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freesurfer segmentation results extraction activity example BIDS-Prov #60

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@dbkeator dbkeator commented Jun 17, 2021

See README.md file for additional information. This is an example derived from ABIDE NIDM files containing Freesurfer segmentation statistics.

Remi Adon and others added 30 commits March 5, 2020 18:35
[ADD] a basic README
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[ADD] CLI to visualize prov files
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init jsonld files for spm_default
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improve spm_default/realign.json
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[RM] types for parameters & simplify reading
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mke all examples use a context.json at the root
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spm_default realign uses entity from copies
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gitignore graphviz files
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[MV] context local URIs to remote URIs
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realign.json more infos on SPM
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[ADD] copy activity & explicit exp_dit in paths
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[ADD] entity link realign and coreg
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[RM] auditory fmri for now, may restore this later
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[ADD] type indexing for spm_default
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[RM] misleading references to bids namespace
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[RM] link to bids in context
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[remove] exp_dir definition
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type indexing agents in copies.json
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Merge pull request bids-standard#4 from Inria-Visages/spm_default
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init jsonld files for spm_default
define SPM Agent in realign.json
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Merge branch 'master' of https://github.com/Inria-Visages/BIDS-prov i…
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…nto spm_default_v2
instatiate semgent activity in realign.json
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mutliple copies && ids instead of labels
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add coreg, segment & normalise
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[ADD] .svg file for spm default
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[ADD] smoothing on functional img
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[ADD] model estimation
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add report to PDF
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reformat json files, graph is just a dict
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explicit name for copy and unzip
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remiadon and others added 25 commits February 19, 2021 14:54
@remiadon
SPM parser link activities via close names AND reference numbers
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Merge pull request bids-standard#50 from bids-standard/spm_parser
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[WIP]v0 for spm parser
@remiadon
SPM parser config is now external
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@remiadon
[FIX] CI for bids_prov.spm_parser
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@remiadon
SPM default graph in config
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@remiadon
spm_parser : hard coded mappings in yaml file
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@remiadon
[ADD] missing requirement
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@remiadon
SPM [FIX] duplicate gunzipped files
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@remiadon
SPM [ADD] predefined outputs in static config
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@remiadon
rename spm_config.py to avoid confusion
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@remiadon
[ADD] bids_prov/README
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@cmaumet
fix: avoid overwriting used dependency in the presence of used entities
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@cmaumet
Merge pull request bids-standard#54 from bids-standard/spm_parser_config
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SPM parser config is now external
@cmaumet
rename static_map
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@tiborauer
FIX - remove redundancy in README
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@tiborauer
FIX - typo in README
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@cmaumet
Merge pull request bids-standard#55 from tiborauer/patch-1
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FIX - README
@remiadon
SPM parser improve [DOC] and [RM] dead code
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@remiadon
SPM parser improve [DOC]
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@remiadon
[RM] reprecated closest_activity
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@remiadon
spm_parser set prov:atLocation for activities with default outputs
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@dbkeator
freesurfer segmentation results extraction example BIDS-Prov
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@dbkeator
fixing typo
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@dbkeator
beautifying indentation...lol
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@dbkeator
added link to freesurfer segmentation statistics -> NIDM / jsonld tool
cd87bc7
remiadon
remiadon reviewed Jun 18, 2021
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@cmaumet I make a few comments on this PR. There are relayed to the discussion we are having in the google doc

But this PR adds an interesting example to the ones we already have !

examples/freesurfer_segs/freesurfer_provenance.jsonld
"freesurfer:Title": "Segmentation Statistics",
"freesurfer:VoxelVolume_mm3": "1",
"freesurfer:anatomy_type": "volume",
"freesurfer:cmdline": "mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /opt/freesurfer-6.0.0-min/ASegStatsLUT.txt --subject sub-0050660",
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@remiadon remiadon Jun 18, 2021 •
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A command field has been added (as REQUIRED) in the definition of a Activity from our gdoc

So I guess freesurfer:cmdline should be renamed command and placed above (eg. after startedAtTime)

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Got it, will make the change....

examples/freesurfer_segs/freesurfer_provenance.jsonld
"@id": "niiri:ff2754fe-1585-11eb-b1e7-1094bbf2086c",
"description": "Freesurfer segmentation statistics",
"startedAtTime": "2018-11-27T21:42:49",
"wasAttributedTo": "RRID:SCR_001847",
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we used wasAssociatedWith to record the fact that an activity is a running instance of an Agent

an example here

And the def of this term in our common context here

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cmaumet commented May 21, 2024

(Note for @bclenet: let's keep this PR open as it is)

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djarecka commented Mar 17, 2025 •
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@cmaumet or others - is this PR a good start if I need to see an example for FS? Is it more or less align with the current idea? Or anyone has a better example?

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cmaumet commented Mar 17, 2025

@djarecka - this example is not up to date with current specification, sorry! Most current (and validated) examples are in: https://github.com/bids-standard/BEP028_BIDSprov/tree/master/examples/from_parsers. More examples (including dicom to nifti conversion and derivatives) are in progress.

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@dbkeator @cmaumet @djarecka @remiadon @tiborauer