/mouse/bet/main.nf'
+include { BET } from './subworkflows/local/bet/main.nf'
 include { MOUSE_N4 } from './modules/local/mouse/n4/main.nf'
 include { IMAGE_RESAMPLE as RESAMPLE_DWI} from './modules/nf-neuro/image/resample/main.nf'
 include { IMAGE_RESAMPLE as RESAMPLE_MASK} from './modules/nf-neuro/image/resample/main.nf'
@@ -143,14 +143,15 @@ workflow {
     else {
         ch_after_eddy = ch_eddy
     }
-
+    
+    ch_bet = data.anat
     if (params.invivo){
-        MOUSE_BET(data.anat)
+        BET(ch_bet)
         ch_after_eddy = ch_eddy.join(
-            MOUSE_BET.out.mask)
+            BET.out.mask)
     }
     else {
-        ch_after_eddy = ch_eddy
+        ch_after_eddy = ch_eddy 
     }
 
     UTILS_EXTRACTB0(ch_after_eddy)
diff --git a/modules/local/mouse/bet/environment.yml b/modules/local/mouse/brainextraction/environment.yml
similarity index 100%
rename from modules/local/mouse/bet/environment.yml
rename to modules/local/mouse/brainextraction/environment.yml
diff --git a/modules/local/mouse/bet/main.nf b/modules/local/mouse/brainextraction/main.nf
similarity index 82%
rename from modules/local/mouse/bet/main.nf
rename to modules/local/mouse/brainextraction/main.nf
index 5d679e9..04bd79f 100644
--- a/modules/local/mouse/bet/main.nf
+++ b/modules/local/mouse/brainextraction/main.nf
@@ -1,4 +1,5 @@
-process MOUSE_BET {
+process MOUSE_BRAINEXTRACTION {
+    tag "$meta.id"
     label 'process_high'
 
     container "scilus/antspynet:dev"
@@ -17,8 +18,6 @@ process MOUSE_BET {
 
     """
     antsMouseBrainExtraction $anat ${prefix}__mask.nii.gz
-    fslmaths ${prefix}__mask.nii.gz -bin ${prefix}__mask.nii.gz
-    scil_volume_math convert ${prefix}__mask.nii.gz ${prefix}__mask.nii.gz -f --data_type int8
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/mouse/bet/meta.yml b/modules/local/mouse/brainextraction/meta.yml
similarity index 91%
rename from modules/local/mouse/bet/meta.yml
rename to modules/local/mouse/brainextraction/meta.yml
index b5358d4..f6c6a88 100755
--- a/modules/local/mouse/bet/meta.yml
+++ b/modules/local/mouse/brainextraction/meta.yml
@@ -1,11 +1,10 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/scilus/nf-neuro/main/modules/meta-schema.json
-name: "preproc_singleeddy"
-description: Apply Eddy (and Topup if already run)
+name: "brainextraction"
+description: Extraction of the brain from anatomical images using BET
 keywords:
   - BET
   - T1
-  - eddy
 tools:
   - "scilpy":
       description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
diff --git a/modules/local/mouse/convertbet/environment.yml b/modules/local/mouse/convertbet/environment.yml
new file mode 100644
index 0000000..b92d504
--- /dev/null
+++ b/modules/local/mouse/convertbet/environment.yml
@@ -0,0 +1,3 @@
+channels: []
+dependencies: []
+name: "mouse_convertbet"  
diff --git a/modules/local/mouse/convertbet/main.nf b/modules/local/mouse/convertbet/main.nf
new file mode 100644
index 0000000..aebb95f
--- /dev/null
+++ b/modules/local/mouse/convertbet/main.nf
@@ -0,0 +1,48 @@
+process MOUSE_CONVERTBET {
+    tag "$meta.id"
+    label 'process_low'
+ 
+    container "scilus/scilus:2.2.0"
+
+    input:
+        tuple val(meta), path(image)
+    output:
+        tuple val(meta), path("*_mask.nii.gz")                      , emit: mask
+        path "versions.yml"                                         , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def nb_vox = task.ext.nb_vox ?: ""
+    """
+    fslmaths ${image} -bin ${prefix}_mask.nii.gz
+
+    scil_volume_math erosion ${prefix}_mask.nii.gz $nb_vox ${prefix}_mask.nii.gz --data_type uint8 -f
+    ImageMath 3 ${prefix}_mask.nii.gz  GetLargestComponent ${prefix}_mask.nii.gz 
+    scil_volume_math dilation ${prefix}_mask.nii.gz $nb_vox ${prefix}_mask.nii.gz --data_type uint8 -f
+    ImageMath 3 ${prefix}_mask.nii.gz  FillHoles ${prefix}_mask.nii.gz 
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    fslmaths
+    scil_volume_math -h
+    ImageMath
+
+    touch ${prefix}_mask.nii.gz 
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+        fsl: \$(flirt -version 2>&1 | sed -n 's/FLIRT version \\([0-9.]\\+\\)/\\1/p')
+    END_VERSIONS
+    """
+}
\ No newline at end of file
diff --git a/modules/local/mouse/convertbet/meta.yml b/modules/local/mouse/convertbet/meta.yml
new file mode 100755
index 0000000..fc7e4b5
--- /dev/null
+++ b/modules/local/mouse/convertbet/meta.yml
@@ -0,0 +1,44 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/scilus/nf-neuro/main/modules/meta-schema.json
+name: "mouse_convertjson"
+description: Convert stats to JSON
+keywords:
+  - stats
+  - convert
+tools:
+  - "scilpy":
+      description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
+      homepage: "https://github.com/scilus/scilpy.git"
+input:
+  # Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - stats:
+      type: list
+      description: DWI Nifti image
+      pattern: "*.{nii,nii.gz}"
+
+output:
+  #Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - stats_json:
+      type: file
+      description: File with stats
+      pattern: "stats_reorganized.json"
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@EliseCos"
\ No newline at end of file
diff --git a/modules/local/mouse/convertjson/main.nf b/modules/local/mouse/convertjson/main.nf
index 5702964..f112f1a 100644
--- a/modules/local/mouse/convertjson/main.nf
+++ b/modules/local/mouse/convertjson/main.nf
@@ -25,6 +25,7 @@ process MOUSE_CONVERTJSON {
     """
 
     stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}__stats_reorganized.json
 
diff --git a/modules/local/mouse/preparebet/environment.yml b/modules/local/mouse/preparebet/environment.yml
new file mode 100644
index 0000000..9e99afe
--- /dev/null
+++ b/modules/local/mouse/preparebet/environment.yml
@@ -0,0 +1,3 @@
+channels: []
+dependencies: []
+name: "mouse_preparebet"
diff --git a/modules/local/mouse/preparebet/main.nf b/modules/local/mouse/preparebet/main.nf
new file mode 100644
index 0000000..e4c8759
--- /dev/null
+++ b/modules/local/mouse/preparebet/main.nf
@@ -0,0 +1,40 @@
+process MOUSE_PREPAREBET {
+    tag "$meta.id"
+    label 'process_high'
+
+    container "scilus/scilus:2.2.0"
+
+    input:
+        tuple val(meta), path(image)
+    output:
+        tuple val(meta), path("*_n4_second.nii.gz")          , emit: betready
+        path "versions.yml"                                  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+
+    N4BiasFieldCorrection -d 3 -i ${image} -o ${prefix}__n4_first.nii.gz -s 4 -c [20x20x10,1e-6]
+    N4BiasFieldCorrection -d 3 -i ${prefix}__n4_first.nii.gz -o ${prefix}__n4_second.nii.gz -s 2 -c [30x20x10,1e-6]
+
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    N4BiasFieldCorrection -h
+
+    touch ${prefix}__n4_second.nii.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    ants: \$(N4BiasFieldCorrection --version 2>&1 | sed -n 's/ANTs Version: v\\([0-9.]\\+\\)/\\1/p')
+    END_VERSIONS
+    """
+}
diff --git a/modules/local/mouse/preparebet/meta.yml b/modules/local/mouse/preparebet/meta.yml
new file mode 100755
index 0000000..2ab9ed4
--- /dev/null
+++ b/modules/local/mouse/preparebet/meta.yml
@@ -0,0 +1,40 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/scilus/nf-neuro/main/modules/meta-schema.json
+name: "preparebet"
+description: Prepare anatomical images for brain extraction with BET
+keywords:
+  - volume
+  - mask
+tools:
+  - "scilpy":
+      description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
+      homepage: "https://github.com/scilus/scilpy.git"
+input:
+  # Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - anat:
+      type: list
+      description: Anat Nifti image
+      pattern: "*.{nii,nii.gz}"
+
+
+output:
+  #Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@EliseCos"
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index 2780da2..0a09354 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -268,8 +268,7 @@ process {
     }
 
     withName: "MOUSE_BET" {
-        container = 'scilus/antspynet:dev'
-        containerOptions = '--entrypoint ""'
+        ext.nb_vox = 3
     }
 
     withName: "UTILS_EXTRACTB0" {
diff --git a/subworkflows/.DS_Store b/subworkflows/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..806193f8fc10dc7faa51772381bda09350c1dae8
GIT binary patch
literal 6148
zcmeHK%}T>S5Z<+|O({YS3VK`cS}+A`DPBUYFJMFuDm5`hgE3p0)Er77cYPsW#OHBl
zcLOa3k0N#kcE8#A+0A^A{b7vp;XLdzW;4btXowt@3PE$FYs&;9ay3UB<mohsWl%BA
z-!$R3H(1Ohdtg3W{r-<&8b@j7IG=p0R&Q)Kt)|ts?z|_Ndzqij)1g1R!O^9ZaZu`h
za1~ARvAugHlgy8j$xJ0g;RHf%ucIWC`B2W2Fjcvpc33T|HMS2Hi*C>9cSNt>TXw`^
za6AD0#91y|*52XK>Baateo5q;W|9NtN_GsE@D9pKNw3~4iDmK#)-t1vBqRoi0b+m{
z*hmJ<abUGKvU)0-7$63IVgUCC0S(bLSZGvR2XuISMt>a<1$2B%APR%7!9pW=K)6l?
z)T!J&F}O|#yD)LC!9t@>XI!le^O%*(#|u}hgI%a_#$Aon69dG+Is-L5wDJ5uhhL`h
zk-wfoBVvFU_-738`p6p%p(t~<ek%{pS^@1I8Vbf0sDOaJb_sw1?j!rksr>?Vh;t1V
V8gUl1t8_rR2q;3RBL;qffiF(zOAP=3

