Replace normalize by flirt

Author: bclenet

examples/nipype/code/merge_prov.py

@@ -8,20 +8,20 @@
 
 # List of available prov files
 prov_soft_files = [
-	'prov/prov-normalize_soft.prov.json'
+	'prov/prov-flirt_soft.prov.json'
 ]
 prov_env_files = [
-	'prov/prov-normalize_env.prov.json'
+	'prov/prov-flirt_env.prov.json'
 ]
 prov_act_files = [
-	'derivatives/normalize/sub-001/anat/sub-001_prov-normalize_act.prov.json'
+	'derivatives/flirt/sub-001/anat/sub-001_prov-flirt_act.prov.json'
 ]
 prov_ent_files = [
-	'prov/prov-normalize_ent.prov.json'
+	'prov/prov-flirt_ent.prov.json'
 ]
 sidecar_files = [
-	'derivatives/normalize/sub-001/anat/sub-001_T1w_brain.json',
-	'derivatives/normalize/sub-001/anat/sub-001_space-mni152nlin2009casym_T1w_brain.json'
+	'derivatives/flirt/sub-001/anat/sub-001_T1w_brain.json',
+	'derivatives/flirt/sub-001/anat/sub-001_space-mni152nlin2009casym_T1w_brain.json'
 ]
 
 # Base jsonld
@@ -34,7 +34,7 @@
 }
 
 # Add context and version
-with open('prov/prov-normalize_base.prov.json', encoding = 'utf-8') as file:
+with open('prov/prov-flirt_base.prov.json', encoding = 'utf-8') as file:
 	base_provenance.update(json.load(file))
 
 # Parse Software
@@ -90,5 +90,5 @@
 					})
 
 # Write jsonld
-with open('prov/merged/prov-normalize.prov.jsonld', 'w', encoding = 'utf-8') as file:
+with open('prov/merged/prov-flirt.prov.jsonld', 'w', encoding = 'utf-8') as file:
 	file.write(json.dumps(base_provenance, indent = 2))

examples/nipype/code/normalize.py

@@ -19,9 +19,9 @@
 brain_extraction = Node(BET(), name = 'brain_extraction')
 brain_extraction.inputs.in_file = abspath('sub-001/anat/sub-001_T1w.nii.gz')
 
-normalization = Node(FLIRT(), name = 'normalization')
-normalization.inputs.reference = Info.standard_image('MNI152_T1_1mm_brain.nii.gz')
-workflow.connect(brain_extraction, 'out_file', normalization, 'in_file')
+flirt = Node(FLIRT(), name = 'flirt')
+flirt.inputs.reference = Info.standard_image('MNI152_T1_1mm_brain.nii.gz')
+workflow.connect(brain_extraction, 'out_file', flirt, 'in_file')
 
 export_brain = Node(ExportFile(), name = 'export_brain')
 export_brain.inputs.clobber = True

examples/nipype/derivatives/flirt/sub-001/anat/sub-001_prov-flirt_act.prov.json

@@ -13,7 +13,7 @@
     ]
   },
   "bids::prov/#flirt-xzje9hjh": {
-    "Label": "normalization",
+    "Label": "flirt",
     "Command": "flirt -in /work/derivatives/bids_prov_workflow/brain_extraction/sub-001_T1w_brain.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out sub-001_T1w_brain_flirt.nii.gz -omat sub-001_T1w_brain_flirt.mat",
     "AssociatedWith": "bids::prov/#fsl-e1oq534p",
     "Used": [
@@ -42,7 +42,7 @@
     "AssociatedWith": "bids::prov/#nipype-s9w94f9u",
     "Used": [
       {
-        "Id": "bids::derivatives/bids_prov_workflow/normalization/sub-001_T1w_brain_flirt.nii.gz",
+        "Id": "bids::derivatives/bids_prov_workflow/flirt/sub-001_T1w_brain_flirt.nii.gz",
         "Type": "Entity",
         "Label": "sub-001_T1w_brain_flirt.nii.gz",
         "GeneratedBy": "bids::prov/#flirt-xzje9hjh"