diff --git a/modules/nf-neuro/reconst/noddi/main.nf b/modules/nf-neuro/reconst/noddi/main.nf
index 56bcbd8d..d64d1898 100644
--- a/modules/nf-neuro/reconst/noddi/main.nf
+++ b/modules/nf-neuro/reconst/noddi/main.nf
@@ -31,14 +31,8 @@ process RECONST_NODDI {
     def set_kernels = kernels ? "--load_kernels $kernels" : "--save_kernels kernels/"
     def set_mask = mask ? "--mask $mask" : ""
     def compute_only = task.ext.compute_only && !kernels ? "--compute_only" : ""
-    def ignore_single_shell = task.ext.ignore_single_shell ?: false
 
     """
-    # Set home directory. This is problematic if the container is run
-    # with non-root user which does not create a home directory, whilst
-    # AMICO attempts to write in the home directory, raising an error.
-    export HOME=/tmp
-
     # Check if data are multi-shell based on b-values and set number of clusters accordingly
     # Set tolerance threshold (default 40 if not specified)
     b_threshold=${task.ext.b_thr ?: 40}
@@ -58,27 +52,29 @@ process RECONST_NODDI {
 
     if [ \$clusters -lt 3 ]; then
         echo "Error: NODDI reconstruction requires multi-shell data (at least 2 non-zero b-value shells). Detected only \$clusters shell(s) with b-values: \${uniq_bvals[@]}"
-        if [ "$ignore_single_shell" = "false" ]; then
-            exit 1
-        fi
+        exit 1
     else
         echo "Detected \$clusters unique b-value shells: \${uniq_bvals[@]}"
+    fi
 
+    # Set home directory. This is problematic if the container is run
+    # with non-root user which does not create a home directory, whilst
+    # AMICO attempts to write in the home directory, raising an error.
+    export HOME=/tmp
 
-        scil_NODDI_maps $dwi $bval $bvec $para_diff_str $iso_diff_str $lambda1 \
-            $lambda2 $nb_threads $b_thr $set_mask $set_kernels --skip_b0_check $compute_only
+    scil_NODDI_maps $dwi $bval $bvec $para_diff_str $iso_diff_str $lambda1 \
+        $lambda2 $nb_threads $b_thr $set_mask $set_kernels --skip_b0_check $compute_only
 
-        if [ -z "${compute_only}" ];
-        then
-            mv results/fit_dir.nii.gz ${prefix}__dir.nii.gz
-            mv results/fit_NDI.nii.gz ${prefix}__icvf.nii.gz    # ICVF -> NDI
-            mv results/fit_FWF.nii.gz ${prefix}__isovf.nii.gz   # ISOVF -> FWF
-            mv results/fit_ODI.nii.gz ${prefix}__odi.nii.gz     # ODI -> OD
+    if [ -z "${compute_only}" ];
+    then
+        mv results/fit_dir.nii.gz ${prefix}__dir.nii.gz
+        mv results/fit_NDI.nii.gz ${prefix}__icvf.nii.gz    # ICVF -> NDI
+        mv results/fit_FWF.nii.gz ${prefix}__isovf.nii.gz   # ISOVF -> FWF
+        mv results/fit_ODI.nii.gz ${prefix}__odi.nii.gz     # ODI -> OD
 
-            scil_volume_math subtraction 1 ${prefix}__isovf.nii.gz ${prefix}__ecvf.nii.gz
+        scil_volume_math subtraction 1 ${prefix}__isovf.nii.gz ${prefix}__ecvf.nii.gz
 
-            rm -rf results
-        fi
+        rm -rf results
     fi
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-neuro/reconst/noddi/meta.yml b/modules/nf-neuro/reconst/noddi/meta.yml
index 061a8e70..7fe53609 100644
--- a/modules/nf-neuro/reconst/noddi/meta.yml
+++ b/modules/nf-neuro/reconst/noddi/meta.yml
@@ -79,9 +79,7 @@ args:
   - compute_only:
       type: boolean
       description: Compute kernels only.
-  - ignore_single_shell:
-      type: boolean
-      description: Ignore single shell data instead of raising an error. With this flag enabled, simply no output will be produced for single shell data.
+
 output:
   dir:
     - - meta:
diff --git a/subworkflows/nf-neuro/reconst_fw_noddi/main.nf b/subworkflows/nf-neuro/reconst_fw_noddi/main.nf
index 05cc8483..85d77930 100644
--- a/subworkflows/nf-neuro/reconst_fw_noddi/main.nf
+++ b/subworkflows/nf-neuro/reconst_fw_noddi/main.nf
@@ -197,6 +197,13 @@ workflow RECONST_FW_NODDI {
             ch_noddi_input = ch_noddi_custom_subj
                 .mix( ch_noddi_custom )
                 .mix( ch_noddi_computed )
+                .filter{ _meta, _dwi, bval, _bvec, _b0_mask, _para, _iso ->
+                    def is_multi_shell = bval.text.tokenize().unique().size() > 2
+                    if (!is_multi_shell && !options.silence_single_shell_warnings){
+                        log.warn "Subject ${_meta.id} has single-shell data. Skipping NODDI reconstruction."
+                    }
+                    return is_multi_shell
+                }
                 .map{ meta, dwi, bval, bvec, b0_mask, para, iso ->
                     [meta, dwi, bval, bvec, b0_mask, [], para, iso] }
 
diff --git a/subworkflows/nf-neuro/reconst_fw_noddi/meta.yml b/subworkflows/nf-neuro/reconst_fw_noddi/meta.yml
index a1d1e8f0..f90439b6 100644
--- a/subworkflows/nf-neuro/reconst_fw_noddi/meta.yml
+++ b/subworkflows/nf-neuro/reconst_fw_noddi/meta.yml
@@ -113,6 +113,10 @@ input:
           type: boolean
           description: If 'true', the diffusivity priors computed from the RECONST/DIFFUSIVITYPRIORS module will be averaged across all subjects. (Recommended)
           default: false
+        silence_single_shell_warnings:
+          type: boolean
+          description: If 'true', the workflow will silence warnings about single-shell data (e.g. when filtering subjects for NODDI).
+          default: false
       mandatory: false
 output:
   - noddi_dir: