From f217d164af0e05771e48e6e42a14c168e71ac9e0 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 16 May 2024 15:19:59 -0400
Subject: [PATCH] Get it building at least.
---
src/fmripost_aroma/cli/workflow.py | 25 -----------------------
src/fmripost_aroma/data/io_spec.json | 2 ++
src/fmripost_aroma/data/tests/config.toml | 1 -
src/fmripost_aroma/workflows/base.py | 15 ++++++++++++++
4 files changed, 17 insertions(+), 26 deletions(-)
diff --git a/src/fmripost_aroma/cli/workflow.py b/src/fmripost_aroma/cli/workflow.py
index 9505f85..b612dee 100644
--- a/src/fmripost_aroma/cli/workflow.py
+++ b/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:
diff --git a/src/fmripost_aroma/data/io_spec.json b/src/fmripost_aroma/data/io_spec.json
index 750d3cd..cb1b2e4 100644
--- a/src/fmripost_aroma/data/io_spec.json
+++ b/src/fmripost_aroma/data/io_spec.json
@@ -69,6 +69,8 @@
null
],
"space": null,
+ "res": null,
+ "den": null,
"desc": "confounds",
"suffix": "timeseries",
"extension": [
diff --git a/src/fmripost_aroma/data/tests/config.toml b/src/fmripost_aroma/data/tests/config.toml
index d19940b..8dc1353 100644
--- a/src/fmripost_aroma/data/tests/config.toml
+++ b/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
diff --git a/src/fmripost_aroma/workflows/base.py b/src/fmripost_aroma/workflows/base.py
index 74d2e47..9605192 100644
--- a/src/fmripost_aroma/workflows/base.py
+++ b/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']