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Some provenance traces for func files
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8 files changed

+327
-25
lines changed

8 files changed

+327
-25
lines changed

‎examples/fmriprep/derivatives/fmriprep/code/merge_prov.py‎

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -14,11 +14,13 @@
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'prov/prov-fmriprep_env.prov.json'
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]
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prov_act_files = [
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'sub-001/anat/sub-001_prov-fmriprep_act.prov.json'
17+
'sub-001/anat/sub-001_T1w_prov-fmriprep_act.prov.json',
18+
'sub-001/func/sub-001_task-MGT_bold_prov-fmriprep_act.prov.json'
1819
]
1920
prov_ent_files = [
2021
'prov/prov-fmriprep_ent.prov.json',
21-
'sub-001/anat/sub-001_prov-fmriprep_ent.prov.json'
22+
'sub-001/anat/sub-001_T1w_prov-fmriprep_ent.prov.json',
23+
'sub-001/func/sub-001_task-MGT_bold_prov-fmriprep_ent.prov.json'
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]
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sidecar_files = [
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]

‎examples/fmriprep/derivatives/fmriprep/prov/merged/prov-fmriprep.prov.jsonld‎

Lines changed: 158 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -7,22 +7,32 @@
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"AltIdentifier": "RRID:SCR_016216",
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"Id": "bids::prov/fmriprep-ughfyb4k"
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},
10+
{
11+
"Label": "Nipype",
12+
"Version": "1.1.2",
13+
"AltIdentifier": "RRID:SCR_002502",
14+
"prov:actedOnBehalfOf": "bids::prov/fmriprep-ughfyb4k",
15+
"Id": "bids::prov/nipype-s9w94f9u"
16+
},
1017
{
1118
"Label": "ANTs",
1219
"Version": "2.2.0",
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"AltIdentifier": "RRID:SCR_004757",
21+
"prov:actedOnBehalfOf": "bids::prov/nipype-s9w94f9u",
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"Id": "urn:ants-bagzrxi0"
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},
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{
1725
"Label": "FreeSurfer",
1826
"Version": "6.0.1",
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"AltIdentifier": "RRID:SCR_001847",
28+
"prov:actedOnBehalfOf": "bids::prov/nipype-s9w94f9u",
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"Id": "urn:freesurfer-bqv4h9k2"
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},
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{
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"Label": "FSL",
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"Version": "5.0.9",
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"AltIdentifier": "RRID:SCR_002823",
35+
"prov:actedOnBehalfOf": "bids::prov/nipype-s9w94f9u",
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"Id": "urn:fsl-e1oq534p"
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}
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],
@@ -31,8 +41,7 @@
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"Label": "Correction for intensity non-uniformity (INU)",
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"Command": "N4BiasFieldCorrection",
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"AssociatedWith": [
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"urn:ants-bagzrxi0",
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"bids::prov/fmriprep-ughfyb4k"
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"urn:ants-bagzrxi0"
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],
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"Used": [
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{
@@ -47,8 +56,7 @@
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"Label": "Skull stripping",
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"Command": "antsBrainExtraction.sh",
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"AssociatedWith": [
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"urn:ants-bagzrxi0",
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"bids::prov/fmriprep-ughfyb4k"
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"urn:ants-bagzrxi0"
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],
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"Used": [
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"https://github.com/brainspaces/OASIS/blob/master/OASIS-2x2x2.nii.gz",
@@ -60,8 +68,7 @@
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"Label": "Brain surface reconstruction",
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"Command": "recon-all",
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"AssociatedWith": [
63-
"urn:freesurfer-bqv4h9k2",
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"bids::prov/fmriprep-ughfyb4k"
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"urn:freesurfer-bqv4h9k2"
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],
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"Used": [],
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"Id": "bids::prov/brain-surface-reconstruction-uac8ysmu"
@@ -70,8 +77,7 @@
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"Label": "Spatial normalization to the ICBM 152",
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"Command": "antsRegistration",
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"AssociatedWith": [
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"urn:ants-bagzrxi0",
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"bids::prov/fmriprep-ughfyb4k"
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"urn:ants-bagzrxi0"
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],
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"Used": [
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"http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_sym_09c_nifti.zip",
@@ -88,11 +94,115 @@
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"Label": "Brain tissue segmentation",
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"Command": "feat",
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"AssociatedWith": [
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"urn:fsl-e1oq534p",
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"bids::prov/fmriprep-ughfyb4k"
97+
"urn:fsl-e1oq534p"
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],
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"Used": [],
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"Id": "bids::prov/brain-segmentation-egbeiwg9"
101+
},
102+
{
103+
"Label": "Generation of reference volume",
104+
"Command": "",
105+
"AssociatedWith": [
106+
"urn:fmriprep-ughfyb4k"
107+
],
108+
"Used": [
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{
110+
"Id": "bids:ds001734:sub-001/func/sub-001_task-MGT_run-01_bold.nii.gz",
111+
"Type": "Entity",
112+
"Label": "sub-001_task-MGT_run-01_bold.nii.gz"
113+
}
114+
],
115+
"Id": "bids::prov/reference-volume-6rnvuhfg"
116+
},
117+
{
118+
"Label": "Fielmap Estimation",
119+
"Command": "epidewarp.fsl",
120+
"AssociatedWith": [
121+
"urn:fsl-e1oq534p"
122+
],
123+
"Used": [
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{
125+
"Id": "bids:ds001734:sub-001/fmap/sub-001_magnitude1.nii.gz",
126+
"Type": "Entity",
127+
"Label": "sub-001_magnitude1.nii.gz"
128+
},
129+
{
130+
"Id": "bids:ds001734:sub-001/fmap/sub-001_magnitude2.nii.gz",
131+
"Type": "Entity",
132+
"Label": "sub-001_magnitude2.nii.gz"
133+
},
134+
{
135+
"Id": "bids:ds001734:sub-001/fmap/sub-001_phasediff.json",
136+
"Type": "Entity",
137+
"Label": "sub-001_phasediff.json"
