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Completed first version of the pipeline
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@bclenet
bclenet committed Apr 11, 2024
1 parent 5100256 commit 54d04b8
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82 changes: 32 additions & 50 deletions narps_open/pipelines/team_B5I6.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
from nipype.interfaces.fsl import (
IsotropicSmooth, Level1Design, FEATModel,
L2Model, Merge, FLAMEO, FILMGLS, MultipleRegressDesign,
Cluster, SmoothEstimate, FSLCommand, Randomise
FSLCommand, Randomise
)
from nipype.algorithms.modelgen import SpecifyModel
from nipype.interfaces.fsl.maths import MultiImageMaths
Expand Down Expand Up @@ -595,8 +595,8 @@ def get_group_level_analysis_sub_workflow(self, method):
estimate_model = Node(FLAMEO(), name = 'estimate_model')
estimate_model.inputs.run_mode = 'flame1'
group_level.connect(mask_intersection, 'out_file', estimate_model, 'mask_file')
group_level.connect(merge_copes, estimate_model, [('merged_file', 'cope_file')]),
group_level.connect(merge_varcopes, estimate_model, [('merged_file', 'var_cope_file')]),
group_level.connect(merge_copes, 'merged_file', estimate_model, 'cope_file')
group_level.connect(merge_varcopes, 'merged_file', estimate_model, 'var_cope_file')
group_level.connect(specify_model, 'design_mat', estimate_model, 'design_file')
group_level.connect(specify_model, 'design_con', estimate_model, 't_con_file')
group_level.connect(specify_model, 'design_grp', estimate_model, 'cov_split_file')
Expand All @@ -608,33 +608,23 @@ def get_group_level_analysis_sub_workflow(self, method):
synchronize = True)
randomise.inputs.tfce = True
randomise.inputs.num_perm = 10000
randomise.inputs. = True
randomise.inputs.pthreshold = 0.05
randomise.inputs.c_thresh = 0.05
group_level.connect(mask_intersection, 'out_file', randomise, 'mask')
group_level.connect(merge_copes, 'merged_file', randomise, 'in_file')
group_level.connect(specify_model, 'design_con', randomise, 'tcon')
group_level.connect(specify_model, 'design_mat', randomise, 'design_mat')


tcon
mask
fcon
design_mat

(estimate_model, randomise,
('zstats', 'in_file')
('copes', 'cope_file'))




# Datasink Node - save important files
# Datasink Node - Save important files
data_sink = Node(DataSink(), name = 'data_sink')
data_sink.inputs.base_directory = self.directories.output_dir
(estimate_model, data_sink, [
('zstats', f'group_level_analysis_{method}_nsub_{nb_subjects}.@zstats'),
('tstats', f'group_level_analysis_{method}_nsub_{nb_subjects}.@tstats')
]),
(cluster, data_sink, [
('threshold_file', f'group_level_analysis_{method}_nsub_{nb_subjects}.@thresh'),
('pval_file', f'group_level_analysis_{method}_nsub_{nb_subjects}.@pval')])
])
group_level.connect(estimate_model, 'zstats', data_sink,
f'group_level_analysis_{method}_nsub_{nb_subjects}.@zstats')
group_level.connect(estimate_model, 'tstats', data_sink,
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 All @@ -653,6 +643,8 @@ 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')

# Function Node get_one_sample_t_test_regressors
# Get regressors in the equalRange and equalIndifference method case
Expand All @@ -664,14 +656,8 @@ def get_group_level_analysis_sub_workflow(self, method):
),
name = 'regressors_one_sample',
)

# Add missing connections
group_level_analysis.connect([
(get_group_subjects, get_copes, [('out_list', 'elements')]),
(get_group_subjects, get_varcopes, [('out_list', 'elements')]),
(get_group_subjects, regressors_one_sample, [('out_list', 'subject_list')]),
(regressors_one_sample, specify_model, [('regressors', 'regressors')])
])
group_level.connect(get_group_subjects, 'out_list', regressors_one_sample, 'subject_list')
group_level.connect(regressors_one_sample, 'regressors', specify_model, 'regressors')

elif method == 'groupComp':

Expand Down Expand Up @@ -726,19 +712,15 @@ def get_group_level_analysis_sub_workflow(self, method):
regressors_two_sample.inputs.subject_list = self.subject_list

# Add missing connections
group_level_analysis.connect([
(get_equal_range_subjects, regressors_two_sample, [
('out_list', 'equal_range_ids')
]),
(get_equal_indifference_subjects, regressors_two_sample, [
('out_list', 'equal_indifference_ids')
]),
(regressors_two_sample, specify_model, [
('regressors', 'regressors'),
('groups', 'groups')])
])

return group_level_analysis
group_level.connect(
get_equal_range_subjects, 'out_list', regressors_two_sample, 'equal_range_ids')
group_level.connect(
get_equal_indifference_subjects, 'out_list',
regressors_two_sample, 'equal_indifference_ids')
group_level.connect(regressors_two_sample, 'regressors', specify_model, 'regressors')
group_level.connect(regressors_two_sample, 'groups', specify_model, 'groups')

return group_level

def get_group_level_outputs(self):
""" Return all names for the files the group level analysis is supposed to generate. """
Expand All @@ -748,7 +730,7 @@ def get_group_level_outputs(self):
'contrast_id': self.contrast_list,
'method': ['equalRange', 'equalIndifference'],
'file': [
'_cluster0/zstat1_pval.nii.gz',
'_cluster0/zstat1_pval.nii.gz', # TODO : output for randomise
'_cluster0/zstat1_threshold.nii.gz',
'_cluster1/zstat2_pval.nii.gz',
'_cluster1/zstat2_threshold.nii.gz',
Expand All @@ -772,7 +754,7 @@ def get_group_level_outputs(self):
parameters = {
'contrast_id': self.contrast_list,
'file': [
'_cluster0/zstat1_pval.nii.gz',
'_cluster0/zstat1_pval.nii.gz', # TODO : output for randomise
'_cluster0/zstat1_threshold.nii.gz',
'tstat1.nii.gz',
'zstat1.nii.gz'
Expand Down
10 changes: 2 additions & 8 deletions tests/pipelines/test_team_B5I6.py
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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, 4*6*4*1, 4*4*1 + 4*1, 8*4*2 + 4*4, 18])
helpers.test_pipeline_outputs(pipeline, [0, 4*6*4*1, 4*6*4*1 + 4*1, 8*4*2 + 4*4, 18])

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

@staticmethod
@mark.unit_test
Expand Down Expand Up @@ -138,9 +138,6 @@ def test_confounds_file_no_outliers(temporary_data_dir):
temporary_data_dir, confounds_node.name, 'confounds_file_sub-sid_run-rid.tsv'))
assert exists(created_confounds_file)

from shutil import copy
copy(created_confounds_file, '/work/toot.tsv')

# Check contents
assert cmp(reference_file, created_confounds_file)

Expand Down Expand Up @@ -174,9 +171,6 @@ def test_confounds_file_outliers(temporary_data_dir):
temporary_data_dir, confounds_node.name, 'confounds_file_sub-sid_run-rid.tsv'))
assert exists(created_confounds_file)

from shutil import copy
copy(created_confounds_file, '/work/toot_outl.tsv')

# Check contents
assert cmp(reference_file, created_confounds_file)

Expand Down

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