diff --git a/conf/modules/preproc_dwi.config b/conf/modules/preproc_dwi.config
index af5ff19..26cd73a 100644
--- a/conf/modules/preproc_dwi.config
+++ b/conf/modules/preproc_dwi.config
@@ -33,8 +33,8 @@ process {
     withName: ".*:TRACTOFLOW:PREPROC_DWI:TOPUP_EDDY:PREPROC_TOPUP" {
         ext.prefix_topup            = params.prefix_topup
         ext.default_config_topup    = params.config_topup
-        ext.encoding                = params.encoding_direction  //FIXME : this is subject bound, pass through meta ?
-        ext.readout                 = params.readout             //FIXME : this is subject bound, pass through meta ?
+        ext.encoding                = params.encoding_direction
+        ext.readout                 = params.readout
         ext.b0_thr_extract_b0       = params.b0_thr_extract_b0
     }
 
@@ -46,8 +46,9 @@ process {
         ext.dilate_b0_mask_prelim_brain_extraction  = params.dilate_b0_mask_prelim_brain_extraction
         ext.bet_prelim_f                            = params.bet_prelim_f
         ext.b0_thr_extract_b0                       = params.b0_thr_extract_b0
-        ext.encoding                                = params.encoding_direction  //FIXME : this is subject bound, pass through meta ?
-        ext.readout                                 = params.readout //FIXME : this is subject bound, pass through meta ?
+        ext.encoding                                = params.encoding_direction
+        ext.readout                                 = params.readout
+        ext.extra_args                              = params.eddy_extra_args
         ext.run_qc                                  = true
         publishDir = [
             path: { meta.session ? "${params.outdir}/${meta.id}/${meta.session}/dwi/" : "${params.outdir}/${meta.id}/dwi/" },
diff --git a/modules.json b/modules.json
index bd00b1b..98774ba 100644
--- a/modules.json
+++ b/modules.json
@@ -147,7 +147,7 @@
                     },
                     "preproc/eddy": {
                         "branch": "main",
-                        "git_sha": "31193a9ea0839d2ce29898504812ffdb515b67dc",
+                        "git_sha": "d8b76bf2572247daced80a770df4bd36204480c1",
                         "installed_by": ["topup_eddy"]
                     },
                     "preproc/gibbs": {
@@ -167,7 +167,7 @@
                     },
                     "preproc/topup": {
                         "branch": "main",
-                        "git_sha": "cada787da3b1857454bcfbb49038d438b375b990",
+                        "git_sha": "cd43a735aebf4742acb0186597917bbeb1da9860",
                         "installed_by": ["topup_eddy"]
                     },
                     "qc/multiqc": {
@@ -366,7 +366,7 @@
                     },
                     "preproc_dwi": {
                         "branch": "main",
-                        "git_sha": "e08971ac9ff68fd7df4c52fa6a1bce1db8162a03",
+                        "git_sha": "d50587b763e4dc6932b3f44e96688d5ff8f0d303",
                         "installed_by": ["tractoflow"]
                     },
                     "preproc_t1": {
@@ -386,12 +386,12 @@
                     },
                     "topup_eddy": {
                         "branch": "main",
-                        "git_sha": "913afe95df67300a0e9434374a59b866449f277b",
