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[FIX] Fix the data parser util #95

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[FIX] Fix the data parser util #95

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165 changes: 82 additions & 83 deletions ibc_public/utils_data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -144,7 +144,7 @@ def data_parser(derivatives=DERIVATIVES, conditions=CONDITIONS,
# T1 images
for subject in subject_list:
t1_path = 'sub-*/ses-*/anat/w%s_ses-00_T1w.nii.gz' % subject
t1_abs_path = os.path.join(DERIVATIVES, t1_path)
t1_abs_path = os.path.join(derivatives, t1_path)
t1_imgs_ = glob.glob(os.path.join(t1_abs_path))
for img in t1_imgs_:
session = img.split('/')[-3]
Expand All @@ -159,7 +159,7 @@ def data_parser(derivatives=DERIVATIVES, conditions=CONDITIONS,

for subject in subject_list:
t1bet_path = 'sub-*/ses-*/anat/w%s_ses-00_T1w_bet.nii.gz' % subject
t1bet_abs_path = os.path.join(DERIVATIVES, t1bet_path)
t1bet_abs_path = os.path.join(derivatives, t1bet_path)
t1bet_imgs_ = glob.glob(os.path.join(t1bet_abs_path))
for img in t1bet_imgs_:
session = img.split('/')[-3]
Expand All @@ -174,7 +174,7 @@ def data_parser(derivatives=DERIVATIVES, conditions=CONDITIONS,

for subject in subject_list:
ht1_path = 'sub-*/ses-*/anat/w%s*_acq-highres_T1w_bet.nii.gz' % subject
ht1_abs_path = os.path.join(DERIVATIVES, ht1_path)
ht1_abs_path = os.path.join(derivatives, ht1_path)
ht1_imgs_ = glob.glob(os.path.join(ht1_abs_path))
for img in ht1_imgs_:
session = img.split('/')[-3]
Expand All @@ -190,7 +190,7 @@ def data_parser(derivatives=DERIVATIVES, conditions=CONDITIONS,
# gray-matter images
for subject in subject_list:
mwc1_path = 'sub-*/ses-*/anat/mwc1%s_ses-00_T1w.nii.gz' % subject
mwc1_abs_path = os.path.join(DERIVATIVES, mwc1_path)
mwc1_abs_path = os.path.join(derivatives, mwc1_path)
mwc1_imgs_ = glob.glob(os.path.join(mwc1_abs_path))
for img in mwc1_imgs_:
session = img.split('/')[-3]
Expand All @@ -205,7 +205,7 @@ def data_parser(derivatives=DERIVATIVES, conditions=CONDITIONS,

for subject in subject_list:
hmwc1_path = 'sub-*/ses-*/anat/mwc1%s*_acq-highres_T1w.nii.gz' % subject
hmwc1_abs_path = os.path.join(DERIVATIVES, hmwc1_path)
hmwc1_abs_path = os.path.join(derivatives, hmwc1_path)
hmwc1_imgs_ = glob.glob(os.path.join(hmwc1_abs_path))
for img in hmwc1_imgs_:
session = img.split('/')[-3]
Expand All @@ -221,7 +221,7 @@ def data_parser(derivatives=DERIVATIVES, conditions=CONDITIONS,
# white-matter image
for subject in subject_list:
mwc2_path = 'sub-*/ses-*/anat/mwc2%s_ses-00_T1w.nii.gz' % subject
mwc2_abs_path = os.path.join(DERIVATIVES, mwc2_path)
mwc2_abs_path = os.path.join(derivatives, mwc2_path)
mwc2_imgs_ = glob.glob(os.path.join(mwc2_abs_path))
for img in mwc2_imgs_:
session = img.split('/')[-3]
Expand All @@ -235,84 +235,83 @@ def data_parser(derivatives=DERIVATIVES, conditions=CONDITIONS,
acquisitions.append('')

# preprocessed bold images and corresponding motion parameters
if derivatives in [DERIVATIVES, THREE_MM]:
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@bthirion bthirion Sep 14, 2025

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why do you remove that loop ?

