Subject Id changes

bclenet · bclenet · commit 8728b1390fab · 2025-02-05T15:01:43.000+01:00
diff --git a/examples/heudiconv/code/merge_prov.py b/examples/heudiconv/code/merge_prov.py
@@ -20,8 +20,8 @@
 	'prov/prov-heudiconv_ent.prov.json'
 ]
 sidecar_files = [
-	'sub-None/func/sub-None_task-oneback_run-01_bold.json',
-	'sub-None/anat/sub-None_run-1_T1w.json'
+	'sub-001/func/sub-001_task-oneback_run-01_bold.json',
+	'sub-001/anat/sub-001_run-1_T1w.json'
 ]
 
 # Base jsonld
diff --git a/examples/heudiconv/participants.tsv b/examples/heudiconv/participants.tsv
@@ -1,2 +1,3 @@
 participant_id	age	sex	group
 sub-02	42	F	control
+sub-anon	42	F	control
diff --git a/examples/heudiconv/prov/merged/prov-heudiconv.prov.jsonld b/examples/heudiconv/prov/merged/prov-heudiconv.prov.jsonld
@@ -2,15 +2,15 @@
   "Records": {
     "Software": [
       {
-        "Label": "Heudiconv",
+        "Label": "heudiconv",
         "Version": "v1.3.2",
         "Id": "bids::prov/heudiconv-a9x5yd3j"
       }
     ],
     "Activities": [
       {
         "Label": "Conversion",
-        "Command": "heudiconv --files sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/*.dcm -o . -f sourcedata/hirni-demo/code/hirni-toolbox/converters/heudiconv/hirni_heuristic.py -s 01 -ss acq1 -c dcm2niix -b --minmeta --overwrite",
+        "Command": "heudiconv --files sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/*.dcm -o . -f sourcedata/hirni-demo/code/hirni-toolbox/converters/heudiconv/hirni_heuristic.py -s 02 -ss acq1 -c dcm2niix -b --minmeta --overwrite",
         "AssociatedWith": "bids::prov/heudiconv-a9x5yd3j",
         "Used": [
           "bids::prov/fedora-1cu6r6ou",
@@ -22,7 +22,7 @@
       },
       {
         "Label": "Conversion",
-        "Command": "heudiconv --files sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/* -o . -f sourcedata/hirni-demo/code/hirni-toolbox/converters/heudiconv/hirni_heuristic.py -s 01 -ss acq2 -c dcm2niix -b --minmeta --overwrite",
+        "Command": "heudiconv --files sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/* -o . -f sourcedata/hirni-demo/code/hirni-toolbox/converters/heudiconv/hirni_heuristic.py -s 02 -ss acq2 -c dcm2niix -b --minmeta --overwrite",
         "AssociatedWith": "bids::prov/heudiconv-a9x5yd3j",
         "Used": [
           "bids::prov/fedora-pgrzf567",
@@ -51,7 +51,7 @@
         "Id": "bids::prov/fedora-pgrzf567"
       },
       {
-        "Label": "heuristics",
+        "Label": "heuristic",
         "Id": "bids::sourcedata/hirni-demo/code/hirni-toolbox/converters/heudiconv/hirni_heuristic.py"
       },
       {
@@ -127,11 +127,11 @@
         "Id": "bids::task-oneback_bold.json"
       },
       {
-        "Id": "bids::sub-None/func/sub-None_task-oneback_run-01_bold.nii.gz",
+        "Id": "bids::sub-001/func/sub-001_task-oneback_run-01_bold.nii.gz",
         "GeneratedBy": "bids::prov/conversion-5a66f5be"
       },
       {
-        "Id": "bids::sub-None/anat/sub-None_run-1_T1w.nii.gz",
+        "Id": "bids::sub-001/anat/sub-001_run-1_T1w.nii.gz",
         "GeneratedBy": "bids::prov/conversion-00f3a18f"
       }
     ]
diff --git a/examples/heudiconv/prov/merged/prov-heudiconv.prov.png b/examples/heudiconv/prov/merged/prov-heudiconv.prov.png
diff --git a/examples/heudiconv/prov/prov-heudiconv_act.prov.json b/examples/heudiconv/prov/prov-heudiconv_act.prov.json
@@ -1,7 +1,7 @@
 {
   "bids::prov/conversion-00f3a18f": {
     "Label": "Conversion",
-    "Command": "heudiconv --files sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/*.dcm -o . -f sourcedata/hirni-demo/code/hirni-toolbox/converters/heudiconv/hirni_heuristic.py -s 01 -ss acq1 -c dcm2niix -b --minmeta --overwrite",
+    "Command": "heudiconv --files sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/*.dcm -o . -f sourcedata/hirni-demo/code/hirni-toolbox/converters/heudiconv/hirni_heuristic.py -s 02 -ss acq1 -c dcm2niix -b --minmeta --overwrite",
     "AssociatedWith": "bids::prov/heudiconv-a9x5yd3j",
     "Used": [
       "bids::prov/fedora-1cu6r6ou",
@@ -12,7 +12,7 @@
   },
   "bids::prov/conversion-5a66f5be": {
     "Label": "Conversion",
-    "Command": "heudiconv --files sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/* -o . -f sourcedata/hirni-demo/code/hirni-toolbox/converters/heudiconv/hirni_heuristic.py -s 01 -ss acq2 -c dcm2niix -b --minmeta --overwrite",
+    "Command": "heudiconv --files sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/* -o . -f sourcedata/hirni-demo/code/hirni-toolbox/converters/heudiconv/hirni_heuristic.py -s 02 -ss acq2 -c dcm2niix -b --minmeta --overwrite",
     "AssociatedWith": "bids::prov/heudiconv-a9x5yd3j",
     "Used": [
       "bids::prov/fedora-pgrzf567",
diff --git a/examples/heudiconv/prov/prov-heudiconv_soft.prov.json b/examples/heudiconv/prov/prov-heudiconv_soft.prov.json
@@ -1,6 +1,6 @@
 {
-  "bids::prov/heudiconv-a9x5yd3j": {    
-    "Label": "Heudiconv",
+  "bids::prov/heudiconv-a9x5yd3j": {
+    "Label": "heudiconv",
     "Version": "v1.3.2"
   }
 }
diff --git a/examples/heudiconv/sub-001/anat/sub-001_run-1_T1w.json b/examples/heudiconv/sub-001/anat/sub-001_run-1_T1w.json
@@ -17,4 +17,6 @@
   "SeriesNumber": 401,
   "SliceThickness": 0.666667,
   "SoftwareVersions": "0.4.11",
-  "SpacingBetweenSlices": 0.666667}
+  "SpacingBetweenSlices": 0.666667,
+  "GeneratedBy": "bids::prov/conversion-00f3a18f"
+}
diff --git a/examples/heudiconv/sub-001/anat/sub-001_run-1_T1w.nii.gz b/examples/heudiconv/sub-001/anat/sub-001_run-1_T1w.nii.gz
diff --git a/examples/heudiconv/sub-001/func/sub-001_task-oneback_run-01_bold.json b/examples/heudiconv/sub-001/func/sub-001_task-oneback_run-01_bold.json
@@ -59,4 +59,6 @@
   "SpacingBetweenSlices": 3.3,
   "TaskName": "oneback",
   "UsePhilipsFloatNotDisplayScaling": 1,
-  "WaterFatShift": 12.4991}
+  "WaterFatShift": 12.4991,
+  "GeneratedBy": "bids::prov/conversion-5a66f5be"
+}
diff --git a/examples/heudiconv/sub-001/func/sub-001_task-oneback_run-01_bold.nii.gz b/examples/heudiconv/sub-001/func/sub-001_task-oneback_run-01_bold.nii.gz
diff --git a/examples/heudiconv/sub-001/func/sub-001_task-oneback_run-01_events.tsv b/examples/heudiconv/sub-001/func/sub-001_task-oneback_run-01_events.tsv
@@ -0,0 +1 @@
+onset	duration	trial_type	response_time	stim_file	TODO -- fill in rows and add more tab-separated columns if desired
diff --git a/examples/heudiconv/sub-001/sub-001_scans.tsv b/examples/heudiconv/sub-001/sub-001_scans.tsv
@@ -0,0 +1,3 @@
+filename	acq_time	operator	randstr
+anat/sub-001_run-1_T1w.nii.gz	2013-07-17T13:25:18	n/a	e72d11b8
+func/sub-001_task-oneback_run-01_bold.nii.gz	2014-04-25T16:04:22.680000	n/a	c2b66122
diff --git a/examples/heudiconv/task-oneback_bold.json b/examples/heudiconv/task-oneback_bold.json
@@ -12,6 +12,7 @@
   "EstimatedEffectiveEchoSpacing": 0.000355975,
   "EstimatedTotalReadoutTime": 0.028122,
   "FlipAngle": 90,
+  "GeneratedBy": "bids::prov/conversion-5a66f5be",
   "HeudiconvVersion": "1.3.2",
