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Ignore system stuff.
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tsalo committed Nov 4, 2024

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1 parent fb5a571 commit aef915b
Showing 3 changed files with 6 additions and 6 deletions.
2 changes: 1 addition & 1 deletion xcp_d/interfaces/restingstate.py
Original file line number Diff line number Diff line change
@@ -243,7 +243,7 @@ def _run_interface(self, runtime):
else:
mask_cmd = ''

os.system(f'3dReHo -inset {in_file} {mask_cmd} -nneigh 27 -prefix {out_file}')
os.system(f'3dReHo -inset {in_file} {mask_cmd} -nneigh 27 -prefix {out_file}') # noqa: S605
self._results['out_file'] = out_file


8 changes: 4 additions & 4 deletions xcp_d/tests/test_smoothing.py
Original file line number Diff line number Diff line change
@@ -25,7 +25,7 @@ def test_smoothing_nifti(fmriprep_without_freesurfer_data):

# Run AFNI'S FWHMx via CLI, the nipype interface doesn't have what we need
os.system(
f'3dFWHMx -ShowMeClassicFWHM -acf -detrend -input {in_file} -mask {mask} '
f'3dFWHMx -ShowMeClassicFWHM -acf -detrend -input {in_file} -mask {mask} ' # noqa: S605
'-detprefix detrend.nii.gz -out test_file.out > test_fwhm.out'
)

@@ -56,7 +56,7 @@ def test_smoothing_nifti(fmriprep_without_freesurfer_data):
# Run AFNI'S FWHMx via CLI, the nipype interface doesn't have what we need
# i.e : the "ShowMeClassicFWHM" option
os.system(
f'3dFWHMx -ShowMeClassicFWHM -acf -detrend -input {out_file} -mask {mask} '
f'3dFWHMx -ShowMeClassicFWHM -acf -detrend -input {out_file} -mask {mask} ' # noqa: S605
'-detprefix detrend.nii.gz -out test_file.out > test_fwhm.out'
)

@@ -105,7 +105,7 @@ def test_smoothing_cifti(ds001419_data, tmp_path_factory, sigma_lx=None):

# Estimate the smoothness of the unsmoothed file
in_file_smoothness = os.popen(
f'wb_command -cifti-estimate-fwhm {in_file} '
f'wb_command -cifti-estimate-fwhm {in_file} ' # noqa: S605
f'-surface CORTEX_LEFT {left_surf} '
f'-surface CORTEX_RIGHT {right_surf} '
'-whole-file -merged-volume'
@@ -137,7 +137,7 @@ def test_smoothing_cifti(ds001419_data, tmp_path_factory, sigma_lx=None):

# Estimate the smoothness of the smoothed file
out_file_smoothness = os.popen(
f'wb_command -cifti-estimate-fwhm {out_file} '
f'wb_command -cifti-estimate-fwhm {out_file} ' # noqa: S605
f'-surface CORTEX_LEFT {left_surf} '
f'-surface CORTEX_RIGHT {right_surf} '
'-whole-file -merged-volume'
2 changes: 1 addition & 1 deletion xcp_d/utils/concatenation.py
Original file line number Diff line number Diff line change
@@ -59,4 +59,4 @@ def concatenate_niimgs(files, out_file):
concat_preproc_img = concat_imgs(files)
concat_preproc_img.to_filename(out_file)
else:
os.system(f"wb_command -cifti-merge {out_file} -cifti {' -cifti '.join(files)}")
os.system(f'wb_command -cifti-merge {out_file} -cifti {" -cifti ".join(files)}') # noqa: S605

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