Skip to content

Commit

Permalink
Correcting bugs in group level analyses
Browse files Browse the repository at this point in the history
  • Loading branch information
@bclenet
bclenet committed Apr 16, 2024
1 parent 0a1add4 commit 783c79e
Show file tree
Hide file tree
Showing 2 changed files with 70 additions and 26 deletions.
67 changes: 43 additions & 24 deletions narps_open/pipelines/team_4SZ2.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -214,6 +214,7 @@ def get_two_sample_t_test_regressors(
equal_range_ids: list,
equal_indifference_ids: list,
subject_list: list,
run_list: list
) -> dict:
"""
Create dictionary of regressors for two sample t-test group analysis.
Expand All @@ -222,19 +223,24 @@ def get_two_sample_t_test_regressors(
- equal_range_ids: ids of subjects in equal range group
- equal_indifference_ids: ids of subjects in equal indifference group
- subject_list: ids of subject for which to do the analysis
- run_list: ids of runs for which to do the analysis
Returns:
- regressors, dict: containing named lists of regressors.
- groups, list: group identifiers to distinguish groups in FSL analysis.
"""

# Create 2 lists containing n_sub values which are
# Create 2 lists containing a value for each run, which is
# * 1 if the participant is on the group
# * 0 otherwise
equal_range_regressors = [1 if i in equal_range_ids else 0 for i in subject_list]
equal_indifference_regressors = [
1 if i in equal_indifference_ids else 0 for i in subject_list
]
equal_range_regressors = []
equal_indifference_regressors = []

for subject_id in subject_list:
value_er = 1 if subject_id in equal_range_ids else 0
value_ei = 1 if subject_id in equal_indifference_ids else 0
for _ in run_list:
equal_range_regressors.append(value_er)
equal_indifference_regressors.append(value_ei)

# Create regressors output : a dict with the two list
regressors = dict(
Expand Down Expand Up @@ -268,9 +274,14 @@ def get_group_level_analysis_sub_workflow(self, method):
Returns:
- group_level: nipype.WorkFlow
"""
# Compute the number of participants used to do the analysis
# Compute the number of participants in the analysis
nb_subjects = len(self.subject_list)

# Compute the number of participants in the group
nb_subjects_in_group = nb_subjects
if method in ['equalIndifference', 'equalRange']:
nb_subjects_in_group = len([s for s in self.subject_list if s in get_group(method)])

# Declare the workflow
group_level = Workflow(
base_dir = self.directories.working_dir,
Expand All @@ -294,9 +305,13 @@ def get_group_level_analysis_sub_workflow(self, method):
'sub-*_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
group_level.connect(information_source, 'contrast_id', select_files, 'contrast_id')

# Create a function to complete the subject ids out from the get_*_subjects node
complete_subject_ids = lambda l : [f'_subject_id_{a}' for a in l]
complete_sub_ids = lambda l : [f'sub-{a}' for a in l]

# Function Node elements_in_string
# Get contrast of parameter estimates (cope) for subjects in a given group
# Note : using a MapNode with elements_in_string requires using clean_list to remove
Expand Down Expand Up @@ -348,14 +363,15 @@ def get_group_level_analysis_sub_workflow(self, method):

# Split Node - Split mask list to serve them as inputs of the MultiImageMaths node.
split_masks = Node(Split(), name = 'split_masks')
split_masks.inputs.splits = [1, len(self.subject_list) - 1]
split_masks.inputs.splits = [1, (nb_subjects_in_group * len(self.run_list)) - 1]
split_masks.inputs.squeeze = True # Unfold one-element splits removing the list
group_level.connect(get_masks, ('out_list', clean_list), split_masks, 'inlist')

# MultiImageMaths Node - Create a subject mask by
# computing the intersection of all run masks.
mask_intersection = Node(MultiImageMaths(), name = 'mask_intersection')
mask_intersection.inputs.op_string = '-mul %s ' * (len(self.subject_list) - 1)
mask_intersection.inputs.op_string = '-mul %s ' * \
((nb_subjects_in_group * len(self.run_list)) - 1)
group_level.connect(split_masks, 'out1', mask_intersection, 'in_file')
group_level.connect(split_masks, 'out2', mask_intersection, 'operand_files')

Expand Down Expand Up @@ -411,9 +427,12 @@ def get_group_level_analysis_sub_workflow(self, method):
)
get_group_subjects.inputs.list_1 = get_group(method)
get_group_subjects.inputs.list_2 = self.subject_list
group_level.connect(get_group_subjects, 'out_list', get_copes, 'elements')
group_level.connect(get_group_subjects, 'out_list', get_varcopes, 'elements')
group_level.connect(get_group_subjects, 'out_list', get_masks, 'elements')
group_level.connect(
get_group_subjects, ('out_list', complete_subject_ids), get_copes, 'elements')
group_level.connect(
get_group_subjects, ('out_list', complete_subject_ids), get_varcopes, 'elements')
group_level.connect(
get_group_subjects, ('out_list', complete_sub_ids), get_masks, 'elements')

# Function Node get_one_sample_t_test_regressors
# Get regressors in the equalRange and equalIndifference method case
Expand All @@ -425,16 +444,17 @@ def get_group_level_analysis_sub_workflow(self, method):
),
name = 'regressors_one_sample',
)
group_level.connect(get_group_subjects, 'out_list', regressors_one_sample, 'subject_list')
regressors_one_sample.inputs.subject_list = range(
nb_subjects_in_group * len(self.run_list))
group_level.connect(regressors_one_sample, 'regressors', specify_model, 'regressors')

elif method == 'groupComp':