   "ImageOrientationPatientDICOM": [0.999805, -0.0114282, 0.0161145, 0.0147905, 0.973763, -0.227084],
   "ImageType": [

Original file line number	Diff line number	Diff line change
`@@ -20,8 +20,8 @@`
`20`	`20`	`'prov/prov-heudiconv_ent.prov.json'`
`21`	`21`	`]`
`22`	`22`	`sidecar_files = [`
`23`		`- 'sub-None/func/sub-None_task-oneback_run-01_bold.json',`
`24`		`- 'sub-None/anat/sub-None_run-1_T1w.json'`
	`23`	`+ 'sub-001/func/sub-001_task-oneback_run-01_bold.json',`
	`24`	`+ 'sub-001/anat/sub-001_run-1_T1w.json'`
`25`	`25`	`]`
`26`	`26`
`27`	`27`	`# Base jsonld`
Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,3 @@`
`1`	`1`	`participant_id age sex group`
`2`	`2`	`sub-02 42 F control`
	`3`	`+sub-anon 42 F control`
Original file line number	Diff line number	Diff line change
`@@ -2,15 +2,15 @@`
`2`	`2`	`"Records": {`
`3`	`3`	`"Software": [`
`4`	`4`	`{`
`5`		`- "Label": "Heudiconv",`
	`5`	`+ "Label": "heudiconv",`
`6`	`6`	`"Version": "v1.3.2",`
`7`	`7`	`"Id": "bids::prov/heudiconv-a9x5yd3j"`
`8`	`8`	`}`
`9`	`9`	`],`
`10`	`10`	`"Activities": [`
`11`	`11`	`{`
`12`	`12`	`"Label": "Conversion",`
`13`		`- "Command": "heudiconv --files sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/*.dcm -o . -f sourcedata/hirni-demo/code/hirni-toolbox/converters/heudiconv/hirni_heuristic.py -s 01 -ss acq1 -c dcm2niix -b --minmeta --overwrite",`
	`13`	`+ "Command": "heudiconv --files sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/*.dcm -o . -f sourcedata/hirni-demo/code/hirni-toolbox/converters/heudiconv/hirni_heuristic.py -s 02 -ss acq1 -c dcm2niix -b --minmeta --overwrite",`
`14`	`14`	`"AssociatedWith": "bids::prov/heudiconv-a9x5yd3j",`
`15`	`15`	`"Used": [`
`16`	`16`	`"bids::prov/fedora-1cu6r6ou",`
`@@ -22,7 +22,7 @@`
`22`	`22`	`},`
`23`	`23`	`{`
`24`	`24`	`"Label": "Conversion",`
`25`		`- "Command": "heudiconv --files sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/* -o . -f sourcedata/hirni-demo/code/hirni-toolbox/converters/heudiconv/hirni_heuristic.py -s 01 -ss acq2 -c dcm2niix -b --minmeta --overwrite",`
	`25`	`+ "Command": "heudiconv --files sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/* -o . -f sourcedata/hirni-demo/code/hirni-toolbox/converters/heudiconv/hirni_heuristic.py -s 02 -ss acq2 -c dcm2niix -b --minmeta --overwrite",`
`26`	`26`	`"AssociatedWith": "bids::prov/heudiconv-a9x5yd3j",`
`27`	`27`	`"Used": [`
`28`	`28`	`"bids::prov/fedora-pgrzf567",`
`@@ -51,7 +51,7 @@`
`51`	`51`	`"Id": "bids::prov/fedora-pgrzf567"`
`52`	`52`	`},`
`53`	`53`	`{`
`54`		`- "Label": "heuristics",`
	`54`	`+ "Label": "heuristic",`
`55`	`55`	`"Id": "bids::sourcedata/hirni-demo/code/hirni-toolbox/converters/heudiconv/hirni_heuristic.py"`
`56`	`56`	`},`
`57`	`57`	`{`
`@@ -127,11 +127,11 @@`
`127`	`127`	`"Id": "bids::task-oneback_bold.json"`
`128`	`128`	`},`
`129`	`129`	`{`
`130`		`- "Id": "bids::sub-None/func/sub-None_task-oneback_run-01_bold.nii.gz",`
	`130`	`+ "Id": "bids::sub-001/func/sub-001_task-oneback_run-01_bold.nii.gz",`
`131`	`131`	`"GeneratedBy": "bids::prov/conversion-5a66f5be"`
`132`	`132`	`},`
`133`	`133`	`{`
`134`		`- "Id": "bids::sub-None/anat/sub-None_run-1_T1w.nii.gz",`
	`134`	`+ "Id": "bids::sub-001/anat/sub-001_run-1_T1w.nii.gz",`
`135`	`135`	`"GeneratedBy": "bids::prov/conversion-00f3a18f"`
`136`	`136`	`}`
`137`	`137`	`]`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`		`- "bids::prov/heudiconv-a9x5yd3j": {`
`3`		`- "Label": "Heudiconv",`
	`2`	`+ "bids::prov/heudiconv-a9x5yd3j": {`
	`3`	`+ "Label": "heudiconv",`
`4`	`4`	`"Version": "v1.3.2"`
`5`	`5`	`}`
`6`	`6`	`}`