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[FIX] Ignore real and imaginary scans in ADNI #1029

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merged 5 commits into from
Dec 8, 2023
Merged

[FIX] Ignore real and imaginary scans in ADNI #1029

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54f10ef
log dcm2niix command in debug or warning mode depending on sucess or …
NicolasGensollen Dec 4, 2023
9e67d9f
remove unused imports and explicit level of logging
NicolasGensollen Dec 4, 2023
943b742
remove unused imports and explicit level of logging again
NicolasGensollen Dec 4, 2023
193e97b
Use Pathlib in path_to_bids and remove real and imaginary images gene…
NicolasGensollen Dec 4, 2023
a293c03
Apply suggestions from code review
NicolasGensollen Dec 5, 2023
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10 changes: 7 additions & 3 deletions clinica/iotools/bids_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -833,10 +833,10 @@ def _build_dcm2niix_command(
bids_sidecar: bool = True,
) -> list:
"""Generate the dcm2niix command from user inputs."""
command = ["dcm2niix", "-w", "0", "-f", output_fmt, "-o", output_dir]
command = ["dcm2niix", "-w", "0", "-f", output_fmt, "-o", str(output_dir)]
command += ["-9", "-z", "y"] if compress else ["-z", "n"]
command += ["-b", "y", "-ba", "y"] if bids_sidecar else ["-b", "n"]
command += [input_dir]
command += [str(input_dir)]

return command

Expand Down Expand Up @@ -889,12 +889,16 @@ def run_dcm2niix(
cprint(
msg=(
"DICOM to BIDS conversion with dcm2niix failed:\n"
f"command: {command}\n"
f"command: {' '.join(command)}\n"
f"{completed_process.stdout.decode('utf-8')}"
),
lvl="warning",
)
return False
cprint(
f"DICOM to BIDS conversion with dcm2niix failed:\ncommand: {' '.join(command)}\n",
lvl="debug",
)
return True


Expand Down
9 changes: 3 additions & 6 deletions clinica/iotools/converters/adni_to_bids/adni_modalities/adni_flair.py
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Expand Up @@ -40,10 +40,6 @@ def convert_adni_flair(
If specified, it should be between 1 and the number of available CPUs.
Default=1.
"""
from os import path

import pandas as pd

from clinica.iotools.converters.adni_to_bids.adni_utils import (
load_clinical_csv,
paths_to_bids,
Expand All @@ -55,10 +51,11 @@ def convert_adni_flair(
subjects = list(adni_merge.PTID.unique())

cprint(
f"Calculating paths of FLAIR images. Output will be stored in {conversion_dir}."
f"Calculating paths of FLAIR images. Output will be stored in {conversion_dir}.",
lvl="info",
)
images = compute_flair_paths(source_dir, csv_dir, subjects, conversion_dir)
cprint("Paths of FLAIR images found. Exporting images into BIDS ...")
cprint("Paths of FLAIR images found. Exporting images into BIDS ...", lvl="info")
# flair_paths_to_bids(images, dest_dir)
paths_to_bids(
images, destination_dir, "flair", mod_to_update=mod_to_update, n_procs=n_procs
Expand Down
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