diff --git a/sdcflows/fieldmaps.py b/sdcflows/fieldmaps.py
index 0909592ee8..c03b52890e 100644
--- a/sdcflows/fieldmaps.py
+++ b/sdcflows/fieldmaps.py
@@ -446,7 +446,8 @@ def get_workflow(self, set_inputs=True, **kwargs):
return self._wf
# Override workflow name
- kwargs["name"] = f"wf_{self.bids_id}"
+ clean_bids_id = re.sub(r'[^a-zA-Z0-9]', '', self.bids_id)
+ kwargs["name"] = f"wf_{clean_bids_id}"
if self.method in (EstimatorType.MAPPED, EstimatorType.PHASEDIFF):
from .workflows.fit.fieldmap import init_fmap_wf
diff --git a/sdcflows/workflows/base.py b/sdcflows/workflows/base.py
index 7c9c609d10..4a9f632fdd 100644
--- a/sdcflows/workflows/base.py
+++ b/sdcflows/workflows/base.py
@@ -21,6 +21,8 @@
# https://www.nipreps.org/community/licensing/
#
"""Estimate fieldmaps for :abbr:`SDC (susceptibility distortion correction)`."""
+import re
+
from nipype import logging
from nipype.pipeline import engine as pe
from nipype.interfaces import utility as niu
@@ -106,6 +108,7 @@ def init_fmap_preproc_wf(
)
for n, estimator in enumerate(estimators, 1):
+ clean_bids_id = re.sub(r'[^a-zA-Z0-9]', '', estimator.bids_id)
est_wf = estimator.get_workflow(
omp_nthreads=omp_nthreads,
debug=debug,
@@ -116,7 +119,7 @@ def init_fmap_preproc_wf(
]
out_map = pe.Node(
- niu.IdentityInterface(fields=out_fields), name=f"out_{estimator.bids_id}"
+ niu.IdentityInterface(fields=out_fields), name=f"out_{clean_bids_id}"
)
out_map.inputs.fmap_id = estimator.bids_id
@@ -124,7 +127,7 @@ def init_fmap_preproc_wf(
output_dir=str(output_dir),
write_coeff=True,
bids_fmap_id=estimator.bids_id,
- name=f"fmap_derivatives_wf_{estimator.bids_id}",
+ name=f"fmap_derivatives_wf_{clean_bids_id}",
)
fmap_derivatives_wf.inputs.inputnode.source_files = source_files
fmap_derivatives_wf.inputs.inputnode.fmap_meta = [
@@ -135,7 +138,7 @@ def init_fmap_preproc_wf(
output_dir=str(output_dir),
fmap_type=str(estimator.method).rpartition(".")[-1].lower(),
bids_fmap_id=estimator.bids_id,
- name=f"fmap_reports_wf_{estimator.bids_id}",
+ name=f"fmap_reports_wf_{clean_bids_id}",
)
fmap_reports_wf.inputs.inputnode.source_files = source_files
@@ -143,7 +146,7 @@ def init_fmap_preproc_wf(
fields = INPUT_FIELDS[estimator.method]
inputnode = pe.Node(
niu.IdentityInterface(fields=fields),
- name=f"in_{estimator.bids_id}",
+ name=f"in_{clean_bids_id}",
)
# fmt:off
workflow.connect([
diff --git a/sdcflows/workflows/fit/base.py b/sdcflows/workflows/fit/base.py
index 1010b8b65f..09fc928221 100644
--- a/sdcflows/workflows/fit/base.py
+++ b/sdcflows/workflows/fit/base.py
@@ -25,6 +25,8 @@
def init_sdcflows_wf():
"""Create a multi-subject, multi-estimator *SDCFlows* workflow."""
+ import re
+
from nipype.pipeline.engine import Workflow
from niworkflows.utils.bids import collect_participants
@@ -51,6 +53,8 @@ def init_sdcflows_wf():
for subject, sub_estimators in estimators_record.items():
for estim in sub_estimators:
+ clean_bids_id = re.sub(r'[^a-zA-Z0-9]', '', estim.bids_id)
+
estim_wf = estim.get_workflow(
omp_nthreads=config.nipype.omp_nthreads,
sloppy=False,
@@ -61,7 +65,7 @@ def init_sdcflows_wf():
output_dir=config.execution.output_dir,
bids_fmap_id=estim.bids_id,
write_coeff=True,
- name=f"fmap_derivatives_{estim.bids_id}",
+ name=f"fmap_derivatives_{clean_bids_id}",
)
source_paths = [
@@ -76,7 +80,7 @@ def init_sdcflows_wf():
fmap_type=estim.method,
output_dir=config.execution.output_dir,
bids_fmap_id=estim.bids_id,
- name=f"fmap_reports_{estim.bids_id}",
+ name=f"fmap_reports_{clean_bids_id}",
)
reportlets_wf.inputs.inputnode.source_files = source_paths
diff --git a/sdcflows/workflows/outputs.py b/sdcflows/workflows/outputs.py
index 24e3d559bf..35e0c72004 100644
--- a/sdcflows/workflows/outputs.py
+++ b/sdcflows/workflows/outputs.py
@@ -21,6 +21,8 @@
# https://www.nipreps.org/community/licensing/
#
"""Writing out outputs."""
+import re
+
from nipype.pipeline import engine as pe
from nipype.interfaces import utility as niu
from niworkflows.interfaces.bids import DerivativesDataSink as _DDS
@@ -77,7 +79,7 @@ def init_fmap_reports_wf(
custom_entities = custom_entities or {}
if bids_fmap_id:
- custom_entities["fmapid"] = bids_fmap_id.replace("_", "")
+ custom_entities["fmapid"] = re.sub(r'[^a-zA-Z0-9]', '', bids_fmap_id)
workflow = pe.Workflow(name=name)
inputnode = pe.Node(
@@ -156,7 +158,7 @@ def init_fmap_derivatives_wf(
"""
custom_entities = custom_entities or {}
if bids_fmap_id:
- custom_entities["fmapid"] = bids_fmap_id.replace("_", "")
+ custom_entities["fmapid"] = re.sub(r'[^a-zA-Z0-9]', '', bids_fmap_id)
workflow = pe.Workflow(name=name)
inputnode = pe.Node(
diff --git a/sdcflows/workflows/tests/test_base.py b/sdcflows/workflows/tests/test_base.py
index b31222fecc..ac782a0bc0 100644
--- a/sdcflows/workflows/tests/test_base.py
+++ b/sdcflows/workflows/tests/test_base.py
@@ -23,7 +23,10 @@
"""Test the base workflow."""
from pathlib import Path
import os
+import re
+
import pytest
+
from sdcflows import fieldmaps as fm
from sdcflows.utils.wrangler import find_estimators
from sdcflows.workflows.base import init_fmap_preproc_wf
@@ -55,7 +58,8 @@ def test_fmap_wf(tmpdir, workdir, outdir, bids_layouts, dataset, subject):
if estimator.method != fm.EstimatorType.PEPOLAR:
continue
- inputnode = wf.get_node(f"in_{estimator.bids_id}")
+ clean_bids_id = re.sub(r'[^a-zA-Z0-9]', '', estimator.bids_id)
+ inputnode = wf.get_node(f"in_{clean_bids_id}")
inputnode.inputs.in_data = [str(f.path) for f in estimator.sources]
inputnode.inputs.metadata = [f.metadata for f in estimator.sources]