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Update to match neurodatascience/nipoppy:main #52

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Apr 25, 2024
Merged

Update to match neurodatascience/nipoppy:main #52

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20 changes: 18 additions & 2 deletions nipoppy/extractors/fmriprep/run_FC.py
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Original file line number Diff line number Diff line change
Expand Up @@ -148,12 +148,18 @@ def run_FC(

logger.info("Running FC assessment...")
logger.info("-"*50)

func_file = f"{fmriprep_dir}/{participant_id}/ses-{session_id}/func/{participant_id}_ses-{session_id}_{task}_{run}_{space}_desc-preproc_bold.nii.gz"
# check if the func file exists
if not os.path.exists(func_file):
logger.error(f"func file not found: {func_file}")
logger.error(f"Skipping participant: {participant_id}")
return

try:
for brain_atlas in brain_atlas_list:
logger.info('******** running ' + brain_atlas)
### extract time series
func_file = f"{fmriprep_dir}/{participant_id}/ses-{session_id}/func/{participant_id}_ses-{session_id}_{task}_{run}_{space}_desc-preproc_bold.nii.gz"
if 'schaefer' in brain_atlas:
time_series, labels = extract_timeseries(func_file, brain_atlas, confound_strategy)
elif brain_atlas=='DKT':
Expand All @@ -170,10 +176,11 @@ def run_FC(
if not os.path.exists(folder):
os.makedirs(folder)
np.save(f"{folder}/{participant_id}_ses-{session_id}_{task}_{space}_FC_{brain_atlas}.npy", FC)
logger.info(f"Successfully completed FC assessment for participant: {participant_id}")
except Exception as e:
logger.error(f"FC assessment failed with exceptions: {e}")
logger.error(f"Failed participant: {participant_id}")

logger.info(f"Successfully completed FC assessment for participant: {participant_id}")
logger.info("-"*75)
logger.info("")

Expand Down Expand Up @@ -226,6 +233,15 @@ def run(participant_id: str,
DKT_dir = f"{DATASET_ROOT}/derivatives/networks/0.9.0/output"
FC_dir = f"{output_dir}/FC"

# check if the func/ exists in fmriprep_dir
func_dir = f"{fmriprep_dir}/{participant_id}/ses-{session_id}/func/"
if not os.path.exists(func_dir):
logger.error(
f"func data not found: {func_dir}"
)
logger.error(f"Skipping participant: {participant_id}")
return

# assess FC
run_FC(
participant_id,
Expand Down
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