# Select copes and varcopes corresponding to the selected subjects
# Indeed the SelectFiles node asks for all (*) subjects available
get_copes.inputs.elements = self.subject_list
get_varcopes.inputs.elements = self.subject_list
get_masks.inputs.elements = self.subject_list
get_copes.inputs.elements = complete_subject_ids(self.subject_list)
get_varcopes.inputs.elements = complete_subject_ids(self.subject_list)
get_masks.inputs.elements = complete_sub_ids(self.subject_list)

# Setup a two sample t-test
specify_model.inputs.contrasts = [
Expand Down Expand Up @@ -474,12 +494,14 @@ def get_group_level_analysis_sub_workflow(self, method):
'equal_range_ids',
'equal_indifference_ids',
'subject_list',
'run_list'
],
output_names = ['regressors', 'groups']
),
name = 'regressors_two_sample',
)
regressors_two_sample.inputs.subject_list = self.subject_list
regressors_two_sample.inputs.run_list = self.run_list

# Add missing connections
group_level.connect(
Expand All @@ -500,9 +522,7 @@ def get_group_level_outputs(self):
'contrast_id': self.contrast_list,
'method': ['equalRange', 'equalIndifference'],
'file': [
'_cluster0/zstat1_pval.nii.gz',
'_cluster0/zstat1_threshold.nii.gz',
'_cluster1/zstat2_pval.nii.gz',
'_cluster1/zstat2_threshold.nii.gz',
'tstat1.nii.gz',
'tstat2.nii.gz',
Expand All @@ -524,7 +544,6 @@ 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',
'tstat1.nii.gz',
'zstat1.nii.gz'
Expand Down Expand Up @@ -564,13 +583,13 @@ def get_hypotheses_outputs(self):
join(f'group_level_analysis_equalRange_nsub_{nb_sub}',
'_contrast_id_1', 'zstat1.nii.gz'),
join(f'group_level_analysis_equalIndifference_nsub_{nb_sub}',
'_contrast_id_2', '_cluster0', 'zstat1_threshold.nii.gz'),
'_contrast_id_2', '_cluster1', 'zstat2_threshold.nii.gz'),
join(f'group_level_analysis_equalIndifference_nsub_{nb_sub}',
'_contrast_id_2', 'zstat1.nii.gz'),
'_contrast_id_2', 'zstat2.nii.gz'),
join(f'group_level_analysis_equalRange_nsub_{nb_sub}',
'_contrast_id_2', '_cluster0', 'zstat1_threshold.nii.gz'),
'_contrast_id_2', '_cluster1', 'zstat2_threshold.nii.gz'),
join(f'group_level_analysis_equalRange_nsub_{nb_sub}',
'_contrast_id_2', 'zstat1.nii.gz'),
'_contrast_id_2', 'zstat2.nii.gz'),
join(f'group_level_analysis_equalIndifference_nsub_{nb_sub}',
'_contrast_id_2', '_cluster0', 'zstat1_threshold.nii.gz'),
join(f'group_level_analysis_equalIndifference_nsub_{nb_sub}',
Expand Down
29 changes: 27 additions & 2 deletions tests/pipelines/test_team_4SZ2.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -52,11 +52,11 @@ def test_outputs():

# 1 - 1 subject outputs
pipeline.subject_list = ['001']
helpers.test_pipeline_outputs(pipeline, [0, 2*4*1*4, 0, 8*2*2 + 4*2, 18])
helpers.test_pipeline_outputs(pipeline, [0, 2*4*1*4, 0, 6*2*2 + 3*2, 18])

# 2 - 4 subjects outputs
pipeline.subject_list = ['001', '002', '003', '004']
helpers.test_pipeline_outputs(pipeline, [0, 2*4*4*4, 0, 8*2*2 + 4*2, 18])
helpers.test_pipeline_outputs(pipeline, [0, 2*4*4*4, 0, 6*2*2 + 3*2, 18])

@staticmethod
@mark.unit_test
Expand Down Expand Up @@ -86,6 +86,31 @@ def test_subject_information():
[6.0, 14.0, 19.0, 15.0, 17.0]
])

@staticmethod
@mark.unit_test
def test_one_sample_t_test_regressors():
""" Test the get_one_sample_t_test_regressors method """

result = PipelineTeam4SZ2.get_one_sample_t_test_regressors(['001', '002', '003', '004'])
assert result == {'group_mean' : [1]*4}

@staticmethod
@mark.unit_test
def test_two_sample_t_test_regressors():
""" Test the get_two_sample_t_test_regressors method """

result_1, result_2 = PipelineTeam4SZ2.get_two_sample_t_test_regressors(
['001', '003'], # equal_range_ids
['002', '004'], # equal_indifference_ids
['001', '002', '003', '004'], # subject_list
['01', '02'] # run_list
)
assert result_1 == {
'equalRange' : [1, 1, 0, 0, 1, 1, 0, 0],
'equalIndifference' : [0, 0, 1, 1, 0, 0, 1, 1]
}
assert result_2 == [1, 1, 2, 2, 1, 1, 2, 2]

@staticmethod
@mark.pipeline_test
def test_execution():
Expand Down

0 comments on commit 783c79e

Please sign in to comment.