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improvements in brainvisa schemas
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@denisri
denisri committed Jul 19, 2023
1 parent 1db0920 commit 8250b63
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Showing 2 changed files with 389 additions and 237 deletions.
167 changes: 163 additions & 4 deletions capsul/schemas/brainvisa.py
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Original file line number Diff line number Diff line change
Expand Up @@ -115,11 +115,78 @@ def _path_list(self):
return path_list


morphologist_datasets = {
't1mri': 'input',
'PrepareSubject_Normalization_Normalization_AimsMIRegister_anatomical_template': 'shared',
'PrepareSubject_TalairachFromNormalization_normalized_referential': 'shared',
'PrepareSubject_TalairachFromNormalization_transform_chain_ACPC_to_Normalized': 'shared',
'PrepareSubject_TalairachFromNormalization_acpc_referential': 'shared',
'PrepareSubject_StandardACPC_older_MNI_normalization': None,
'PrepareSubject_Normalization_commissures_coordinates': None,
'PrepareSubject_Normalization_NormalizeFSL_template': 'shared',
'PrepareSubject_Normalization_NormalizeSPM_template': 'shared',
'PrepareSubject_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_normalized_volume': None,
'PrepareSubject_Normalization_NormalizeBaladin_template': 'shared',
'PrepareSubject_Normalization_Normalization_AimsMIRegister_mni_to_acpc': 'shared',
'BrainSegmentation_lesion_mask': None,
'Renorm_template': 'shared',
'Renorm_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_normalized_volume': None,
'Renorm_Normalization_Normalization_AimsMIRegister_mni_to_acpc': 'shared',
'HeadMesh_remove_mask': None,
'SplitBrain_split_template': 'shared',
'GreyWhiteClassification_lesion_mask': None,
'SulciRecognition_SPAM_recognition09_global_recognition_labels_priors': 'shared',
'SulciRecognition_SPAM_recognition09_global_recognition_initial_transformation': None,
'SulciRecognition_SPAM_recognition09_global_recognition_model': 'shared',
'SulciRecognition_SPAM_recognition09_local_recognition_model': 'shared',
'SulciRecognition_SPAM_recognition09_local_recognition_local_referentials': 'shared',
'SulciRecognition_SPAM_recognition09_local_recognition_direction_priors': 'shared',
'SulciRecognition_SPAM_recognition09_local_recognition_angle_priors': 'shared',
'SulciRecognition_SPAM_recognition09_local_recognition_translation_priors': 'shared',
'SulciRecognition_SPAM_recognition09_markovian_recognition_model': 'shared',
'SulciRecognition_SPAM_recognition09_markovian_recognition_segments_relations_model': 'shared',
'SulciRecognition_CNN_recognition19_model_file': 'shared',
'SulciRecognition_CNN_recognition19_param_file': 'shared',
'GreyWhiteClassification_1_lesion_mask': None,
'SulciRecognition_1_SPAM_recognition09_global_recognition_labels_priors': 'shared',
'SulciRecognition_1_SPAM_recognition09_global_recognition_initial_transformation': None,
'SulciRecognition_1_SPAM_recognition09_global_recognition_model': 'shared',
'SulciRecognition_1_SPAM_recognition09_local_recognition_model': 'shared',
'SulciRecognition_1_SPAM_recognition09_local_recognition_local_referentials': 'shared',
'SulciRecognition_1_SPAM_recognition09_local_recognition_direction_priors': 'shared',
'SulciRecognition_1_SPAM_recognition09_local_recognition_angle_priors': 'shared',
'SulciRecognition_1_SPAM_recognition09_local_recognition_translation_priors': 'shared',
'SulciRecognition_1_SPAM_recognition09_markovian_recognition_model': 'shared',
'SulciRecognition_1_SPAM_recognition09_markovian_recognition_segments_relations_model': 'shared',
'SulciRecognition_1_CNN_recognition19_model_file': 'shared',
'SulciRecognition_1_CNN_recognition19_param_file': 'shared',
'SPAM_recognition_labels_translation_map': 'shared',
'SulciRecognition_recognition2000_model': 'shared',
'SulciRecognition_1_recognition2000_model': 'shared',
'sulcal_morphometry_sulci_file': 'shared',
'GlobalMorphometry_subject': 'output',
'Report_normative_brain_stats': None,
'Report_subject': 'output',
}
''' standard, shared datasets associated with shared input data for
Morphologist
'''


def declare_morpho_schemas(morpho_module):
''' Declares Morphologist and sub-processes completion schemas for
BIDS, BrainVisa and shared organizations.
It may apply to the "real" Morphologist pipeline (morphologist.capsul
parent module), or to the "fake" morphologist test replica
(capsul.pipeline.test.fake_morphologist parent module)
'''

axon_module = morpho_module
cnn_module = '{}.sulcideeplabeling'.format(morpho_module)
if morpho_module.startswith('morphologist.'):
axon_module = '{}.axon'.format(morpho_module)
cnn_module = 'deepsulci.sulci_labeling.capsul.labeling'

morphologist = importlib.import_module(
'{}.morphologist'.format(morpho_module))
Expand Down Expand Up @@ -163,8 +230,11 @@ def declare_morpho_schemas(morpho_module):
'{}.sulcilabellingspamlocal'.format(axon_module))
sulcilabellingspammarkov = importlib.import_module(
'{}.sulcilabellingspammarkov'.format(axon_module))
sulcideeplabeling = importlib.import_module(
'{}.sulcideeplabeling'.format(axon_module))
sulcideeplabeling = importlib.import_module(cnn_module)
brainvolumes = importlib.import_module(
'{}.brainvolumes'.format(axon_module))
morpho_report = importlib.import_module(
'{}.morpho_report'.format(axon_module))