literal 0
HcmV?d00001

diff --git a/subworkflows/local/bet/main.nf b/subworkflows/local/bet/main.nf
new file mode 100644
index 0000000..be97e8f
--- /dev/null
+++ b/subworkflows/local/bet/main.nf
@@ -0,0 +1,27 @@
+include { MOUSE_PREPAREBET } from '../../../modules/local/mouse/preparebet/main.nf'
+include { MOUSE_BRAINEXTRACTION } from '../../../modules/local/mouse/brainextraction/main.nf'
+include { MOUSE_CONVERTBET } from '../../../modules/local/mouse/convertbet/main.nf'
+
+workflow BET {
+
+    take:
+        ch_bet           // channel: [ val(meta), dwi, bval, b0, mask]
+
+    main:
+
+        ch_versions = Channel.empty()
+        ch_multiqc_files = Channel.empty()
+
+
+        MOUSE_PREPAREBET(ch_bet)
+
+        MOUSE_BRAINEXTRACTION(MOUSE_PREPAREBET.out.betready)
+
+        MOUSE_CONVERTBET(MOUSE_BRAINEXTRACTION.out.mask)
+
+
+    emit:
+        mask = MOUSE_CONVERTBET.out.mask                     // channel: [ val(meta), mask ]
+        mqc                 = ch_multiqc_files              // channel: [ val(meta), mqc ]
+        versions            = ch_versions                   // channel: [ versions.yml ]
+}

From fffc8fd042be9c07c1081663de131e6cf05449e6 Mon Sep 17 00:00:00 2001
From: EliseCos <elise.cosenza@u-bordeaux.fr>
Date: Wed, 29 Apr 2026 17:42:29 +0200
Subject: [PATCH 06/15] [ENH] adapt to masks from different sources

Co-authored-by: Copilot <copilot@github.com>
---
 main.nf                                | 72 ++++++++++++++++----------
 modules/local/mouse/preparebet/main.nf |  4 +-
 nextflow.config                        |  9 ++++
 3 files changed, 56 insertions(+), 29 deletions(-)

diff --git a/main.nf b/main.nf
index 587e715..e1fa1ca 100644
--- a/main.nf
+++ b/main.nf
@@ -37,13 +37,17 @@ workflow get_data {
             log.info ""
             log.info "                         [input]"
             log.info "                           ├-- S1"
-            log.info "                           |   ├-- *dwi.nii.gz"
             log.info "                           |   ├-- *dwi.bval"
-            log.info "                           |   └-- *dwi.bvec"
+            log.info "                           |   ├-- *dwi.bvec"
+            log.info "                           |   ├-- *dwi.nii.gz"
+            log.info "                           |   ├-- *anat.nii.gz (optional)"
+            log.info "                           |   └-- *mask.nii.gz (optional)"
             log.info "                           └-- S2"
-            log.info "                                ├-- *dwi.nii.gz"
-            log.info "                                ├-- *dwi.bval"
-            log.info "                                └-- *dwi.bvec"
+            log.info "                               ├-- *dwi.bval"
+            log.info "                               ├-- *dwi.bvec"
+            log.info "                               ├-- *dwi.nii.gz"
+            log.info "                               ├-- *anat.nii.gz (optional)"
+            log.info "                               └-- *mask.nii.gz (optional)"
             log.info ""
             log.info ""
             error "Please resubmit your command with the previous file structure."
@@ -102,6 +106,8 @@ workflow {
         }
     ch_ref_rgb = data.template_rgb
     ch_lut = data.lut
+    ch_bet = data.anat
+    ch_mask = Channel.empty()
 
     if ( params.run_preqc ) {
         PRE_QC(ch_dwi_bvalbvec.dwi.join(ch_dwi_bvalbvec.bvs_files).combine(ch_ref_rgb))
@@ -144,30 +150,40 @@ workflow {
         ch_after_eddy = ch_eddy
     }
     
-    ch_bet = data.anat
-    if (params.invivo){
+    UTILS_EXTRACTB0(ch_after_eddy)
+
+    if (params.invivo) {
         BET(ch_bet)
-        ch_after_eddy = ch_eddy.join(
-            BET.out.mask)
+        ch_mask = BET.out.mask
     }
     else {
-        ch_after_eddy = ch_eddy 
-    }
+        ch_eddy_with_optional_mask = ch_after_eddy
+            .join(data.mask, by: 0, remainder: true)
 
-    UTILS_EXTRACTB0(ch_after_eddy)
-    ch_nnunet = ch_after_eddy.join(UTILS_EXTRACTB0.out.b0)
-    .join(data.mask, by: 0, remainder: true)
-            .map { meta, dwi, bval, bvec, b0, mask ->   
-                [meta, dwi, bval, b0, mask ?: [   ]]}  // Use empty list if mask is null
+        ch_mask_split = ch_eddy_with_optional_mask
+            .branch { meta, dwi, bval, bvec, mask ->
+                with_mask: mask != null
+                no_mask:   mask == null}
+
+        ch_mask_from_input = ch_mask_split.with_mask
+            .map { meta, dwi, bval, bvec, mask ->
+                tuple(meta, mask)}
+
+        ch_nnunet = ch_mask_split.no_mask
+            .join(UTILS_EXTRACTB0.out.b0)
+            .map { meta, dwi, bval, bvec, mask, b0 ->
+                tuple(meta, dwi, bval, b0, [])}
     
