More work.

docs/usage.rst

@@ -4,6 +4,12 @@
 
 Usage Notes
 ===========
+
+.. warning::
+   *fMRIPost-AROMA* requires preprocessing outputs in MNI152NLin6Asym space with
+   2 mm3 voxels (i.e., ``res-02``).
+   Make sure you run fMRIPrep with ``--output-spaces MNI152NLin6Asym:res-02``.
+
 .. warning::
    *fMRIPost-AROMA* includes a tracking system to report usage statistics and errors
    for debugging and grant reporting purposes.

src/fmripost_aroma/interfaces/resampler.py

@@ -36,12 +36,7 @@ class _ResamplerOutputSpec(TraitedSpec):
 
 
 class Resampler(SimpleInterface):
-    """Extract timeseries and compute connectivity matrices.
-
-    Write out time series using Nilearn's NiftiLabelMasker
-    Then write out functional correlation matrix of
-    timeseries using numpy.
-    """
+    """Apply the resampler workflow."""
 
     input_spec = _ResamplerInputSpec
     output_spec = _ResamplerOutputSpec

src/fmripost_aroma/workflows/base.py

@@ -343,6 +343,27 @@ def init_single_run_wf(bold_file):
             ),
         )
 
+    config.loggers.workflow.info(
+        (
+            f'Collected run data for {os.path.basename(bold_file)}:\n'
+            f'{yaml.dump(functional_cache, default_flow_style=False, indent=4)}'
+        ),
+    )
+
+    if config.workflow.dummy_scans is not None:
+        skip_vols = config.workflow.dummy_scans
+    else:
+        if not functional_cache['confounds']:
+            raise ValueError(
+                'No confounds detected. '
+                'Automatical dummy scan detection cannot be performed. '
+                'Please set the `--dummy-scans` flag explicitly.'
+            )
+        skip_vols = get_nss(functional_cache['confounds'])
+
+    ica_aroma_wf.inputs.inputnode.confounds = functional_cache['confounds']
+    ica_aroma_wf.inputs.inputnode.skip_vols = skip_vols
+
     mni6_buffer = pe.Node(
         niu.IdentityInterface(
             fields=['bold_mni152nlin6asym', 'bold_mask_mni152nlin6asym'],
@@ -381,27 +402,6 @@ def init_single_run_wf(bold_file):
         ]),
     ])  # fmt:skip
 
-    config.loggers.workflow.info(
-        (
-            f'Collected run data for {os.path.basename(bold_file)}:\n'
-            f'{yaml.dump(functional_cache, default_flow_style=False, indent=4)}'
-        ),
-    )
-
-    if config.workflow.dummy_scans is not None:
-        skip_vols = config.workflow.dummy_scans
-    else:
-        if not functional_cache['confounds']:
-            raise ValueError(
-                'No confounds detected. '
-                'Automatical dummy scan detection cannot be performed. '
-                'Please set the `--dummy-scans` flag explicitly.'
-            )
-        skip_vols = get_nss(functional_cache['confounds'])
-
-    ica_aroma_wf.inputs.inputnode.confounds = functional_cache['confounds']
-    ica_aroma_wf.inputs.inputnode.skip_vols = skip_vols
-
     if config.workflow.denoise_method:
         # Now denoise the output-space BOLD data using ICA-AROMA
         denoise_wf = init_denoise_wf(bold_file=bold_file)