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Last checks on 4TQ6
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@bclenet
bclenet committed Apr 18, 2024
1 parent e7efbca commit 9394b53
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Showing 2 changed files with 30 additions and 26 deletions.
54 changes: 29 additions & 25 deletions narps_open/pipelines/team_4TQ6.py
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Original file line number Diff line number Diff line change
Expand Up @@ -226,10 +226,10 @@ def get_subject_level_analysis(self):
'run_level_analysis', '_run_id_*_subject_id_{subject_id}', 'results',
'varcope{contrast_id}.nii.gz'),
'masks' : join('derivatives', 'fmriprep', 'sub-{subject_id}', 'func',
'sub-{subject_id}_task-MGT_run-{run_id}_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz')
'sub-{subject_id}_task-MGT_run-*_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz')
}
select_files = Node(SelectFiles(templates), name = 'select_files')
select_files.inputs.base_directory= self.directories.results_dir
select_files.inputs.base_directory= self.directories.dataset_dir
subject_level.connect(information_source, 'subject_id', select_files, 'subject_id')
subject_level.connect(information_source, 'contrast_id', select_files, 'contrast_id')

Expand Down Expand Up @@ -308,7 +308,7 @@ def get_subject_level_outputs(self):
template = join(
self.directories.output_dir,
'subject_level_analysis', '_contrast_id_{contrast_id}_subject_id_{subject_id}',
'sub-{subject_id}_task-MGT_run-01_bold_space-MNI152NLin2009cAsym_preproc_brain_mask_maths.nii.gz'
'sub-{subject_id}_task-MGT_run-01_bold_space-MNI152NLin2009cAsym_brainmask_maths.nii.gz'
)
return_list += [template.format(**dict(zip(parameters.keys(), parameter_values)))\
for parameter_values in parameter_sets]
Expand Down Expand Up @@ -410,7 +410,7 @@ def get_group_level_analysis_sub_workflow(self, method):
'varcope1.nii.gz'),
'masks': join(self.directories.output_dir,
'subject_level_analysis', '_contrast_id_1_subject_id_*',
'sub-*_task-MGT_run-*_bold_space-MNI152NLin2009cAsym_preproc_brain_mask_maths.nii.gz')
'sub-*_task-MGT_run-*_bold_space-MNI152NLin2009cAsym_brainmask_maths.nii.gz')
}
select_files = Node(SelectFiles(templates), name = 'select_files')
select_files.inputs.base_directory = self.directories.results_dir
Expand Down Expand Up @@ -499,8 +499,6 @@ def get_group_level_analysis_sub_workflow(self, method):
f'group_level_analysis_{method}_nsub_{nb_subjects}.@tstats')
group_level.connect(randomise,'t_corrected_p_files', data_sink,
f'group_level_analysis_{method}_nsub_{nb_subjects}.@t_corrected_p_files')
group_level.connect(randomise,'t_p_files', data_sink,
f'group_level_analysis_{method}_nsub_{nb_subjects}.@t_p_files')

if method in ('equalIndifference', 'equalRange'):
# Setup a one sample t-test
Expand Down Expand Up @@ -606,10 +604,8 @@ def get_group_level_outputs(self):
'contrast_id': self.contrast_list,
'method': ['equalRange', 'equalIndifference'],
'file': [
'_cluster0/zstat1_pval.nii.gz', # TODO : output for randomise
'_cluster0/zstat1_threshold.nii.gz',
'_cluster1/zstat2_pval.nii.gz',
'_cluster1/zstat2_threshold.nii.gz',
'randomise_tfce_corrp_tstat1.nii.gz',
'randomise_tfce_corrp_tstat2.nii.gz',
'tstat1.nii.gz',
'tstat2.nii.gz',
'zstat1.nii.gz',
Expand All @@ -630,8 +626,7 @@ def get_group_level_outputs(self):
parameters = {
'contrast_id': self.contrast_list,
'file': [
'_cluster0/zstat1_pval.nii.gz', # TODO : output for randomise
'_cluster0/zstat1_threshold.nii.gz',
'randomise_tfce_corrp_tstat1.nii.gz',
'tstat1.nii.gz',
'zstat1.nii.gz'
]
Expand All @@ -653,40 +648,49 @@ def get_hypotheses_outputs(self):