+                        "git_sha": "7755bea10e388c2f47412f99e383e41695662b21",
                         "installed_by": ["preproc_dwi"]
                     },
                     "tractoflow": {
                         "branch": "main",
-                        "git_sha": "bd3302172e63f11c08db8ebb22f8653dfff21af7",
+                        "git_sha": "d50587b763e4dc6932b3f44e96688d5ff8f0d303",
                         "installed_by": ["subworkflows"]
                     },
                     "tractometry": {
diff --git a/modules/nf-neuro/preproc/eddy/main.nf b/modules/nf-neuro/preproc/eddy/main.nf
index 520b9c3..1c925ed 100644
--- a/modules/nf-neuro/preproc/eddy/main.nf
+++ b/modules/nf-neuro/preproc/eddy/main.nf
@@ -12,6 +12,7 @@ process PREPROC_EDDY {
         tuple val(meta), path("*__dwi_eddy_corrected.bval")             , emit: bval_corrected
         tuple val(meta), path("*__dwi_eddy_corrected.bvec")             , emit: bvec_corrected
         tuple val(meta), path("*__b0_bet_mask.nii.gz")                  , emit: b0_mask
+        tuple val(meta), env("nan_percentage")                          , emit: nan_percentage
         tuple val(meta), path("*__dwi_eddy_mqc.gif")                    , emit: dwi_eddy_mqc, optional:true
         tuple val(meta), path("*__rev_dwi_eddy_mqc.gif")                , emit: rev_dwi_eddy_mqc, optional:true
         tuple val(meta), path("*__dwi_eddy_restricted_movement_rms.txt"), emit: eddy_fd_mqc, optional:true
@@ -26,8 +27,8 @@ process PREPROC_EDDY {
     def bet_topup_before_eddy_f = task.ext.bet_topup_before_eddy_f ?: ""
     def prefix_topup = task.ext.prefix_topup ? task.ext.prefix_topup : ""
     def b0_thr_extract_b0 = task.ext.b0_thr_extract_b0 ? task.ext.b0_thr_extract_b0 : ""
-    def encoding = task.ext.encoding ? task.ext.encoding : ""
-    def readout = task.ext.readout ? task.ext.readout : ""
+    def encoding = meta.dir ?: (task.ext.encoding ?: "")
+    def readout = meta.readout ?: (task.ext.readout ?: "")
     def dilate_b0_mask_prelim_brain_extraction = task.ext.dilate_b0_mask_prelim_brain_extraction ? task.ext.dilate_b0_mask_prelim_brain_extraction : ""
     def eddy_cmd = task.ext.eddy_cmd ? task.ext.eddy_cmd : "eddy_cpu"
     def bet_prelim_f = task.ext.bet_prelim_f ? task.ext.bet_prelim_f : ""
@@ -45,6 +46,8 @@ process PREPROC_EDDY {
     export ANTS_RANDOM_SEED=${task.ext.ants_rng_seed ? task.ext.ants_rng_seed : "1234"}
     export MRTRIX_RNG_SEED=${task.ext.mrtrix_rng_seed ? task.ext.mrtrix_rng_seed : "1234"}
 
+    nan_percentage=0
+
     orig_bval=$bval
     # Concatenate DWIs
     number_rev_dwi=0
@@ -112,6 +115,16 @@ process PREPROC_EDDY {
     # Rename framewise displacement file to include subject id
     mv dwi_eddy_corrected.eddy_restricted_movement_rms ${prefix}__dwi_eddy_restricted_movement_rms.txt
 
+    nb_voxels=\$(mrstats ${prefix}__dwi_corrected.nii.gz -mask ${prefix}__b0_bet_mask.nii.gz -quiet -output count -allvolumes)
+    nb_nan=\$(mrcalc ${prefix}__dwi_corrected.nii.gz  -isnan - | mrstats - -quiet -output count -ignorezero -allvolumes)
+    nan_percentage=\$(awk "BEGIN {print \${nb_nan} * 100 / \${nb_voxels}}")
+
+    if [[ \${nan_percentage} -gt 0 ]];
+    then
+        echo "Warning: \${nan_percentage}% of voxels in the brain mask are NaN after eddy correction."
