MEG examples by chrisgorgo · Pull Request #45 · bids-standard/bids-examples

chrisgorgo · 2018-01-29T15:52:08Z

@robertoostenveld @jasmainak let me know if everything is up to date.

…ler/ds000117_R1.0.0_empty

added example dataset with MEG+EEG+fMRI

include BrainStorm sample auditory dataset in BIDS-MEG format

include example BIDS dataset from MNE

…lters

fid.json --> coordsystem.json

…he name Coodsystem, Headshape and Photo, files don't need to include *_task-label in the name. They are session specific

Merge remote-tracking branch 'guiomar/bep008_meg' into bep008_meg

jasmainak · 2018-03-23T15:50:43Z

ds000117/.bidsignore

-sub-16/ses-mri/anat/sub-16_ses-mri_run-2_echo-5_FLASH.nii.gz
-sub-16/ses-mri/anat/sub-16_ses-mri_run-2_echo-6_FLASH.nii.gz
-sub-16/ses-mri/anat/sub-16_ses-mri_run-2_echo-7_FLASH.nii.gz
+run-*_echo-*_FLASH.json


@chrisfilo I am not 100% sure but it seems to me that number ranges like [0-9] is not working here. So, I used the more permissive * for now instead of [1-16] or so

jasmainak · 2018-03-23T16:11:01Z

@chrisfilo how do we go about merging this? Travis will fail of course because the validator is not aware of MEG specifications. Do we test both the validator and the datasets locally and then merge them simultaneously?

chrisgorgo · 2018-03-23T16:23:37Z

If you think it's ready please go ahead and merge

fix ds000248

jasmainak · 2018-03-26T09:40:04Z

@chrisfilo okay with a squash and merge? we might have many intermediate PRs where big files were added and removed

jasmainak · 2018-03-26T13:26:43Z

@guiomar I still see two errors, arfff. Do you see this too?

	1: Subject label in the filename doesn't match with the path of the file. File seems to be saved in incorrect subject directory. (code: 64 - SUBJECT_LABEL_IN_FILENAME_DOESNOT_MATCH_DIRECTORY)
		./derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_proc-sss_meg.json
			Evidence: File: /derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_proc-sss_meg.json is saved in incorrect subject directory as per sub-id in filename.
		./derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-01_proc-sss_log.txt
			Evidence: File: /derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-01_proc-sss_log.txt is saved in incorrect subject directory as per sub-id in filename.
		./derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-01_proc-sss_meg.fif.gz
			Evidence: File: /derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-01_proc-sss_meg.fif.gz is saved in incorrect subject directory as per sub-id in filename.
		./derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-02_proc-sss_log.txt
			Evidence: File: /derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-02_proc-sss_log.txt is saved in incorrect subject directory as per sub-id in filename.
		./derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-02_proc-sss_meg.fif.gz
			Evidence: File: /derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-02_proc-sss_meg.fif.gz is saved in incorrect subject directory as per sub-id in filename.
		./derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-03_proc-sss_log.txt
			Evidence: File: /derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-03_proc-sss_log.txt is saved in incorrect subject directory as per sub-id in filename.
		./derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-03_proc-sss_meg.fif.gz
			Evidence: File: /derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-03_proc-sss_meg.fif.gz is saved in incorrect subject directory as per sub-id in filename.
		./derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-04_proc-sss_log.txt
			Evidence: File: /derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-04_proc-sss_log.txt is saved in incorrect subject directory as per sub-id in filename.
		./derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-04_proc-sss_meg.fif.gz
			Evidence: File: /derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-04_proc-sss_meg.fif.gz is saved in incorrect subject directory as per sub-id in filename.
		./derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-05_proc-sss_log.txt
			Evidence: File: /derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-05_proc-sss_log.txt is saved in incorrect subject directory as per sub-id in filename.
		... and 182 more files having this issue (Use --verbose to see them all).

	2: Session label in the filename doesn't match with the path of the file. File seems to be saved in incorrect session directory. (code: 65 - SESSION_LABEL_IN_FILENAME_DOESNOT_MATCH_DIRECTORY)
		./derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_proc-sss_meg.json
			Evidence: File: /derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_proc-sss_meg.json is saved in incorrect session directory as per ses-id in filename.
		./derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-01_proc-sss_log.txt
			Evidence: File: /derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-01_proc-sss_log.txt is saved in incorrect session directory as per ses-id in filename.
		./derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-01_proc-sss_meg.fif.gz
			Evidence: File: /derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-01_proc-sss_meg.fif.gz is saved in incorrect session directory as per ses-id in filename.
		./derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-02_proc-sss_log.txt
			Evidence: File: /derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-02_proc-sss_log.txt is saved in incorrect session directory as per ses-id in filename.
		./derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-02_proc-sss_meg.fif.gz
			Evidence: File: /derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-02_proc-sss_meg.fif.gz is saved in incorrect session directory as per ses-id in filename.
		./derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-03_proc-sss_log.txt
			Evidence: File: /derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-03_proc-sss_log.txt is saved in incorrect session directory as per ses-id in filename.
		./derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-03_proc-sss_meg.fif.gz
			Evidence: File: /derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-03_proc-sss_meg.fif.gz is saved in incorrect session directory as per ses-id in filename.
		./derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-04_proc-sss_log.txt
			Evidence: File: /derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-04_proc-sss_log.txt is saved in incorrect session directory as per ses-id in filename.
		./derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-04_proc-sss_meg.fif.gz
			Evidence: File: /derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-04_proc-sss_meg.fif.gz is saved in incorrect session directory as per ses-id in filename.
		./derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-05_proc-sss_log.txt
			Evidence: File: /derivatives/meg_derivatives/sub-01/ses-meg/meg/sub-01_ses-meg_task-facerecognition_run-05_proc-sss_log.txt is saved in incorrect session directory as per ses-id in filename.
		... and 182 more files having this issue (Use --verbose to see them all).

