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FIX: skipping dcm2niix shouldn't allow collisions #360

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FIX: skipping dcm2niix shouldn't allow collisions #360

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26acae0
skipping dcm2niix shouldn't allow collisions
joey-scanga Mar 2, 2026
9dbb618
added log back in
joey-scanga Mar 2, 2026
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8 changes: 5 additions & 3 deletions dcm2bids/dcm2niix_gen.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
import tarfile
import zipfile
from glob import glob
from pathlib import Path

from dcm2bids.utils.io import valid_path
from dcm2bids.utils.utils import DEFAULT, run_shell_command
Expand Down Expand Up @@ -153,8 +154,9 @@ def execute(self):
self.logger.info("Check log file for dcm2niix output\n")
else:
for dicomDir in self.dicom_dirs:
shutil.copytree(dicomDir, self.output_dir, dirs_exist_ok=True)
cmd = ['cp', '-r', dicomDir, self.output_dir]
self.logger.info("Running: %s", " ".join(str(item) for item in cmd))
for filepath in Path(dicomDir).rglob("*"):
if filepath.is_file():
shutil.copy(filepath, Path(self.output_dir / f"{Path(dicomDir).name}_{filepath.name}"), follow_symlinks=True)
self.logger.info("Copying NIFTI files/sidecars from: %s", dicomDir)

self.logger.info("Not running dcm2niix\n")
12 changes: 6 additions & 6 deletions dcm2bids/sidecar.py
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Original file line number Diff line number Diff line change
Expand Up @@ -302,9 +302,9 @@ def compare(name, pattern):
def compare_list(name, pattern):
try:
subResult = [
len(name) == len(pattern),
isinstance(pattern, list),
]
len(name) == len(pattern),
isinstance(pattern, list),
]
for subName, subPattern in zip(name, pattern):
subResult.append(compare(subName, subPattern))
except Exception:
Expand Down Expand Up @@ -436,8 +436,8 @@ def build_acquisitions(self, participant):
acquisitions.append(acq)

self.logger.info(
f"{acq.dstFile.replace(f'{acq.participant.prefix}-', '')}"
f" <- {sidecarName}")
f"{acq.dstFile.replace(f'{acq.participant.prefix}-', '')}"
f" <- {sidecarName}")

elif len(valid_descriptions) == 0:
self.logger.info(f"No Pairing <- {sidecarName}")
Expand Down Expand Up @@ -578,6 +578,6 @@ def duplicates(seq):
dup = dup[0:-1]

for runNum, acqInd in enumerate(dup):
runStr = templateDup.format(runNum+1)
runStr = templateDup.format(runNum + 1)
self.acquisitions[acqInd].custom_entities += runStr
self.acquisitions[acqInd].setDstFile()
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