+        mrcalc ${prefix}__dwi_corrected.nii.gz -finite ${prefix}__dwi_corrected.nii.gz 0.0 -if ${prefix}__dwi_corrected.nii.gz -force
+    fi
+
     if $run_qc;
     then
         extract_dim=\$(mrinfo ${dwi} -size)
@@ -214,6 +227,7 @@ process PREPROC_EDDY {
     touch ${prefix}__dwi_eddy_corrected.bvec
     touch ${prefix}__b0_bet_mask.nii.gz
     touch ${prefix}__dwi_eddy_restricted_movement_rms.txt
+    nan_percentage=1
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-neuro/preproc/eddy/meta.yml b/modules/nf-neuro/preproc/eddy/meta.yml
index 0043d25..cee1447 100644
--- a/modules/nf-neuro/preproc/eddy/meta.yml
+++ b/modules/nf-neuro/preproc/eddy/meta.yml
@@ -184,6 +184,16 @@ output:
           pattern: "*__b0_bet_mask.nii.gz"
           ontologies:
             - edam: http://edamontology.org/format_3989 # GZIP format
+  nan_percentage:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - nan_percentage:
+          type: float
+          description: Percentage of NaN voxels in the brain mask after Eddy correction.
+          ontologies: []
   dwi_eddy_mqc:
     - - meta:
           type: map
diff --git a/modules/nf-neuro/preproc/eddy/tests/main.nf.test b/modules/nf-neuro/preproc/eddy/tests/main.nf.test
index 0fdcfcb..066bae4 100644
--- a/modules/nf-neuro/preproc/eddy/tests/main.nf.test
+++ b/modules/nf-neuro/preproc/eddy/tests/main.nf.test
@@ -32,7 +32,7 @@ nextflow_process {
                 """
                 input[0] = LOAD_DATA.out.test_data_directory
                     .map{ test_data_directory -> [
-                    [ id:'test', session:'ses-01' ], // meta map
+                    [ id:'test', session:'ses-01', dir:'y', readout:0.062 ], // meta map
                     file("\${test_data_directory}/sub-01_dir-AP_dwi.nii.gz", checkIfExists: true),
                     file("\${test_data_directory}/sub-01_dir-AP_dwi.bval", checkIfExists: true),
                     file("\${test_data_directory}/sub-01_dir-AP_dwi.bvec", checkIfExists: true),
@@ -55,6 +55,7 @@ nextflow_process {
                     process.out.bval_corrected,
                     file(process.out.bvec_corrected.get(0).get(1)).name,
                     process.out.b0_mask,
+                    process.out.nan_percentage,
                     file(process.out.dwi_eddy_mqc.get(0).get(1)).name,
                     file(process.out.rev_dwi_eddy_mqc.get(0).get(1)).name,
                     file(process.out.eddy_fd_mqc.get(0).get(1)).name,
@@ -91,6 +92,7 @@ nextflow_process {
                     process.out.bval_corrected,
                     file(process.out.bvec_corrected.get(0).get(1)).name,
                     process.out.b0_mask,
+                    process.out.nan_percentage,
                     file(process.out.dwi_eddy_mqc.get(0).get(1)).name,
                     file(process.out.eddy_fd_mqc.get(0).get(1)).name,
                     process.out.versions
diff --git a/modules/nf-neuro/preproc/eddy/tests/main.nf.test.snap b/modules/nf-neuro/preproc/eddy/tests/main.nf.test.snap
index c4bfb7f..2b84200 100644
--- a/modules/nf-neuro/preproc/eddy/tests/main.nf.test.snap
+++ b/modules/nf-neuro/preproc/eddy/tests/main.nf.test.snap
@@ -6,7 +6,9 @@
                 [
                     {
                         "id": "test",
-                        "session": "ses-01"
+                        "session": "ses-01",
+                        "dir": "y",
+                        "readout": 0.062
                     },
                     "test_ses-01__dwi_eddy_corrected.bval:md5,4c61c53078316c31b4d5daf446a3d6ac"
                 ]
@@ -16,11 +18,24 @@
                 [
                     {
                         "id": "test",
-                        "session": "ses-01"
+                        "session": "ses-01",
+                        "dir": "y",