-    NNUNET(ch_nnunet)
+        NNUNET(ch_nnunet)
+        ch_mask = ch_mask_from_input.mix(NNUNET.out.mask)
+        }
 
     if ( params.run_n4 ) {
         ch_N4 = ch_after_eddy
             .map{ meta, dwi, _bval, _bvec ->
                     tuple(meta, dwi)}
             .join(UTILS_EXTRACTB0.out.b0)
-            .join(NNUNET.out.mask)
+            .join(ch_mask)
         MOUSE_N4(ch_N4)
         ch_after_n4 = MOUSE_N4.out.dwi_n4
     }
@@ -178,7 +194,7 @@ workflow {
 
     if ( params.run_resampling ) {
         RESAMPLE_DWI(ch_after_n4.map{ meta, dwi -> [meta, dwi, []] }) // Add an empty list for the optional reference image
-        RESAMPLE_MASK(NNUNET.out.mask.map{ meta, mask -> [meta, mask, []] })
+        RESAMPLE_MASK(ch_mask.map{ meta, mask -> [meta, mask, []] })
         IMAGE_CONVERT(RESAMPLE_MASK.out.image)
 
         dwi_after_resample = RESAMPLE_DWI.out.image
@@ -186,7 +202,7 @@ workflow {
     }
     else {
         dwi_after_resample = ch_after_n4
-        IMAGE_CONVERT(NNUNET.out.mask)
+        IMAGE_CONVERT(ch_mask)
         mask_after_resample = IMAGE_CONVERT.out.image
     }
     
@@ -204,13 +220,15 @@ workflow {
     ch_multiqc_files = ch_multiqc_files.mix(RECONST_DTIMETRICS.out.mqc)
 
     /* FODF */ 
-    RECONST_FRF(ch_for_reconst.map{ it + [[], [], []]})
-    ch_for_reconst_fodf = ch_for_reconst
-                            .join(RECONST_DTIMETRICS.out.fa)
-                            .join(RECONST_DTIMETRICS.out.md)
-                            .join(RECONST_FRF.out.frf)
-                            .map{ it + [[], []]}
-    RECONST_FODF(ch_for_reconst_fodf)
+    if ( params.run_fodf_metrics ) {
+        RECONST_FRF(ch_for_reconst.map{ it + [[], [], []]})
+        ch_for_reconst_fodf = ch_for_reconst
+                                .join(RECONST_DTIMETRICS.out.fa)
+                                .join(RECONST_DTIMETRICS.out.md)
+                                .join(RECONST_FRF.out.frf)
+                                .map{ it + [[], []]}
+        RECONST_FODF(ch_for_reconst_fodf)
+    }
 
     /* QBALL */
     RECONST_QBALL(ch_for_reconst)
diff --git a/modules/local/mouse/preparebet/main.nf b/modules/local/mouse/preparebet/main.nf
index e4c8759..365730f 100644
--- a/modules/local/mouse/preparebet/main.nf
+++ b/modules/local/mouse/preparebet/main.nf
@@ -5,7 +5,7 @@ process MOUSE_PREPAREBET {
     container "scilus/scilus:2.2.0"
 
     input:
-        tuple val(meta), path(image)
+        tuple val(meta), path(anat)
     output:
         tuple val(meta), path("*_n4_second.nii.gz")          , emit: betready
         path "versions.yml"                                  , emit: versions
@@ -17,7 +17,7 @@ process MOUSE_PREPAREBET {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
 
-    N4BiasFieldCorrection -d 3 -i ${image} -o ${prefix}__n4_first.nii.gz -s 4 -c [20x20x10,1e-6]
+    N4BiasFieldCorrection -d 3 -i ${anat} -o ${prefix}__n4_first.nii.gz -s 4 -c [20x20x10,1e-6]
     N4BiasFieldCorrection -d 3 -i ${prefix}__n4_first.nii.gz -o ${prefix}__n4_second.nii.gz -s 2 -c [30x20x10,1e-6]
 
 
diff --git a/nextflow.config b/nextflow.config
index 0a09354..b1432ec 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -31,6 +31,7 @@ params {
     nvox_min = 100
 
     // FODF || QBALL
+    run_fodf_metrics = true
     use_fodf_for_tracking = false
     sh_order = 6
     min_fodf_value = 1000
@@ -228,6 +229,14 @@ profiles {
 
     pre_qc {
         params.run_preqc = true
+        params.use_preqc = true
+    }
+
+    invivo {
+        params.invivo = true
+        params.run_resampling = false
+        params.run_fodf_metrics = false
+        params.run_tracking = false
     }
 }
 

From 71408e581dffce40a1ede5c9889c55cdd5372041 Mon Sep 17 00:00:00 2001
From: EliseCos <elise.cosenza@u-bordeaux.fr>
Date: Thu, 30 Apr 2026 11:59:31 +0000
Subject: [PATCH 07/15] [ENH] correct main.nf + .config

