freesurfer segmentation results extraction activity example BIDS-Prov #60
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init jsonld files for spm_default
…nto spm_default_v2
[WIP]v0 for spm parser
SPM parser config is now external
FIX - README
remiadon
reviewed
Jun 18, 2021
| "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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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....
| "@id": "niiri:ff2754fe-1585-11eb-b1e7-1094bbf2086c", | ||
| "description": "Freesurfer segmentation statistics", | ||
| "startedAtTime": "2018-11-27T21:42:49", | ||
| "wasAttributedTo": "RRID:SCR_001847", |
|
(Note for @bclenet: let's keep this PR open as it is) |
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See README.md file for additional information. This is an example derived from ABIDE NIDM files containing Freesurfer segmentation statistics.