rwblair’s gists

rwblair / gist:6e0871b454ad0e73a1e4b11ee3e59208

Last active April 20, 2023 19:24

deno_bids_examples_errors

	issue key filename schema path
	┌───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
	│ eeg_rest_fmri │
	└───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
	DWI_MISSING_BVEC sub-36_acq-NODDI10DIR_dwi.nii.gz schema.rules.checks.dwi.DWIMissingBvec

	DWI_MISSING_BVAL sub-36_acq-NODDI10DIR_dwi.nii.gz schema.rules.checks.dwi.DWIMissingBval

rwblair / gist:77f68a2d1dec63567b5e92400fc3fd80

Created April 15, 2022 18:47

oneliner used to generate common derivatives datatypes run from inside datatypes dir.

grep -oP "^\w*:" *.yaml | sed -r 's/^(.*).yaml:(.*):/\1_\2_common:\n  \$ref: schema.rules.datatypes.\1.\2\n  entities:\n    \$ref: schema.rules.datatypes.\1.\2.entities\n    space: OPTIONAL\n    desc: OPTIONAL\n/' > common_derivatives.yaml

rwblair / root.yaml

Created March 24, 2022 20:24

	---
	root:
	filename:
	entities:
	- any
	extensions:
	- '/'
	children:
	_use:
	- ./top_level_files.yaml

rwblair / example_ds002837_versions.txt

Last active May 13, 2021 17:33

$ aws s3api --no-sign-request list-object-versions --bucket=openneuro.org --prefix ds002837/derivatives/sub-9/func/sub-9_task-500daysofsummer_bold_preprocessedICA.nii.gz

	{
	"Versions": [
	{
	"ETag": "\"0d6a47221c91f039c105b28fbde7da27-2\"",
	"Size": 1854105076,
	"StorageClass": "STANDARD",
	"Key": "ds002837/derivatives/sub-9/func/sub-9_task-500daysofsummer_bold_preprocessedICA.nii.gz",
	"VersionId": "NlyjwYWAx9z36mkHMPHII6A6J3TqGIp2",
	"IsLatest": true,
	"LastModified": "2021-04-20T23:34:42.000Z"

rwblair / age_by_ds.txt

Created April 28, 2020 17:04

for file in $(find . -maxdepth 2 -name participants.tsv -exec grep -lP "\tage" {} \;); do echo $file && csvcut -t -c age $file | sort | uniq; done > age_by_ds.txt

	./ds001544/participants.tsv
	0
	age
	./ds000001/participants.tsv
	19
	20
	21
	22
	24
	26

rwblair / sex_by_ds.txt

Created April 28, 2020 16:17

for file in $(find . -maxdepth 2 -name participants.tsv -exec grep -lP "\tsex" {} \;); do echo $file && csvcut -t -c sex $file | sort | uniq; done > sex_by_ds.txt

	./ds001544/participants.tsv
	m
	sex
	./ds000001/participants.tsv
	F
	M
	"M,"
	sex
	./ds000244/participants.tsv
	F

rwblair / gist:3ecc156aad2840758e656a14844e6984

Last active March 31, 2020 15:28

Nested objects for pet schema.

	{
	"type": "object",
	"properties": {
	"info": {
	"type": "object"
	"properties": {
	"Modality": {"type": "string"}
	},
	"plasma": {
	"type": "object"

rwblair / gist:dc27f9f5891eca867d855d853f90e1f1

Created October 18, 2018 19:50

ds000001 model

	{
	"name": "ds000001 AFNI model",
	"input": {"task": "balloonanalogrisktask"},
	"blocks": [
	{
	"level": "subject",
	"transformations": [
	{
	"name": "polynomial_expansion",
	"order": 2

rwblair / gist:5a37a080a79f37ed1de2ba9fef81a021

Created July 30, 2018 21:19

	~/projects/s3-test $ aws s3api list-object-versions --bucket 907245365968-test \| grep VersionId
	"VersionId": "7gJ1tHgIOA7DHI4zMCF2WGIKwWheVson",
	"VersionId": "396V1OKMHM0QBnRBSoL8Rh5EdhVoYg63",

	~/projects/s3-test $ curl https://s3.amazonaws.com/907245365968-test/a.txt?versionId=7gJ1tHgIOA7DHI4zMCF2WGIKwWheVson
	<?xml version="1.0" encoding="UTF-8"?>
	<Error><Code>AccessDenied</Code><Message>Access Denied</Message><RequestId>A5D078F3B89ED356</RequestId><HostId>wG6NFU3MLIq6XwNM53fmvCjyZZY+LeSWz1zj3fQrKFAT9uNgATnFWEtOzaoteZwn4HuX+8bV0uY=</HostId></Error>

	~/projects/s3-test $ aws s3api put-object-acl --bucket 907245365968-test --key a.txt --acl public-read --version-id 7gJ1tHgIOA7DHI4zMCF2WGIKwWheVson

rwblair / gist:36ad619233b3d6ac6bddb5e58848e1d4

Created July 4, 2018 18:45

	{
	"blocks" : [
	{
	"transformations" : [
	{
	"input" : [
	"CSF"
	],
	"name" : "scale",
	"rescale" : true,

Ross Blair rwblair