---
 main.nf         | 33 ++++++++++++---------------------
 nextflow.config |  3 +++
 2 files changed, 15 insertions(+), 21 deletions(-)

diff --git a/main.nf b/main.nf
index e1fa1ca..213a179 100644
--- a/main.nf
+++ b/main.nf
@@ -149,34 +149,25 @@ workflow {
     else {
         ch_after_eddy = ch_eddy
     }
-    
-    UTILS_EXTRACTB0(ch_after_eddy)
 
     if (params.invivo) {
         BET(ch_bet)
         ch_mask = BET.out.mask
     }
+    else if ( params.data_masked ) {
+        ch_mask = data.mask
+    }
     else {
-        ch_eddy_with_optional_mask = ch_after_eddy
-            .join(data.mask, by: 0, remainder: true)
-
-        ch_mask_split = ch_eddy_with_optional_mask
-            .branch { meta, dwi, bval, bvec, mask ->
-                with_mask: mask != null
-                no_mask:   mask == null}
-
-        ch_mask_from_input = ch_mask_split.with_mask
-            .map { meta, dwi, bval, bvec, mask ->
-                tuple(meta, mask)}
-
-        ch_nnunet = ch_mask_split.no_mask
-            .join(UTILS_EXTRACTB0.out.b0)
-            .map { meta, dwi, bval, bvec, mask, b0 ->
-                tuple(meta, dwi, bval, b0, [])}
-    
+        UTILS_EXTRACTB0(ch_after_eddy)
+        ch_nnunet = ch_after_eddy.join(UTILS_EXTRACTB0.out.b0)
+        .join(data.mask, by: 0, remainder: true)
+                .map { meta, dwi, bval, bvec, b0, mask ->   
+                    [meta, dwi, bval, b0, mask ?: [   ]]}
+        
         NNUNET(ch_nnunet)
-        ch_mask = ch_mask_from_input.mix(NNUNET.out.mask)
-        }
+        
+        ch_mask = NNUNET.out.mask
+    }
 
     if ( params.run_n4 ) {
         ch_N4 = ch_after_eddy
diff --git a/nextflow.config b/nextflow.config
index b1432ec..056e928 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -15,6 +15,9 @@ params {
     run_eddy = true
     processes = 10
 
+    // Masked
+    data_masked = false
+    
     // Invivo
     invivo = false
     

From f45747a4b47de190dc74a5ee10b60c2a3d553ca0 Mon Sep 17 00:00:00 2001
From: EliseCos <elise.cosenza@u-bordeaux.fr>
Date: Mon, 4 May 2026 11:11:19 +0000
Subject: [PATCH 08/15] fix module b0

---
 main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 213a179..9cf520e 100644
--- a/main.nf
+++ b/main.nf
@@ -149,6 +149,7 @@ workflow {
     else {
         ch_after_eddy = ch_eddy
     }
+    UTILS_EXTRACTB0(ch_after_eddy)
 
     if (params.invivo) {
         BET(ch_bet)
@@ -158,7 +159,6 @@ workflow {
         ch_mask = data.mask
     }
     else {
-        UTILS_EXTRACTB0(ch_after_eddy)
         ch_nnunet = ch_after_eddy.join(UTILS_EXTRACTB0.out.b0)
         .join(data.mask, by: 0, remainder: true)
                 .map { meta, dwi, bval, bvec, b0, mask ->   

From 58e76b26ff8268903285fa239669e3bcc1cb4b2a Mon Sep 17 00:00:00 2001
From: EliseCos <elise.cosenza@u-bordeaux.fr>
Date: Mon, 4 May 2026 16:47:01 +0200
Subject: [PATCH 09/15] remove docker files

---
 assets/Docker/Dockerfile          | 40 -------------------------------
 assets/Docker/brain_extraction.py | 30 -----------------------
 2 files changed, 70 deletions(-)
 delete mode 100644 assets/Docker/Dockerfile
 delete mode 100644 assets/Docker/brain_extraction.py

diff --git a/assets/Docker/Dockerfile b/assets/Docker/Dockerfile
deleted file mode 100644
index c6e7d71..0000000
--- a/assets/Docker/Dockerfile
+++ /dev/null
@@ -1,40 +0,0 @@
-FROM scilus/scilus:2.2.0
-
-USER root
-
-WORKDIR /
-RUN --mount=type=cache,sharing=locked,target=/var/cache/apt \
-    apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \
-        build-essential gcc bc\
-        zlib1g-dev \
-        clinfo \
-        git \
-        libblas-dev \
-        libfreetype6-dev \
-        liblapack-dev \
-        locales \
-        imagemagick && \
-    rm -rf /var/lib/apt/lists/*
-
-WORKDIR /
-
-COPY maskbackgroundnoise /usr/bin/
-COPY ants_generate_iterations.py /ants/bin/
-RUN chmod 777 /ants/bin/ants_generate_iterations.py
-
-COPY ANO_taxonomy_EC_V4.csv /
-RUN chmod 777 /ANO_taxonomy_EC_V4.csv
-
-COPY mouse_extract_masks.py /usr/local/bin/
-RUN chmod 777 /usr/local/bin/mouse_extract_masks.py
-
-COPY brain_extraction.py /usr/local/bin/
-RUN chmod 777 /usr/local/bin/brain_extraction.py
-
-WORKDIR /
-ADD atlas.tar.gz /
-
-ARG NUMBA_CACHE_DIR
-ENV NUMBA_CACHE_DIR="/tmp"
-
-WORKDIR /
diff --git a/assets/Docker/brain_extraction.py b/assets/Docker/brain_extraction.py
deleted file mode 100644
index 5be1f5e..0000000
--- a/assets/Docker/brain_extraction.py
+++ /dev/null
@@ -1,30 +0,0 @@
-#! /usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-"""
-Extract the brain mask from an anatomical image using ants and antspynet.
-"""
-
-import argparse
-import os
-
-import ants
-import antspynet
-import argparse
-from antspynet import mouse_brain_extraction
-
-parser = argparse.ArgumentParser(description="")
-parser.add_argument('input_anat', type=str, help="Path to the anatomical image.")
-parser.add_argument('output_mask', type=str, help="Path to the output mask file.")
-
-args = parser.parse_args()
-
-filename_input=args.input_anat
-filename_output=args.output_mask
-
-mri_image = ants.image_read(filename_input)
-
-output = mouse_brain_extraction(mri_image,modality="t2")
-ants.image_write(output,filename_output)
-
-

