Replace normalize by flirt

Author: bclenet

examples/nipype/README.md

@@ -16,7 +16,7 @@ See [hereafter](#running-the-workflow) for more details on how to run the workfl
 In order to describe provenance records using BIDS Prov, we use:
 
 * the `GeneratedBy` field of JSON sidecar files, already existing in the BIDS specification;
-* modality agnostic files inside the `prov/` directory
+* modality agnostic files inside the `derivatives/flirt/prov/` directory
 * a modality agnostic file inside the `derivatives/flirt/sub-001/anat/` directory
 
 After running the workflow and adding provenance traces, the resulting directory tree looks like this:
@@ -55,7 +55,7 @@ The python script `code/merge_prov.py` aims at merging all provenance records in
 
 ```shell
 pip install bids-prov==0.1.0
-mkdir prov/merged/
+mkdir derivatives/flirt/prov/merged/
 python code/merge_prov.py
 ```
 
@@ -69,7 +69,7 @@ We are then able to visualize these provenance files using the following command
 
 ```shell
 pip install bids-prov==0.1.0
-bids_prov_visualizer --input_file prov/merged/prov-flirt.prov.jsonld --output_file prov/merged/prov-flirt.prov.png
+bids_prov_visualizer --input_file derivatives/flirt/prov/merged/prov-flirt.prov.jsonld --output_file derivatives/flirt/prov/merged/prov-flirt.prov.png
 ```
 
 ![](/examples/nipype/prov/merged/prov-flirt.prov.png)

examples/nipype/code/merge_prov.py

@@ -8,16 +8,16 @@
 
 # List of available prov files
 prov_soft_files = [
-	'prov/prov-flirt_soft.prov.json'
+	'derivatives/flirt/prov/prov-flirt_soft.prov.json'
 ]
 prov_env_files = [
-	'prov/prov-flirt_env.prov.json'
+	'derivatives/flirt/prov/prov-flirt_env.prov.json'
 ]
 prov_act_files = [
 	'derivatives/flirt/sub-001/anat/sub-001_prov-flirt_act.prov.json'
 ]
 prov_ent_files = [
-	'prov/prov-flirt_ent.prov.json'
+	'derivatives/flirt/prov/prov-flirt_ent.prov.json'
 ]
 sidecar_files = [
 	'derivatives/flirt/sub-001/anat/sub-001_T1w_brain.json',
@@ -34,7 +34,7 @@
 }
 
 # Add context and version
-with open('prov/prov-flirt_base.prov.json', encoding = 'utf-8') as file:
+with open('derivatives/flirt/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-flirt.prov.jsonld', 'w', encoding = 'utf-8') as file:
+with open('derivatives/flirt/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

@@ -26,14 +26,14 @@
 export_brain = Node(ExportFile(), name = 'export_brain')
 export_brain.inputs.clobber = True
 export_brain.inputs.out_file = abspath(
-	'derivatives/normalize/sub-001/anat/sub-001_T1w_brain.nii.gz')
+	'derivatives/flirt/sub-001/anat/sub-001_T1w_brain.nii.gz')
 workflow.connect(brain_extraction, 'out_file', export_brain, 'in_file')
 
-export_normalized_brain = Node(ExportFile(), name = 'export_normalized_brain')
-export_normalized_brain.inputs.clobber = True
-export_normalized_brain.inputs.out_file = abspath(
-	'derivatives/normalize/sub-001/anat/sub-001_space-mni152nlin2009casym_T1w_brain.nii.gz')
-workflow.connect(brain_extraction, 'out_file', export_normalized_brain, 'in_file')
+export_brain_MNI_space = Node(ExportFile(), name = 'export_brain_MNI_space')
+export_brain_MNI_space.inputs.clobber = True
+export_brain_MNI_space.inputs.out_file = abspath(
+	'derivatives/flirt/sub-001/anat/sub-001_space-mni152nlin2009casym_T1w_brain.nii.gz')
+workflow.connect(brain_extraction, 'out_file', export_brain_MNI_space, 'in_file')
 
 # Run workflow
 workflow.run()

examples/nipype/derivatives/flirt/prov/merged/prov-flirt.prov.jsonld

@@ -31,7 +31,7 @@
         "Id": "bids::prov/#bet-ys913vx4"
       },
       {
-        "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": [
@@ -57,12 +57,12 @@
         "Id": "bids::prov/#export_file-i1cblvll"
       },
       {
-        "Label": "export_normalized_brain",
+        "Label": "export_brain_MNI_space",
         "Command": "shutil.copy",
         "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"
@@ -83,11 +83,11 @@
         "Id": "/usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz"
       },
       {
-        "Id": "bids::derivatives/normalize/sub-001/anat/sub-001_T1w_brain.nii.gz",
+        "Id": "bids::derivatives/flirt/sub-001/anat/sub-001_T1w_brain.nii.gz",
         "GeneratedBy": "bids::prov/#export_file-i1cblvll"
       },
       {
-        "Id": "bids::derivatives/normalize/sub-001/anat/sub-001_space-mni152nlin2009casym_T1w_brain.nii.gz",
+        "Id": "bids::derivatives/flirt/sub-001/anat/sub-001_space-mni152nlin2009casym_T1w_brain.nii.gz",
         "GeneratedBy": "bids::prov/#export_file-fpw3jrwy"
       }
     ]

examples/nipype/derivatives/flirt/prov/merged/prov-flirt.prov.png

@@ -37,7 +37,7 @@
     ]
   },
   "bids::prov/#export_file-fpw3jrwy": {
-    "Label": "export_normalized_brain",
+    "Label": "export_brain_MNI_space",
     "Command": "shutil.copy",
     "AssociatedWith": "bids::prov/#nipype-s9w94f9u",
     "Used": [