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Return lists of defaced t1w and t2w and define it for t2w #83

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Return lists of defaced t1w and t2w and define it for t2w #83

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788d3e0
Return lists of defaced t1w and t2w and define it for t2w
yarikoptic Jun 12, 2024
5783af4
BF: more of defining defaults to not cause obnoxious crashes
yarikoptic Jun 13, 2024
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3 changes: 2 additions & 1 deletion bidsonym/reports.py
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Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,7 @@ def plot_defaced(bids_dir, subject_label, session=None, t2w=None):
plt.savefig(opj(bidsonym_path,
t1w[t1w.rfind('/')+1:t1w.rfind('.nii')] + '_desc-brainmaskdeid.png'))

defaced_t2w = None
if t2w is not None:
if session is not None:
defaced_t2w = layout.get(subject=subject_label, extension='nii.gz', suffix='T2w',
Expand All @@ -67,7 +68,7 @@ def plot_defaced(bids_dir, subject_label, session=None, t2w=None):
plt.savefig(opj(bids_dir, 'sourcedata/bidsonym/sub-%s' % subject_label,
t2w[t2w.rfind('/')+1:t2w.rfind('.nii')] + '_desc-brainmaskdeid.png'))

return (t1w, t2w)
return (defaced_t1w, defaced_t2w)


def gif_defaced(bids_dir, subject_label, session=None, t2w=None):
Expand Down
23 changes: 13 additions & 10 deletions bidsonym/run_deeid.py
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Original file line number Diff line number Diff line change
Expand Up @@ -107,13 +107,15 @@ def run_deeid():
subjects_to_analyze = layout.get(return_type='id', target='subject')

list_part_prob = []
part = None
session = None

for part in subjects_to_analyze:
if part not in layout.get_subjects():
list_part_prob.append(part)
if len(list_part_prob) >= 1:
raise Exception("The participant(s) you indicated are not present in the BIDS dataset, please check again."
"This refers to:")
print(list_part_prob)
f"This refers to: {list_part_prob}")

if args.session:
list_sessions = args.session
Expand All @@ -133,6 +135,7 @@ def run_deeid():
print(sessions_to_analyze)

list_ses_prob = []
list_t1w = []

if args.session and args.session != ["all"]:

Expand All @@ -148,8 +151,7 @@ def run_deeid():

if len(list_ses_prob) >= 1:
raise Exception("The session(s) you indicated are not present in the BIDS dataset, please check again."
"This refers to:")
print(list_ses_prob)
f"This refers to: {list_ses_prob}")

list_t1w = layout.get(subject=subject_label, extension='nii.gz',
suffix='T1w', return_type='filename',
Expand Down Expand Up @@ -240,6 +242,7 @@ def run_deeid():

if args.deface_t2w:

list_t2w = []
if args.session and args.session != ["all"]:

for ses in args.session:
Expand All @@ -249,8 +252,7 @@ def run_deeid():

if len(list_ses_prob) >= 1:
raise Exception("The session(s) you indicated are not present in the BIDS dataset, please check again."
"This refers to:")
print(list_ses_prob)
f"This refers to: {list_ses_prob}")

list_t2w = layout.get(subject=subject_label,
extension='nii.gz', suffix='T2w',
Expand All @@ -262,7 +264,7 @@ def run_deeid():
extension='nii.gz', suffix='T2w',
return_type='filename')

if list_t2w == []:
if not list_t2w:
raise Exception("You indicated that a T2w image should be defaced as well."
"However, no T2w image exists for subject %s and indicated sessions."
"Please check again." % subject_label)
Expand All @@ -278,6 +280,7 @@ def run_deeid():
source_t2w = copy_no_deid(args.bids_dir, subject_label,
T2_file)

T1_file = None
if 'ses' in T2_file:

session = T2_file[T2_file.rfind('ses')+4:].split("_")[0]
Expand Down Expand Up @@ -324,20 +327,20 @@ def run_deeid():
t2w=None)
clean_up_files(args.bids_dir, subject_label, session=None)

elif len(T1_file) == 1 and args.deface_t2w:
elif len(T1_files) == 1 and args.deface_t2w:
create_graphics(args.bids_dir, subject_label, session=None,
t2w=True)
clean_up_files(args.bids_dir, subject_label, session=None)

elif len(T1_file) >= 1 and args.deface_t2w is False:
elif len(T1_files) >= 1 and args.deface_t2w is False:

for session in sessions_to_analyze:
create_graphics(args.bids_dir, subject_label,
session=session, t2w=None)
clean_up_files(args.bids_dir, subject_label,
session=session)

elif len(T1_file) >= 1 and args.deface_t2w:
elif len(T1_files) >= 1 and args.deface_t2w:

for session in sessions_to_analyze:
create_graphics(args.bids_dir, subject_label,
Expand Down
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