From c63eb8f0409aa837002d5bc8cf41b1d76f37d21d Mon Sep 17 00:00:00 2001
From: EliseCos <elise.cosenza@u-bordeaux.fr>
Date: Mon, 4 May 2026 16:49:42 +0200
Subject: [PATCH 10/15] restore dockerfile

---
 assets/Docker/Dockerfile | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 assets/Docker/Dockerfile

diff --git a/assets/Docker/Dockerfile b/assets/Docker/Dockerfile
new file mode 100644
index 0000000..c6e7d71
--- /dev/null
+++ b/assets/Docker/Dockerfile
@@ -0,0 +1,40 @@
+FROM scilus/scilus:2.2.0
+
+USER root
+
+WORKDIR /
+RUN --mount=type=cache,sharing=locked,target=/var/cache/apt \
+    apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \
+        build-essential gcc bc\
+        zlib1g-dev \
+        clinfo \
+        git \
+        libblas-dev \
+        libfreetype6-dev \
+        liblapack-dev \
+        locales \
+        imagemagick && \
+    rm -rf /var/lib/apt/lists/*
+
+WORKDIR /
+
+COPY maskbackgroundnoise /usr/bin/
+COPY ants_generate_iterations.py /ants/bin/
+RUN chmod 777 /ants/bin/ants_generate_iterations.py
+
+COPY ANO_taxonomy_EC_V4.csv /
+RUN chmod 777 /ANO_taxonomy_EC_V4.csv
+
+COPY mouse_extract_masks.py /usr/local/bin/
+RUN chmod 777 /usr/local/bin/mouse_extract_masks.py
+
+COPY brain_extraction.py /usr/local/bin/
+RUN chmod 777 /usr/local/bin/brain_extraction.py
+
+WORKDIR /
+ADD atlas.tar.gz /
+
+ARG NUMBA_CACHE_DIR
+ENV NUMBA_CACHE_DIR="/tmp"
+
+WORKDIR /

From ba4bce2b27a6c8fae3786a328e5ad2dd47314f99 Mon Sep 17 00:00:00 2001
From: EliseCos <elise.cosenza@u-bordeaux.fr>
Date: Mon, 4 May 2026 18:57:11 +0200
Subject: [PATCH 11/15] remove mask nnunet

---
 assets/Docker/Dockerfile              |  3 ---
 main.nf                               |  5 ++---
 modules/local/mouse/betnnunet/main.nf | 21 ++++++++-------------
 3 files changed, 10 insertions(+), 19 deletions(-)

diff --git a/assets/Docker/Dockerfile b/assets/Docker/Dockerfile
index c6e7d71..18237a0 100644
--- a/assets/Docker/Dockerfile
+++ b/assets/Docker/Dockerfile
@@ -28,9 +28,6 @@ RUN chmod 777 /ANO_taxonomy_EC_V4.csv
 COPY mouse_extract_masks.py /usr/local/bin/
 RUN chmod 777 /usr/local/bin/mouse_extract_masks.py
 
-COPY brain_extraction.py /usr/local/bin/
-RUN chmod 777 /usr/local/bin/brain_extraction.py
-
 WORKDIR /
 ADD atlas.tar.gz /
 
diff --git a/main.nf b/main.nf
index 9cf520e..00e34a5 100644
--- a/main.nf
+++ b/main.nf
@@ -160,9 +160,8 @@ workflow {
     }
     else {
         ch_nnunet = ch_after_eddy.join(UTILS_EXTRACTB0.out.b0)
-        .join(data.mask, by: 0, remainder: true)
-                .map { meta, dwi, bval, bvec, b0, mask ->   
-                    [meta, dwi, bval, b0, mask ?: [   ]]}
+                .map { meta, dwi, bval, bvec, b0 ->   
+                    [meta, dwi, bval, b0 ?: [   ]]}
         
         NNUNET(ch_nnunet)
         
diff --git a/modules/local/mouse/betnnunet/main.nf b/modules/local/mouse/betnnunet/main.nf
index 851b19d..070fb3c 100644
--- a/modules/local/mouse/betnnunet/main.nf
+++ b/modules/local/mouse/betnnunet/main.nf
@@ -5,7 +5,7 @@ process MOUSE_BETNNUNET {
     container "scilus/nnunet_bet_mouse:0.1.0_cpu"
 
