Get it building at least.

src/fmripost_aroma/cli/workflow.py

@@ -40,7 +40,6 @@ def build_workflow(config_file, retval):
     from fmriprep.utils.misc import check_deps
     from nireports.assembler.tools import generate_reports
     from niworkflows.utils.bids import collect_participants
-    from niworkflows.utils.misc import check_valid_fs_license
     from pkg_resources import resource_filename as pkgrf
 
     from fmripost_aroma import config
@@ -116,30 +115,6 @@ def build_workflow(config_file, retval):
 
     retval['workflow'] = init_fmripost_aroma_wf()
 
-    # Check for FS license after building the workflow
-    if not check_valid_fs_license():
-        from fmripost_aroma.utils.misc import fips_enabled
-
-        if fips_enabled():
-            build_log.critical(
-                """\
-ERROR: Federal Information Processing Standard (FIPS) mode is enabled on your system. \
-FreeSurfer (and thus fMRIPost-AROMA) cannot be used in FIPS mode. \
-Contact your system administrator for assistance."""
-            )
-        else:
-            build_log.critical(
-                """\
-ERROR: a valid license file is required for FreeSurfer to run. \
-fMRIPost-AROMA looked for an existing license file at several paths, in this order: \
-1) command line argument ``--fs-license-file``; \
-2) ``$FS_LICENSE`` environment variable; and \
-3) the ``$FREESURFER_HOME/license.txt`` path. \
-Get it (for free) by registering at https://surfer.nmr.mgh.harvard.edu/registration.html"""
-            )
-        retval['return_code'] = 126  # 126 == Command invoked cannot execute.
-        return retval
-
     # Check workflow for missing commands
     missing = check_deps(retval['workflow'])
     if missing:

src/fmripost_aroma/data/io_spec.json

@@ -69,6 +69,8 @@
                     null
                 ],
                 "space": null,
+                "res": null,
+                "den": null,
                 "desc": "confounds",
                 "suffix": "timeseries",
                 "extension": [

src/fmripost_aroma/data/tests/config.toml

@@ -13,7 +13,6 @@ aggr_ses_reports = false
 bids_dir = "/home/runner/work/fmripost-aroma/fmripost-aroma/src/fmripost_aroma/tests/data"
 bids_description_hash = "5d42e27751bbc884eca87cb4e62b9a0cca0cd86f8e578747fe89b77e6c5b21e5"
 boilerplate_only = false
-fs_license_file = "/opt/freesurfer/license.txt"
 log_dir = "/home/runner/work/fmripost-aroma/fmripost-aroma/src/fmripost_aroma/tests/data"
 log_level = 40
 low_mem = false

src/fmripost_aroma/workflows/base.py

@@ -29,9 +29,11 @@
 
 """
 
+import os
 import sys
 from copy import deepcopy
 
+import yaml
 from nipype.pipeline import engine as pe
 from packaging.version import Version
 
@@ -349,9 +351,22 @@ def init_single_subject_wf(subject_id: str):
             ica_aroma_wf.inputs.inputnode.bold_mask_std = functional_cache['bold_mask_std']
             workflow.add_nodes([ica_aroma_wf])
 
+        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']