+                        "readout": 0.062
                     },
                     "test_ses-01__b0_bet_mask.nii.gz:md5,884e1028fb86b5556e1caac18a8d6e1f"
                 ]
             ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "session": "ses-01",
+                        "dir": "y",
+                        "readout": 0.062
+                    },
+                    "0"
+                ]
+            ],
             "test_ses-01__dwi_eddy_mqc.gif",
             "test_ses-01__rev_dwi_eddy_mqc.gif",
             "test_ses-01__dwi_eddy_restricted_movement_rms.txt",
@@ -32,7 +47,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2026-02-26T22:15:32.652065952"
+        "timestamp": "2026-05-05T11:37:36.006704402"
     },
     "eddy_light": {
         "content": [
@@ -54,6 +69,14 @@
                     "test__b0_bet_mask.nii.gz:md5,884e1028fb86b5556e1caac18a8d6e1f"
                 ]
             ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "0"
+                ]
+            ],
             "test__dwi_eddy_mqc.gif",
             "test__dwi_eddy_restricted_movement_rms.txt",
             [
@@ -64,7 +87,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2026-02-26T22:16:33.991059908"
+        "timestamp": "2026-05-05T11:39:42.9821212"
     },
     "eddy - stub-run": {
         "content": [
diff --git a/modules/nf-neuro/preproc/topup/main.nf b/modules/nf-neuro/preproc/topup/main.nf
index 2dc977a..0199602 100644
--- a/modules/nf-neuro/preproc/topup/main.nf
+++ b/modules/nf-neuro/preproc/topup/main.nf
@@ -26,8 +26,8 @@ process PREPROC_TOPUP {
 
     def prefix_topup = task.ext.prefix_topup ?: ""
     config_topup = config_topup ?: task.ext.default_config_topup
-    def encoding = task.ext.encoding ?: ""
-    def readout = task.ext.readout ?: ""
+    def encoding = meta.dir ?: (task.ext.encoding ?: "")
+    def readout = meta.readout ?: (task.ext.readout ?: "")
     def b0_thr_extract_b0 = task.ext.b0_thr_extract_b0 ?: ""
     def run_qc = task.ext.run_qc
     def nthreads = task.ext.single_thread ? 1 : task.cpus
diff --git a/modules/nf-neuro/preproc/topup/tests/main.nf.test b/modules/nf-neuro/preproc/topup/tests/main.nf.test
index 16dc015..f6cc4c0 100644
--- a/modules/nf-neuro/preproc/topup/tests/main.nf.test
+++ b/modules/nf-neuro/preproc/topup/tests/main.nf.test
@@ -32,7 +32,7 @@ nextflow_process {
                 """
                 input[0] = LOAD_DATA.out.test_data_directory
                     .map{ test_data_directory -> [
-                    [ id:'test', single_end:false ], // meta map
+                    [ id:'test', single_end:false, dir:'y', readout:0.062 ], // meta map
                     file("\${test_data_directory}/sub-01_dir-AP_dwi.nii.gz", checkIfExists: true),
                     file("\${test_data_directory}/sub-01_dir-AP_dwi.bval", checkIfExists: true),
                     file("\${test_data_directory}/sub-01_dir-AP_dwi.bvec", checkIfExists: true),
diff --git a/modules/nf-neuro/preproc/topup/tests/main.nf.test.snap b/modules/nf-neuro/preproc/topup/tests/main.nf.test.snap
index 60d2690..59a43b1 100644
--- a/modules/nf-neuro/preproc/topup/tests/main.nf.test.snap
+++ b/modules/nf-neuro/preproc/topup/tests/main.nf.test.snap
@@ -21,7 +21,9 @@
                 [
                     {
                         "id": "test",
-                        "single_end": false
+                        "single_end": false,
+                        "dir": "y",
+                        "readout": 0.062
                     },
                     "test__rev_b0_mean.nii.gz:md5,a0c63d7a8a234d85eeb63045ae2a8f60"
                 ]
@@ -30,7 +32,9 @@
                 [
                     {
                         "id": "test",
-                        "single_end": false
+                        "single_end": false,
+                        "dir": "y",
+                        "readout": 0.062
                     },
                     "test__b0_mean.nii.gz:md5,f50e652bcdd1d45f7a4c592df7eb851a"
                 ]
@@ -45,7 +49,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2026-02-26T22:18:29.533803801"
+        "timestamp": "2026-05-05T07:41:24.661738077"
     },
     "topup - AP DWI | PA sbref": {
         "content": [
diff --git a/nextflow.config b/nextflow.config
index 436f6b5..650c5f2 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -46,6 +46,8 @@ params {
     bet_topup_before_eddy_f                         = 0.16
     use_slice_drop_correction                       = true
     bet_dwi_final_f                                 = 0.16
+    eddy_nan_threshold                              = 0
+    eddy_extra_args                                 = "" 
 
     //**DWI: N4 bias correction options**//
     run_dwi_N4                                      = true
@@ -465,18 +467,22 @@ process.shell = [
 nextflow.enable.configProcessNamesValidation = false
 
 timeline {
+    overwrite = true
     enabled = true
     file    = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html"
 }
 report {
+    overwrite = true
     enabled = true
     file    = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html"
 }
 trace {
+    overwrite = true
     enabled = true
     file    = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt"
 }
 dag {
+    overwrite = true
     enabled = true
     file    = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html"
 }
diff --git a/nextflow_schema.json b/nextflow_schema.json
index b50891d..08c4562 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -199,6 +199,13 @@
                     "help_text": "Run Gibbs correction.",
                     "default": true
                 },
+                "eddy_nan_threshold": {
+                    "type": "number",
+                    "default": 0,
+                    "description": "Eddy nan threshold. If the number of voxels with NaN values after Eddy correction is above this threshold, the Eddy correction will be considered as failed and the uncorrected DWI will be used for the next steps.",
+                    "help_text": "Eddy nan threshold. If the number of voxels with NaN values after Eddy correction is above this threshold, the Eddy correction will be considered as failed and the uncorrected DWI will be used for the next steps.",
+                    "minimum": 0
+                },
                 "run_topup": {
                     "type": "boolean",
                     "default": true,
diff --git a/subworkflows/nf-neuro/preproc_dwi/main.nf b/subworkflows/nf-neuro/preproc_dwi/main.nf
index 3df2c68..2beae4c 100644
--- a/subworkflows/nf-neuro/preproc_dwi/main.nf
+++ b/subworkflows/nf-neuro/preproc_dwi/main.nf
@@ -117,6 +117,7 @@ workflow PREPROC_DWI {
                 ch_rev_b0,
                 ch_config_topup.ifEmpty( "b02b0.cnf" ),
                 [
+                    "eddy_nan_threshold": options.eddy_nan_threshold,
                     "topup_eddy_run_topup": options.topup_eddy_run_topup,
                     "topup_eddy_run_eddy": options.topup_eddy_run_eddy
                 ] )
diff --git a/subworkflows/nf-neuro/preproc_dwi/meta.yml b/subworkflows/nf-neuro/preproc_dwi/meta.yml
index 419fb9e..de2e918 100644
--- a/subworkflows/nf-neuro/preproc_dwi/meta.yml
+++ b/subworkflows/nf-neuro/preproc_dwi/meta.yml
@@ -193,6 +193,10 @@ input:
           type: boolean
           description: Remove Gibbs artifacts using the mrdegibbs method from MRtrix3.
           default: true
+        eddy_nan_threshold:
+          type: float
+          description: Threshold for the percentage of NaN voxels in the brain mask after Eddy correction to raise a warning.