     input:
-        tuple val(meta), path(dwi), path(b0), path(mask)
+        tuple val(meta), path(dwi), path(b0)
     output:
         tuple val(meta), path("*__mask.nii.gz")      , emit: mask
         path "versions.yml"                          , emit: versions
@@ -17,21 +17,16 @@ process MOUSE_BETNNUNET {
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    if [[ -f "$mask" ]]
-    then
-        mv $mask ${prefix}__mask.nii.gz
-    else
 	export nnUNet_raw="Database/RAW/"
 	export nnUNet_preprocessed="Database/PRE/"
 	export nnUNet_results="Database/RESULTS/"
-        mkdir -p Database/RAW/Dataset012_ExVivoBrainFSboth/imagesTs
-        ln -s /Database/RAW/Dataset012_ExVivoBrainFSboth/dataset.json Database/RAW/Dataset012_ExVivoBrainFSboth/dataset.json
-        ln -s /Database/RESULTS Database/RESULTS
-        mv $b0 Database/RAW/Dataset012_ExVivoBrainFSboth/imagesTs/exvivobrain_000_0000.nii.gz
-        mv $dwi Database/RAW/Dataset012_ExVivoBrainFSboth/imagesTs/exvivobrain_000_0001.nii.gz
-        nnUNetv2_predict -i Database/RAW/Dataset012_ExVivoBrainFSboth/imagesTs -o ./ -d 012 -c 3d_fullres -f all -npp 1 -nps 1 -device 'cpu' -tr nnUNetTrainer -chk checkpoint_best.pth
-        mv exvivobrain_000.nii.gz ${prefix}__mask.nii.gz
-    fi  
+    mkdir -p Database/RAW/Dataset012_ExVivoBrainFSboth/imagesTs
+    ln -s /Database/RAW/Dataset012_ExVivoBrainFSboth/dataset.json Database/RAW/Dataset012_ExVivoBrainFSboth/dataset.json
+    ln -s /Database/RESULTS Database/RESULTS
+    mv $b0 Database/RAW/Dataset012_ExVivoBrainFSboth/imagesTs/exvivobrain_000_0000.nii.gz
+    mv $dwi Database/RAW/Dataset012_ExVivoBrainFSboth/imagesTs/exvivobrain_000_0001.nii.gz
+    nnUNetv2_predict -i Database/RAW/Dataset012_ExVivoBrainFSboth/imagesTs -o ./ -d 012 -c 3d_fullres -f all -npp 1 -nps 1 -device 'cpu' -tr nnUNetTrainer -chk checkpoint_best.pth
+    mv exvivobrain_000.nii.gz ${prefix}__mask.nii.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From 4b9d7acde6cb3de5f6b8327bb2907f872039c9e5 Mon Sep 17 00:00:00 2001
From: EliseCos <140726377+EliseCos@users.noreply.github.com>
Date: Fri, 8 May 2026 19:21:42 +0200
Subject: [PATCH 12/15] Delete subworkflows/.DS_Store

---
 subworkflows/.DS_Store | Bin 6148 -> 0 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 subworkflows/.DS_Store

diff --git a/subworkflows/.DS_Store b/subworkflows/.DS_Store
deleted file mode 100644
index 806193f8fc10dc7faa51772381bda09350c1dae8..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 6148
zcmeHK%}T>S5Z<+|O({YS3VK`cS}+A`DPBUYFJMFuDm5`hgE3p0)Er77cYPsW#OHBl
zcLOa3k0N#kcE8#A+0A^A{b7vp;XLdzW;4btXowt@3PE$FYs&;9ay3UB<mohsWl%BA
z-!$R3H(1Ohdtg3W{r-<&8b@j7IG=p0R&Q)Kt)|ts?z|_Ndzqij)1g1R!O^9ZaZu`h
za1~ARvAugHlgy8j$xJ0g;RHf%ucIWC`B2W2Fjcvpc33T|HMS2Hi*C>9cSNt>TXw`^
za6AD0#91y|*52XK>Baateo5q;W|9NtN_GsE@D9pKNw3~4iDmK#)-t1vBqRoi0b+m{
z*hmJ<abUGKvU)0-7$63IVgUCC0S(bLSZGvR2XuISMt>a<1$2B%APR%7!9pW=K)6l?
z)T!J&F}O|#yD)LC!9t@>XI!le^O%*(#|u}hgI%a_#$Aon69dG+Is-L5wDJ5uhhL`h
zk-wfoBVvFU_-738`p6p%p(t~<ek%{pS^@1I8Vbf0sDOaJb_sw1?j!rksr>?Vh;t1V
V8gUl1t8_rR2q;3RBL;qffiF(zOAP=3


From d341d41de0c85818ba2f18f0c72c425fbb099622 Mon Sep 17 00:00:00 2001
From: EliseCos <elise.cosenza@u-bordeaux.fr>
Date: Fri, 8 May 2026 19:23:50 +0200
Subject: [PATCH 13/15] add .gitignore file

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 .gitignore

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..496ee2c
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+.DS_Store
\ No newline at end of file

From c0f546e2e8d8af75223aad936404e3ff54613e2c Mon Sep 17 00:00:00 2001
From: EliseCos <elise.cosenza@u-bordeaux.fr>
Date: Tue, 12 May 2026 17:05:13 +0000
Subject: [PATCH 14/15] fix output registration

