a few fixes in Morphologist schema. Much more needs to be done

populse · Jul 24, 2023 · f54df7c · f54df7c
1 parent d777de8
commit f54df7c
Showing 1 changed file with 19 additions and 0 deletions.
diff --git a/capsul/schemas/brainvisa.py b/capsul/schemas/brainvisa.py
@@ -310,6 +310,13 @@ class MorphologistBrainVISA(ProcessSchema, schema='brainvisa',
             'suffix': None,
             'extension': 'nii.gz',
         }
+        Renorm_skull_stripped = {
+            'extension': 'nii.gz',
+        }
+        normalized_t1mri = {
+            'analysis': undefined,
+            'extension': 'nii.gz',
+        }
         t1mri_nobias = {
             'analysis': lambda **kwargs: f'{kwargs["metadata"].analysis}',
             'side': None,
@@ -319,8 +326,12 @@ class MorphologistBrainVISA(ProcessSchema, schema='brainvisa',
             'extension': 'nii.gz',
         }
         commissure_coordinates = {
+            'analysis': undefined,
             'extension': 'APC',
         }
+        BrainSegmentation_brain_mask = {
+            'extension': 'nii.gz',
+        }
         t1mri_referential = {
             'analysis': undefined,
             'seg_directory': 'registration',
@@ -387,11 +398,13 @@ class AimsNormalizationShared(ProcessSchema, schema='brainvisa_shared',
     class FSLNormalizationBrainVISA(ProcessSchema, schema='brainvisa',
                                     process=Normalization_FSL_reinit):
         transformation_matrix = {
+            'seg_directory': 'registration',
             'analysis': undefined,
             'suffix': 'fsl',
             'extension': 'mat'
         }
         normalized_anatomy_data = {
+            'seg_directory': None,
             'analysis': undefined,
             'prefix': 'normalized_FSL',
             'suffix': None,
@@ -404,6 +417,12 @@ class T1BiasCorrectionBIDS(ProcessSchema, schema='bids',
 
     class T1BiasCorrectionBrainVISA(ProcessSchema, schema='brainvisa',
                                     process=T1BiasCorrection):
+        _ = {
+            '*': {
+                'seg_directory': None,
+                'analysis': lambda **kwargs: f'{kwargs["metadata"].analysis}',
+            }
+        }
         t1mri_nobias = {'prefix': 'nobias'}
         b_field = {'prefix': 'biasfield'}
         hfiltered = {'prefix': 'hfiltered'}