update eddy subworkflow

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/" },

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": {

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}":

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

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

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": [

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

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),

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": [

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"
 }

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,

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
                 ] )

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.

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,

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)

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.