---
 nextflow.config | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index c5d0159..05bffac 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -337,7 +337,7 @@ process {
         ext.atlas_resolution = ""
         ext.run_qc = true
         publishDir = [
-            path: { "${params.outdir}/${meta.id}/anat/"},
+            [ path: { "${params.outdir}/${meta.id}/anat/"},
             saveAs: {
                 filename ->
                 if ( filename.contains("ANO.nii.gz") ) { "${meta.id}_atlas-Allen_desc-ANO_dseg.nii.gz"}
@@ -346,19 +346,18 @@ process {
                 else if ( filename.contains("0GenericAffine.mat") ) { "${meta.id}_from-Allen_to-dwi_affine.mat"}
                 else if ( filename.contains("1Warp.nii.gz") ) { "${meta.id}_from-Allen_to-dwi_warp.nii.gz"}
                 else if ( filename.contains("1InverseWarp.nii.gz") ) { "${meta.id}_from-dwi_to-Allen_warp.nii.gz"}
-                else if ( filename.contains("b0.nii.gz") ) { "${meta.id}_desc-process_b0.nii.gz"}
                 else if ( filename.contains("versions.yml") ) { null }
                 else { params.lean_output ? null : filename }
                 
-            },
-            path: { "${params.outdir}/${meta.id}/anat/"},
+            } ],
+            [ path: { "${params.outdir}/${meta.id}/dwi/"},
             saveAs: {
                 filename ->
                 if ( filename.contains("b0.nii.gz") ) { "${meta.id}_desc-process_b0.nii.gz"}
                 else if ( filename.contains("versions.yml") ) { null }
                 else { params.lean_output ? null : filename }
                 
-            }
+            }]
         ]
     }
 

From 1d2a6af6e623e261545fdf67a4d37e1d0ff05c32 Mon Sep 17 00:00:00 2001
From: EliseCos <elise.cosenza@u-bordeaux.fr>
Date: Fri, 15 May 2026 20:21:22 +0200
Subject: [PATCH 15/15] Answer Arnaud's comments

---
 modules/local/mouse/brainextraction/main.nf | 7 +++----
 modules/local/mouse/convertbet/main.nf      | 5 ++++-
 modules/local/mouse/register/main.nf        | 6 ++++--
 3 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/modules/local/mouse/brainextraction/main.nf b/modules/local/mouse/brainextraction/main.nf
index 04bd79f..2242f0b 100644
--- a/modules/local/mouse/brainextraction/main.nf
+++ b/modules/local/mouse/brainextraction/main.nf
@@ -21,18 +21,17 @@ process MOUSE_BRAINEXTRACTION {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+        ants: \$(antsMouseBrainExtraction --version 2>&1 | sed -n 's/ANTs Version: v\\([0-9.]\\+\\)/\\1/p')
     END_VERSIONS
     """
 
     stub:
     """
-    fslmaths
-    scil_volume_math -h
+    antsMouseBrainExtraction -h
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+        ants: \$(antsMouseBrainExtraction --version 2>&1 | sed -n 's/ANTs Version: v\\([0-9.]\\+\\)/\\1/p')
     END_VERSIONS
     """
 }
\ No newline at end of file
diff --git a/modules/local/mouse/convertbet/main.nf b/modules/local/mouse/convertbet/main.nf
index aebb95f..990d9d2 100644
--- a/modules/local/mouse/convertbet/main.nf
+++ b/modules/local/mouse/convertbet/main.nf
@@ -26,7 +26,9 @@ process MOUSE_CONVERTBET {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+	    scilpy: \$(uv -q -n pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+        fsl: \$(flirt -version 2>&1 | sed -n 's/FLIRT version \\([0-9.]\\+\\)/\\1/p')
+        ants: \$(ImageMath --version 2>&1 | sed -n 's/ANTs Version: v\\([0-9.]\\+\\)/\\1/p')
     END_VERSIONS
     """
 
@@ -43,6 +45,7 @@ process MOUSE_CONVERTBET {
     "${task.process}":
         scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
         fsl: \$(flirt -version 2>&1 | sed -n 's/FLIRT version \\([0-9.]\\+\\)/\\1/p')
+        ants: \$(ImageMath --version 2>&1 | sed -n 's/ANTs Version: v\\([0-9.]\\+\\)/\\1/p')
     END_VERSIONS
     """
 }
\ No newline at end of file
diff --git a/modules/local/mouse/register/main.nf b/modules/local/mouse/register/main.nf
index 01bfec9..0bf5cd7 100644
--- a/modules/local/mouse/register/main.nf
+++ b/modules/local/mouse/register/main.nf
@@ -184,8 +184,9 @@ process MOUSE_REGISTRATION {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-	scilpy: \$(uv -q -n pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+	    scilpy: \$(uv -q -n pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
         fsl: \$(flirt -version 2>&1 | sed -n 's/FLIRT version \\([0-9.]\\+\\)/\\1/p')
+        ants: \$(antsRegistration --version 2>&1 | sed -n 's/ANTs Version: v\\([0-9.]\\+\\)/\\1/p')
     END_VERSIONS
     """
 
@@ -206,9 +207,10 @@ process MOUSE_REGISTRATION {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-	scilpy: \$(uv -q -n pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+	    scilpy: \$(uv -q -n pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
         mrtrix: \$(dwidenoise -version 2>&1 | sed -n 's/== dwidenoise \\([0-9.]\\+\\).*/\\1/p')
         fsl: \$(flirt -version 2>&1 | sed -n 's/FLIRT version \\([0-9.]\\+\\)/\\1/p')
+        ants: \$(antsRegistration --version 2>&1 | sed -n 's/ANTs Version: v\\([0-9.]\\+\\)/\\1/p')
     END_VERSIONS
     """
 }