+          default: 0
         topup_eddy_run_topup:
           type: boolean
           description: Perform Topup correction using FSL's Topup.
diff --git a/subworkflows/nf-neuro/preproc_dwi/tests/main.nf.test b/subworkflows/nf-neuro/preproc_dwi/tests/main.nf.test
index 9ee851d..d775e8b 100644
--- a/subworkflows/nf-neuro/preproc_dwi/tests/main.nf.test
+++ b/subworkflows/nf-neuro/preproc_dwi/tests/main.nf.test
@@ -58,6 +58,7 @@ nextflow_workflow {
                 input[4] = channel.empty()
                 input[5] = channel.from( [] )
                 input[6] = [
+                    "eddy_nan_threshold": 0,
                     "topup_eddy_run_topup": false,
                     "topup_eddy_run_eddy": false,
                     "preproc_dwi_run_denoising": false,
diff --git a/subworkflows/nf-neuro/topup_eddy/main.nf b/subworkflows/nf-neuro/topup_eddy/main.nf
index 6d61ea3..2369624 100644
--- a/subworkflows/nf-neuro/topup_eddy/main.nf
+++ b/subworkflows/nf-neuro/topup_eddy/main.nf
@@ -85,6 +85,13 @@ workflow TOPUP_EDDY {
 
             // ** RUN EDDY **//
             PREPROC_EDDY ( ch_eddy_input )
+
+            PREPROC_EDDY.out.nan_percentage.subscribe { meta, nan_percentage ->
+                if (nan_percentage.toFloat() > options.eddy_nan_threshold) {
+                    log.warn "Subject ${meta.id} has ${nan_percentage}% of voxels in the brain mask that are NaN after eddy correction."
+                }
+            }
+
             ch_versions = ch_versions.mix(PREPROC_EDDY.out.versions.first())
             ch_multiqc_files = ch_multiqc_files.mix(PREPROC_EDDY.out.dwi_eddy_mqc)
             ch_multiqc_files = ch_multiqc_files.mix(PREPROC_EDDY.out.rev_dwi_eddy_mqc)
diff --git a/subworkflows/nf-neuro/topup_eddy/meta.yml b/subworkflows/nf-neuro/topup_eddy/meta.yml
index ba4a42a..5291a1f 100644
--- a/subworkflows/nf-neuro/topup_eddy/meta.yml
+++ b/subworkflows/nf-neuro/topup_eddy/meta.yml
@@ -103,6 +103,10 @@ input:
       description: Map of options for the topup_eddy subworkflow.
       mandatory: false
       entries:
+        eddy_nan_threshold:
+          type: integer
+          description: Threshold for the percentage of NaN voxels in the brain mask after Eddy correction to raise a warning.
+          default: 0
         topup_eddy_run_topup:
           type: boolean
           description: Run FSL Topup for distorsion correction.
diff --git a/subworkflows/nf-neuro/topup_eddy/tests/main.nf.test b/subworkflows/nf-neuro/topup_eddy/tests/main.nf.test
index d4503f8..77c9fd8 100644
--- a/subworkflows/nf-neuro/topup_eddy/tests/main.nf.test
+++ b/subworkflows/nf-neuro/topup_eddy/tests/main.nf.test
@@ -54,7 +54,8 @@ nextflow_workflow {
                 input[4] = channel.from( [] )
                 input[5] = [
                     "topup_eddy_run_topup": false,
-                    "topup_eddy_run_eddy": true
+                    "topup_eddy_run_eddy": true,
+                    "eddy_nan_threshold": 0
                 ]
                 """
             }
@@ -109,7 +110,8 @@ nextflow_workflow {
                 input[4] = channel.from( [] )
                 input[5] = [
                     "topup_eddy_run_topup": true,
-                    "topup_eddy_run_eddy": true
+                    "topup_eddy_run_eddy": true,
+                    "eddy_nan_threshold": 0
                 ]
                 """
             }
@@ -163,7 +165,8 @@ nextflow_workflow {
                 input[4] = channel.from( [] )
                 input[5] = [
                     "topup_eddy_run_topup": true,
-                    "topup_eddy_run_eddy": true
+                    "topup_eddy_run_eddy": true,
+                    "eddy_nan_threshold": 0