138+
},
139+
{
140+
"Id": "bids:ds001734:sub-001/fmap/sub-001_phasediff.nii.gz",
141+
"Type": "Entity",
142+
"Label": "sub-001_phasediff.nii.gz"
143+
}
144+
],
145+
"Id": "bids::prov/fieldmap-estimation-gaodue11"
146+
},
147+
{
148+
"Label": "Unwarping",
149+
"Command": "",
150+
"AssociatedWith": [],
151+
"Used": [
152+
{
153+
"Id": "bids::prov/bold_reference",
154+
"Type": "Entity",
155+
"Label": "Bold reference"
156+
}
157+
],
158+
"Id": "bids::prov/unwarping-vogp4ylg"
159+
},
160+
{
161+
"Label": "Estimation of head motion parameters",
162+
"Command": "mcflirt",
163+
"AssociatedWith": [
164+
"urn:fsl-e1oq534p"
165+
],
166+
"Used": [
167+
{
168+
"Id": "bids::prov/bold_reference",
169+
"Type": "Entity",
170+
"Label": "Bold reference"
171+
}
172+
],
173+
"Id": "bids::prov/head-motion-p1cv54ps"
174+
},
175+
{
176+
"Label": "Resampling to native space",
177+
"Command": "",
178+
"AssociatedWith": [],
179+
"Used": [],
180+
"Id": "bids::prov/resampling-to-nativespace-f0ataumv"
181+
},
182+
{
183+
"Label": "Co-registration",
184+
"Command": "bbregister",
185+
"AssociatedWith": [
186+
"urn:freesurfer-bqv4h9k2"
187+
],
188+
"Used": [],
189+
"Id": "bids::prov/co-registration-f0ataumv"
190+
},
191+
{
192+
"Label": "Resampling to MNI152NLin2009cAsym",
193+
"Command": "",
194+
"AssociatedWith": [],
195+
"Used": [],
196+
"Id": "bids::prov/normalization-22r4wc4k"
197+
},
198+
{
199+
"Label": "Confounding time-series computation",
200+
"Command": "",
201+
"AssociatedWith": [
202+
"bids::prov/nipype-s9w94f9u"
203+
],
204+
"Used": [],
205+
"Id": "bids::prov/confounds-computation-oy8gwd9v"
96206
}
97207
],
98208
"Entities": [
@@ -238,6 +348,44 @@
238348
"Label": "T1w_target-MNI152NLin2009cAsym_warp.h5",
239349
"GeneratedBy": "bids::prov/spatial-normalisation-uuwz1aep",
240350
"Id": "bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_target-MNI152NLin2009cAsym_warp.h5"
351+
},
352+
{
353+
"Label": "task-MGT_run-01_bold_confounds.tsv",
354+
"GeneratedBy": [
355+
"bids::prov/head-motion-p1cv54ps",
356+
"bids::prov/confounds-computation-oy8gwd9v"
357+
],
358+
"Id": "bids:ds001734:derivatives/fmriprep/sub-001/func/sub-001_task-MGT_run-01_bold_confounds.tsv"
359+
},
360+
{
361+
"Label": "task-MGT_run-01_bold_space-fsaverage5.L.func.gii",
362+
"GeneratedBy": "bids::prov/co-registration-f0ataumv",
363+
"Id": "bids:ds001734:derivatives/fmriprep/sub-001/func/sub-001_task-MGT_run-01_bold_space-fsaverage5.L.func.gii"
364+
},
365+
{
366+
"Label": "task-MGT_run-01_bold_space-fsaverage5.R.func.gii",
367+
"GeneratedBy": "bids::prov/co-registration-f0ataumv",
368+
"Id": "bids:ds001734:derivatives/fmriprep/sub-001/func/sub-001_task-MGT_run-01_bold_space-fsaverage5.R.func.gii"
369+
},
370+
{
371+
"Label": "task-MGT_run-01_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz",
372+
"GeneratedBy": "bids::prov/normalization-22r4wc4k",
373+
"Id": "bids:ds001734:derivatives/fmriprep/sub-001/func/sub-001_task-MGT_run-01_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz"
374+
},
375+
{
376+
"Label": "task-MGT_run-01_bold_space-MNI152NLin2009cAsym_preproc.nii.gz",
377+
"GeneratedBy": "bids::prov/normalization-22r4wc4k",
378+
"Id": "bids:ds001734:derivatives/fmriprep/sub-001/func/sub-001_task-MGT_run-01_bold_space-MNI152NLin2009cAsym_preproc.nii.gz"
379+
},
380+
{
381+
"Label": "task-MGT_run-01_bold_space-T1w_label-aparcaseg_roi.nii.gz",
382+
"GeneratedBy": "bids::prov/normalization-22r4wc4k",
383+
"Id": "bids:ds001734:derivatives/fmriprep/sub-001/func/sub-001_task-MGT_run-01_bold_space-T1w_label-aparcaseg_roi.nii.gz"
384+
},
385+
{
386+
"Label": "task-MGT_run-01_bold_space-T1w_label-aseg_roi.nii.gz",
387+
"GeneratedBy": "bids::prov/normalization-22r4wc4k",
388+
"Id": "bids:ds001734:derivatives/fmriprep/sub-001/func/sub-001_task-MGT_run-01_bold_space-T1w_label-aseg_roi.nii.gz"
241389
}
242390
]
243391
},

