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Genfi patch #922

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097f8b1
Enhance verbosity
MatthieuJoulot Apr 13, 2023
1c2f673
convert all runs
MatthieuJoulot Apr 17, 2023
35de330
handle parts of dwi to get them converted
MatthieuJoulot Apr 18, 2023
0a7167e
Handling of philips dwi
MatthieuJoulot Apr 20, 2023
5739891
cleanup 1
MatthieuJoulot Apr 20, 2023
d3d674c
rename variables for clarity
MatthieuJoulot Apr 20, 2023
9c834b0
add docstrings
MatthieuJoulot Apr 20, 2023
bfb59f8
Add some more documentation to compute_philips_parts
MatthieuJoulot Apr 21, 2023
4de1e76
Apply suggestion from review
MatthieuJoulot Apr 24, 2023
ee2bb46
apply helper function as suggested
MatthieuJoulot Apr 24, 2023
7a5b5e8
Update clinica/iotools/converters/genfi_to_bids/genfi_to_bids_utils.py
MatthieuJoulot Apr 24, 2023
0d33f59
Merge branch 'dev' into update-genfi
MatthieuJoulot Apr 24, 2023
bfc45bd
Apply suggestions from code review
MatthieuJoulot Apr 25, 2023
be180a9
update _compute_scan_sequence_number
MatthieuJoulot Apr 25, 2023
2a9f268
Merge remote-tracking branch 'origin/update-genfi' into update-genfi
MatthieuJoulot Apr 25, 2023
13429f3
apply suggestions
MatthieuJoulot Apr 25, 2023
97563b6
modify merge_diffusion_philips
MatthieuJoulot Apr 25, 2023
9eca294
update unit-test
MatthieuJoulot Apr 25, 2023
0705884
Replace pd.NA by np.nan for unit-tests to work
MatthieuJoulot Apr 26, 2023
679ca08
build unit-test for compute_runs
MatthieuJoulot Apr 26, 2023
004f9e6
Add more unit-tests
MatthieuJoulot Apr 26, 2023
dd3eb62
Apply suggestions from code review
MatthieuJoulot Apr 26, 2023
b3f1d5c
handle PhilipsDWI better
MatthieuJoulot Apr 26, 2023
0b9d6c3
handle PhilipsDWI better
MatthieuJoulot Apr 26, 2023
019cdc0
split function
MatthieuJoulot Apr 26, 2023
d80de71
change unit test following the suggestion
MatthieuJoulot Apr 26, 2023
57007d4
apply suggestion from code review
MatthieuJoulot Apr 27, 2023
7b0233f
Apply suggestions from code review
MatthieuJoulot Apr 27, 2023
5a92f1d
correct error from suggestion
MatthieuJoulot Apr 27, 2023
a950cea
Add documentation
MatthieuJoulot Apr 27, 2023
a42284b
apply monkey patch
MatthieuJoulot Apr 27, 2023
387a77b
handle missing manufacturer
MatthieuJoulot Apr 27, 2023
da97d1f
remove problematic mention of manufaturer
MatthieuJoulot Apr 28, 2023
0df4de0
add run_num to index
MatthieuJoulot Apr 28, 2023
ede3405
add drop_duplicates
MatthieuJoulot Apr 28, 2023
27009ad
Add unknown manufacturer correctly
MatthieuJoulot Apr 28, 2023
12e9deb
drop sessions with no manufacturer
MatthieuJoulot Apr 28, 2023
216dc44
add print df
MatthieuJoulot Apr 28, 2023
c7de230
reverse
MatthieuJoulot Apr 28, 2023
10b8abd
function manufacturer
MatthieuJoulot Apr 28, 2023
03fc995
add dcm2niix success as a condition
MatthieuJoulot May 2, 2023
e08b37b
Merge branch 'dev' into update-genfi-patch
MatthieuJoulot May 11, 2023
f972513
remove artefacts
MatthieuJoulot May 11, 2023
3ecda03
remove manufacturer from unit-test
MatthieuJoulot May 11, 2023
ccf5a0d
Improve documentation
MatthieuJoulot May 11, 2023
6787947
add image for documentation
MatthieuJoulot May 11, 2023
487d94d
add bold task_rest
MatthieuJoulot May 11, 2023
f89d61f
update bids-ignore for dwi
MatthieuJoulot May 11, 2023
4aba2ec
correct json writing problem
MatthieuJoulot May 12, 2023
7b19ad3
suggestion from review
MatthieuJoulot May 12, 2023
d7d7b2c
Apply suggestions from code review
MatthieuJoulot May 12, 2023
ecae654
propose refactoring
NicolasGensollen May 12, 2023
2d2a3dc
remove dwi from bidsignore
MatthieuJoulot May 12, 2023
94703ef
remove origin from _compute_source_id_and_source_ses_id
MatthieuJoulot May 12, 2023
20be38b
Apply suggestions from code review
MatthieuJoulot May 12, 2023
71571db
remove useless line and correct unit-tests
MatthieuJoulot May 12, 2023
8b3a4e3
Merge remote-tracking branch 'origin/update-genfi-patch' into update-…
MatthieuJoulot May 12, 2023
fcbd7a4
fix unit-test
MatthieuJoulot May 12, 2023
bae141d
add correct searching length
MatthieuJoulot May 15, 2023
29cf8fb
move task to its right place
MatthieuJoulot May 16, 2023
b9a6467
add try/except
MatthieuJoulot May 17, 2023
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9 changes: 8 additions & 1 deletion clinica/iotools/bids_utils.py
Original file line number Diff line number Diff line change
Expand Up @@ -863,7 +863,7 @@ def run_dcm2niix(
output_fmt: str,
compress: bool = False,
bids_sidecar: bool = True,
) -> None:
) -> bool:
"""Runs the `dcm2niix` command using a subprocess.

Parameters
Expand All @@ -885,6 +885,11 @@ def run_dcm2niix(

bids_sidecar : bool, optional
Whether to generate a BIDS sidecar or not. Default=True.

Returns
-------
bool :
True if the conversion was successful, False otherwise.
"""
import subprocess

Expand All @@ -905,6 +910,8 @@ def run_dcm2niix(
),
lvl="warning",
)
return False
return True


def identify_modality(filename: str) -> Optional[str]:
Expand Down
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