                 ]
                 """
             }
diff --git a/subworkflows/nf-neuro/topup_eddy/tests/main.nf.test.snap b/subworkflows/nf-neuro/topup_eddy/tests/main.nf.test.snap
index dc33dc6..ecd1227 100644
--- a/subworkflows/nf-neuro/topup_eddy/tests/main.nf.test.snap
+++ b/subworkflows/nf-neuro/topup_eddy/tests/main.nf.test.snap
@@ -72,7 +72,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2026-02-26T22:23:35.547426618"
+        "timestamp": "2026-05-05T11:09:28.468045361"
     },
     "topup_eddy - ONLY Eddy - AP DWI | PA sbref": {
         "content": [
@@ -147,7 +147,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2026-02-26T22:23:17.16712078"
+        "timestamp": "2026-05-05T11:08:54.916655227"
     },
     "topup_eddy - AP DWI+sbref | PA DWI+sbref": {
         "content": [
@@ -222,6 +222,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2026-02-26T22:23:53.777548866"
+        "timestamp": "2026-05-05T11:09:59.718470744"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-neuro/tractoflow/main.nf b/subworkflows/nf-neuro/tractoflow/main.nf
index 1a1e842..9aa0b07 100644
--- a/subworkflows/nf-neuro/tractoflow/main.nf
+++ b/subworkflows/nf-neuro/tractoflow/main.nf
@@ -122,6 +122,7 @@ workflow TRACTOFLOW {
             [
                 "preproc_dwi_run_denoising": options.preproc_dwi_run_denoising,
                 "preproc_dwi_run_degibbs": options.preproc_dwi_run_degibbs,
+                "eddy_nan_threshold": options.eddy_nan_threshold,
                 "topup_eddy_run_topup": options.topup_eddy_run_topup,
                 "topup_eddy_run_eddy": options.topup_eddy_run_eddy,
                 "preproc_dwi_run_N4": options.preproc_dwi_run_N4,
diff --git a/subworkflows/nf-neuro/tractoflow/meta.yml b/subworkflows/nf-neuro/tractoflow/meta.yml
index 4df78fb..5ac7a14 100644
--- a/subworkflows/nf-neuro/tractoflow/meta.yml
+++ b/subworkflows/nf-neuro/tractoflow/meta.yml
@@ -546,6 +546,10 @@ input:
           type: boolean
           description: If 'true', the Gibbs artifact removal will be performed using the mrdegibbs method from MRtrix3.
           default: true
+        eddy_nan_threshold:
+          type: float
+          description: Threshold for the percentage of NaN voxels in the brain mask after Eddy correction to raise a warning.
+          default: 0
         topup_eddy_run_topup:
           type: boolean
           description: If 'true', the Topup correction will be performed using FSL's Topup.
diff --git a/subworkflows/nf-neuro/tractoflow/tests/main.nf.test b/subworkflows/nf-neuro/tractoflow/tests/main.nf.test
index 47a82ea..1af9e33 100644
--- a/subworkflows/nf-neuro/tractoflow/tests/main.nf.test
+++ b/subworkflows/nf-neuro/tractoflow/tests/main.nf.test
@@ -95,6 +95,7 @@ nextflow_workflow {
                 input[12] = [
                     "preproc_dwi_run_denoising": true,
                     "preproc_dwi_run_degibbs": false,
+                    "eddy_nan_threshold": 0,
                     "topup_eddy_run_topup": true,
                     "topup_eddy_run_eddy": true,
                     "preproc_dwi_run_N4": true,
diff --git a/workflows/sf-tractomics.nf b/workflows/sf-tractomics.nf
index 56acfe6..80ff67c 100644
--- a/workflows/sf-tractomics.nf
+++ b/workflows/sf-tractomics.nf
@@ -104,6 +104,7 @@ workflow SF_TRACTOMICS {
         [
             "preproc_dwi_run_denoising": params.run_dwi_denoising,
             "preproc_dwi_run_degibbs": params.run_gibbs_correction,
+            "eddy_nan_threshold": params.eddy_nan_threshold,
             "topup_eddy_run_topup": params.run_topup,
             "topup_eddy_run_eddy": params.run_eddy,
             "preproc_dwi_run_synthstrip": params.run_dwi_synthstrip,