‎examples/fmriprep/derivatives/fmriprep/prov/merged/prov-fmriprep.prov.png‎

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‎examples/fmriprep/derivatives/fmriprep/prov/prov-fmriprep_soft.prov.json‎

Lines changed: 12 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -4,19 +4,28 @@
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"Version": "v1.1.6",
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"AltIdentifier": "RRID:SCR_016216"
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},
7+
"bids::prov/nipype-s9w94f9u": {
8+
"Label": "Nipype",
9+
"Version": "1.1.2",
10+
"AltIdentifier": "RRID:SCR_002502",
11+
"prov:actedOnBehalfOf": "bids::prov/fmriprep-ughfyb4k"
12+
},
713
"urn:ants-bagzrxi0": {
814
"Label": "ANTs",
915
"Version": "2.2.0",
10-
"AltIdentifier": "RRID:SCR_004757"
16+
"AltIdentifier": "RRID:SCR_004757",
17+
"prov:actedOnBehalfOf": "bids::prov/nipype-s9w94f9u"
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},
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"urn:freesurfer-bqv4h9k2": {
1320
"Label": "FreeSurfer",
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"Version": "6.0.1",
15-
"AltIdentifier": "RRID:SCR_001847"
22+
"AltIdentifier": "RRID:SCR_001847",
23+
"prov:actedOnBehalfOf": "bids::prov/nipype-s9w94f9u"
1624
},
1725
"urn:fsl-e1oq534p": {
1826
"Label": "FSL",
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"Version": "5.0.9",
20-
"AltIdentifier": "RRID:SCR_002823"
28+
"AltIdentifier": "RRID:SCR_002823",
29+
"prov:actedOnBehalfOf": "bids::prov/nipype-s9w94f9u"
2130
}
2231
}

‎examples/fmriprep/derivatives/fmriprep/sub-001/anat/sub-001_prov-fmriprep_act.prov.json‎ renamed to ‎examples/fmriprep/derivatives/fmriprep/sub-001/anat/sub-001_T1w_prov-fmriprep_act.prov.json‎

Lines changed: 5 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -3,8 +3,7 @@
33
"Label": "Correction for intensity non-uniformity (INU)",
44
"Command": "N4BiasFieldCorrection",
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"AssociatedWith": [
6-
"urn:ants-bagzrxi0",
7-
"bids::prov/fmriprep-ughfyb4k"
6+
"urn:ants-bagzrxi0"
87
],
98
"Used": [
109
{
@@ -18,8 +17,7 @@
1817
"Label": "Skull stripping",
1918
"Command": "antsBrainExtraction.sh",
2019
"AssociatedWith": [
21-
"urn:ants-bagzrxi0",
22-
"bids::prov/fmriprep-ughfyb4k"
20+
"urn:ants-bagzrxi0"
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],
2422
"Used": [
2523
"https://github.com/brainspaces/OASIS/blob/master/OASIS-2x2x2.nii.gz",
@@ -30,8 +28,7 @@
3028
"Label": "Brain surface reconstruction",
3129
"Command": "recon-all",
3230
"AssociatedWith": [
33-
"urn:freesurfer-bqv4h9k2",
34-
"bids::prov/fmriprep-ughfyb4k"
31+
"urn:freesurfer-bqv4h9k2"
3532
],
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"Used": [
3734
]
@@ -40,8 +37,7 @@
4037
"Label": "Spatial normalization to the ICBM 152",
4138
"Command": "antsRegistration",
4239
"AssociatedWith": [
43-
"urn:ants-bagzrxi0",
44-
"bids::prov/fmriprep-ughfyb4k"
40+
"urn:ants-bagzrxi0"
4541
],
4642
"Used": [
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"http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_sym_09c_nifti.zip",
@@ -57,8 +53,7 @@
5753
"Label": "Brain tissue segmentation",
5854
"Command": "feat",
5955
"AssociatedWith": [
60-
"urn:fsl-e1oq534p",
61-
"bids::prov/fmriprep-ughfyb4k"
56+
"urn:fsl-e1oq534p"
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],
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"Used": [
6459
]

‎examples/fmriprep/derivatives/fmriprep/sub-001/anat/sub-001_prov-fmriprep_ent.prov.json‎ renamed to ‎examples/fmriprep/derivatives/fmriprep/sub-001/anat/sub-001_T1w_prov-fmriprep_ent.prov.json‎

File renamed without changes.

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