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@pbarbarant pbarbarant Sep 15, 2025

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It might be a github visualization issue, I'm only removing the if statement

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@bthirion bthirion Sep 16, 2025

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Actually, the point was to sckip that block whenever derivatives == SMOOTH_DERIVATIVES

for sbj in subject_list:
for acq in ['ap', 'pa']:
for task in task_list:
bold_name = 'wrdc%s_ses*_task-%s_dir-%s*_bold.nii.gz' \
% (sbj, task, acq)
bold_path = os.path.join(derivatives, 'sub-*/ses-*/func',
bold_name)
bold = glob.glob(bold_path)
if not bold:
# Add exception for 'bang' task, since 'ap' was
# never part of acq planning
if acq == 'ap' and task == 'Bang':
pass
else:
msg = 'wrdc*.nii.gz file for task ' + \
'%s %s in %s not found!' % (task, acq, sbj)
warnings.warn(msg)
for img in bold:
basename = os.path.basename(img)
parts = basename.split('_')
task_ = None
for part in parts:
if part[4:7] == 'sub':
subject = part[4:10]
elif part[:3] == 'ses':
session = part
elif part[:5] == 'task-':
task_ = part[5:]
elif part[:4] == 'dir-':
acquisition = part[4:]
if task not in task_list:
continue
paths.append(img)
sessions.append(session)
subjects.append(subject)
modalities.append('bold')
contrasts.append('preprocessed')
tasks.append(task_)
acquisitions.append(acquisition)
for sbj in subject_list:
for acq in ['ap', 'pa']:
for task in task_list:
bold_name = 'wrdc%s_ses*_task-%s_dir-%s*_bold.nii.gz' \
% (sbj, task, acq)
bold_path = os.path.join(derivatives, 'sub-*/ses-*/func',
bold_name)
bold = glob.glob(bold_path)
if not bold:
# Add exception for 'bang' task, since 'ap' was
# never part of acq planning
if acq == 'ap' and task == 'Bang':
pass
else:
msg = 'wrdc*.nii.gz file for task ' + \
'%s %s in %s not found!' % (task, acq, sbj)
warnings.warn(msg)
for img in bold:
basename = os.path.basename(img)
parts = basename.split('_')
task_ = None
for part in parts:
if part[4:7] == 'sub':
subject = part[4:10]
elif part[:3] == 'ses':
session = part
elif part[:5] == 'task-':
task_ = part[5:]
elif part[:4] == 'dir-':
acquisition = part[4:]
if task not in task_list:
continue
paths.append(img)
sessions.append(session)
subjects.append(subject)
modalities.append('bold')
contrasts.append('preprocessed')
tasks.append(task_)
acquisitions.append(acquisition)

rps_name = 'rp_dc%s_ses*_task-%s_dir-%s*_bold.txt' \
% (sbj, task, acq)
rps_path = os.path.join(DERIVATIVES, 'sub-*/ses-*/func',
rps_name)
rps = glob.glob(rps_path)
if not rps:
# Add exception for 'bang' task, since 'ap' was
# never part of acq planning
if acq == 'ap' and task == 'Bang':
pass
else:
msg = 'rp-dc*.txt file for task ' + \
'%s %s in %s not found!' % (task, acq, sbj)
warnings.warn(msg)

for rp_file in rps:
basename = os.path.basename(rp_file)
parts = basename.split('_')
task_ = None
for part in parts:
if part[:3] == 'sub':
subject = part
elif part[:3] == 'ses':
session = part
elif part[:5] == 'task-':
task_ = part[5:]
elif part[:4] == 'dir-':
acquisition = part[4:]
if task not in task_list:
continue
paths.append(rp_file)
sessions.append(session)
subjects.append(subject)
modalities.append('bold')
contrasts.append('motion')
tasks.append(task_)
acquisitions.append(acquisition)
rps_name = 'rp_dc%s_ses*_task-%s_dir-%s*_bold.txt' \
% (sbj, task, acq)
rps_path = os.path.join(derivatives, 'sub-*/ses-*/func',
rps_name)
rps = glob.glob(rps_path)
if not rps:
# Add exception for 'bang' task, since 'ap' was
# never part of acq planning
if acq == 'ap' and task == 'Bang':
pass
else:
msg = 'rp-dc*.txt file for task ' + \
'%s %s in %s not found!' % (task, acq, sbj)
warnings.warn(msg)

for rp_file in rps:
basename = os.path.basename(rp_file)
parts = basename.split('_')
task_ = None
for part in parts:
if part[:3] == 'sub':
subject = part
elif part[:3] == 'ses':
session = part
elif part[:5] == 'task-':
task_ = part[5:]
elif part[:4] == 'dir-':
acquisition = part[4:]
if task not in task_list:
continue
paths.append(rp_file)
sessions.append(session)
subjects.append(subject)
modalities.append('bold')
contrasts.append('motion')
tasks.append(task_)
acquisitions.append(acquisition)

# fixed-effects activation images (postprocessed)
con_df = conditions
Expand Down