nb_sub = len(self.subject_list)
files = [
# Hypothesis 1
join(f'group_level_analysis_equalIndifference_nsub_{nb_sub}',
'_contrast_id_1', '_cluster0', 'zstat1_threshold.nii.gz'),
'_contrast_id_1', 'randomise_tfce_corrp_tstat2'),
join(f'group_level_analysis_equalIndifference_nsub_{nb_sub}',
'_contrast_id_1', 'zstat1.nii.gz'),
'_contrast_id_1', 'zstat2.nii.gz'),
# Hypothesis 2
join(f'group_level_analysis_equalRange_nsub_{nb_sub}',
'_contrast_id_1', '_cluster0', 'zstat1_threshold.nii.gz'),
'_contrast_id_1', 'randomise_tfce_corrp_tstat2'),
join(f'group_level_analysis_equalRange_nsub_{nb_sub}',
'_contrast_id_1', 'zstat1.nii.gz'),
'_contrast_id_1', 'zstat2.nii.gz'),
# Hypothesis 3
join(f'group_level_analysis_equalIndifference_nsub_{nb_sub}',
'_contrast_id_1', '_cluster0', 'zstat1_threshold.nii.gz'),
'_contrast_id_1', 'randomise_tfce_corrp_tstat2'),
join(f'group_level_analysis_equalIndifference_nsub_{nb_sub}',
'_contrast_id_1', 'zstat1.nii.gz'),
'_contrast_id_1', 'zstat2.nii.gz'),
# Hypothesis 4
join(f'group_level_analysis_equalRange_nsub_{nb_sub}',
'_contrast_id_1', '_cluster0', 'zstat1_threshold.nii.gz'),
'_contrast_id_1', 'randomise_tfce_corrp_tstat2'),
join(f'group_level_analysis_equalRange_nsub_{nb_sub}',
'_contrast_id_1', 'zstat1.nii.gz'),
'_contrast_id_1', 'zstat2.nii.gz'),
# Hypothesis 5
join(f'group_level_analysis_equalIndifference_nsub_{nb_sub}',
'_contrast_id_2', '_cluster0', 'zstat1_threshold.nii.gz'),
'_contrast_id_2', 'randomise_tfce_corrp_tstat1'),
join(f'group_level_analysis_equalIndifference_nsub_{nb_sub}',
'_contrast_id_2', 'zstat1.nii.gz'),
# Hypothesis 6
join(f'group_level_analysis_equalRange_nsub_{nb_sub}',
'_contrast_id_2', '_cluster0', 'zstat1_threshold.nii.gz'),
'_contrast_id_2', 'randomise_tfce_corrp_tstat1'),
join(f'group_level_analysis_equalRange_nsub_{nb_sub}',
'_contrast_id_2', 'zstat1.nii.gz'),
# Hypothesis 7
join(f'group_level_analysis_equalIndifference_nsub_{nb_sub}',
'_contrast_id_2', '_cluster0', 'zstat1_threshold.nii.gz'),
'_contrast_id_2', 'randomise_tfce_corrp_tstat1'),
join(f'group_level_analysis_equalIndifference_nsub_{nb_sub}',
'_contrast_id_2', 'zstat1.nii.gz'),
# Hypothesis 8
join(f'group_level_analysis_equalRange_nsub_{nb_sub}',
'_contrast_id_2', '_cluster0', 'zstat1_threshold.nii.gz'),
'_contrast_id_2', 'randomise_tfce_corrp_tstat1'),
join(f'group_level_analysis_equalRange_nsub_{nb_sub}',
'_contrast_id_2', 'zstat1.nii.gz'),
# Hypothesis 9
join(f'group_level_analysis_groupComp_nsub_{nb_sub}',
'_contrast_id_2', '_cluster0', 'zstat1_threshold.nii.gz'),
'_contrast_id_2', 'randomise_tfce_corrp_tstat1'),
join(f'group_level_analysis_groupComp_nsub_{nb_sub}',
'_contrast_id_2', 'zstat1.nii.gz')
]
Expand Down
2 changes: 1 addition & 1 deletion narps_open/utils/correlation/__main__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ def main():
parser = ArgumentParser(description = 'Compare reproduced files to original results.')
parser.add_argument('-t', '--team', type = str, required = True,
help = 'the team ID', choices = get_implemented_pipelines())
subjects.add_argument('-n', '--nsubjects', type=str, required = True,
parser.add_argument('-n', '--nsubjects', type=int, required = True,
help='the number of subjects to be selected')
arguments = parser.parse_args()

Expand Down

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