# patch processes to setup their requirements and schemas

Expand Down Expand Up @@ -197,6 +267,8 @@ def declare_morpho_schemas(morpho_module):
SulciLabellingSPAMMarkov \
= sulcilabellingspammarkov.SulciLabellingSPAMMarkov
SulciDeepLabeling = sulcideeplabeling.SulciDeepLabeling
morpho_report = morpho_report.morpho_report
brainvolumes = brainvolumes.brainvolumes

class MorphologistBIDS(ProcessSchema, schema='bids', process=Morphologist):
_ = {
Expand Down Expand Up @@ -236,14 +308,18 @@ class MorphologistBrainVISA(ProcessSchema, schema='brainvisa',
'sidebis': None,
'seg_directory': None,
'suffix': None,
'extension': 'nii',
'extension': 'nii.gz',
}
t1mri_nobias = {
'analysis': lambda **kwargs: f'{kwargs["metadata"].analysis}',
'side': None,
'sidebis': None,
'seg_directory': None,
'suffix': None,
'extension': 'nii',
'extension': 'nii.gz',
}
commissure_coordinates = {
'extension': 'APC',
}
t1mri_referential = {
'analysis': undefined,
Expand All @@ -262,12 +338,17 @@ class MorphologistBrainVISA(ProcessSchema, schema='brainvisa',
'side': None,
'sidebis': None,
'extension': 'trm'}
HeadMesh_head_mesh = {

}
left_labelled_graph = {
'part': 'left_hemi'
}
right_labelled_graph = {
'part': 'right_hemi'
}
Report_subject = {'modality': None}
GlobalMorphometry_subject = {'modality': None}

class SPM12NormalizationBIDS(ProcessSchema, schema='bids',
process=normalization_t1_spm12_reinit):
Expand Down Expand Up @@ -310,6 +391,12 @@ class FSLNormalizationBrainVISA(ProcessSchema, schema='brainvisa',
'suffix': 'fsl',
'extension': 'mat'
}
normalized_anatomy_data = {
'analysis': undefined,
'prefix': 'normalized_FSL',
'suffix': None,
'extension': 'nii.gz'
}

class T1BiasCorrectionBIDS(ProcessSchema, schema='bids',
process=T1BiasCorrection):
Expand Down Expand Up @@ -485,6 +572,78 @@ class SulciDeepLabelingBrainVISA(ProcessSchema, schema='brainvisa',
f'{kwargs["metadata"].sulci_recognition_session}',
'extension': 'arg'}

class BrainVolumesBIDS(ProcessSchema, schema='bids',
process=brainvolumes):
pass

class BrainVolumesBrainVISA(ProcessSchema, schema='brainvisa',
process=brainvolumes):
_ = {
'*': {'seg_directory': 'segmentation'}}
left_csf = {
'prefix': 'csf',
'side': 'L',
'sulci_graph_version': None,
'sulci_recognition_session': None,
'extension': 'nii.gz',
}
right_csf = {
'prefix': 'csf',
'side': 'R',
'sulci_graph_version': None,
'sulci_recognition_session': None,
'extension': 'nii.gz',
}
brain_volumes_file = {
'prefix': 'brain_volumes',
'suffix': None,
'side': None,
'sidebis': None,
'sulci_graph_version': None,
'sulci_recognition_session': None,
'extension': 'csv',
}
subject = {
'seg_directory': None,
'prefix': None,
'center': undefined,
'side': None,
'modality': None,
'acquisition': None,
'analysis': undefined,
'subject_in_filename': False,
'extension': None
}

class MorphoReportBIDS(ProcessSchema, schema='bids',
process=morpho_report):
pass

class MorphoReportBrainVISA(ProcessSchema, schema='brainvisa',
process=morpho_report):
_ = {
'*': {'seg_directory': None}}
report = {
'prefix': None,
'side': None,
'sidebis': None,
'subject_in_filename': False,
'sulci_graph_version': None,
'sulci_recognition_session': None,
'suffix': 'morphologist_report',
'extension': 'pdf'
}
subject = {
'prefix': None,
'center': undefined,
'side': None,
'modality': None,
'acquisition': None,
'analysis': undefined,
'subject_in_filename': False,
'extension': None
}

class MorphologistShared(ProcessSchema, schema='brainvisa_shared',
process=Morphologist):
PrepareSubject_Normalization_Normalization_AimsMIRegister_anatomical_template = {'data_id': 'normalization_template'}
Expand Down
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