guiomar · 2018-03-26T13:30:37Z

@jasmainak Is it in ds000117?

Using your online meg-bids validator, on my local copy of the ds000117 dataset, I only see one error that can be ignored, because it is related to having empty niis.

jasmainak · 2018-03-26T13:47:51Z

I don't know what's going on ... :-\

give me a moment to figure it out

jasmainak · 2018-03-26T14:54:09Z

okay errors fixed

jasmainak · 2018-03-26T17:32:13Z

Merged, finally! 🍻

Thanks everyone who contributed

* added example dataset with MEG+EEG+fMRI from https://github.com/jbwexler/ds000117_R1.0.0_empty * included BrainStorm sample auditory dataset in BIDS-MEG format * added example BIDS dataset from MNE * corrected meg events onsets * replaced empty cells w/ 'n/a' in tsv files * updated channels.tsv files * fixed bids-validator stimuli error * updated publications in README * renamed mef files to comply with BIDS * deleted _trans.fif files * changed proc-sss to proc-tsss in filenames * replaced tsss logs and added new derivatives * FIX - removed gsheet participants table, this addresses #26 * added ds000117/task-facerecognition_proc-tsss_meg.json and softwarefilters * moved _proc-tsss_meg.fif to derivatives * fixed derivatives filenames * added onset and duration columns to beh events * added MEGCoordinatesUnits and LandmarkCoordinateUnits to _fid.json * Fixes after running BIDS validator * updated _fid.json files * added .pos files * added commas to sub-01_ses-meg_task-facerecognition_fid.json * changed AnatomicalMRICoordinateSystem value to NIfTi * made several changes to _meg.json files * Fixes * removed OnlineFilters from _meg.json * DOC - added links to full datasets, see #16 * update CHANGES and dataset_description.json * updated brainstorm_sample_auditory to the latest version from the google drive, as discussed in #38 * passed the json files through https://jsonlint.com to check (all OK) and to format them in a human readable way * updated EpochLength from null to 0 * renamed the brainstorm_sample_auditory and mne_sample_data to be consistent with their representation on openfmri.org, see #38 * added ds000247, modified ds000246 * fid.json --> coordsystem.json fid.json --> coordsystem.json * *_coordsystem.json are session specific * Coodsystem, Headshape, Photo, don't need to include *_task-label in the name Coodsystem, Headshape and Photo, files don't need to include *_task-label in the name. They are session specific * Remove MRI coordinates * Head coils. * update ds00246 and ds00247 * channels.tsv replace 0 by n/a * remove anatomical coordinates * HeadCoildFrequency * update ds000117 from Rik * updating * ENH simpler bidsignore * FIX ds000248 issue with maxfilter * fix ds000248 * replace Neuromag/Elekta by Elekta/Neuromag * Remove derivatives folder Former-commit-id: 4647512

robertoostenveld and others added 30 commits July 12, 2017 14:25

added example dataset with MEG+EEG+fMRI from https://github.com/jbwex…

86ba85f

…ler/ds000117_R1.0.0_empty

included BrainStorm sample auditory dataset in BIDS-MEG format

4e43e90

Merge pull request #23 from robertoostenveld/ds000117

d3993c9

added example dataset with MEG+EEG+fMRI

added example BIDS dataset from MNE

b4a4bde

Merge pull request #22 from robertoostenveld/brainstorm_sample_auditory

43094b1

include BrainStorm sample auditory dataset in BIDS-MEG format

Merge pull request #24 from robertoostenveld/mne_sample_data

3d50bad

include example BIDS dataset from MNE

corrected meg events onsets

20b2e0e

replaced empty cells w/ 'n/a' in tsv files

0a7c52c

updated channels.tsv files

011f212

fixed bids-validator stimuli error

818f3c6

updated publications in README

8d6db57

renamed mef files to comply with BIDS

4ed86bf

deleted _trans.fif files

e32936f

changed proc-sss to proc-tsss in filenames

6f85f54

replaced tsss logs and added new derivatives

6cd58fc

FIX - removed gsheet participants table, this addresses #26

25124b9

added ds000117/task-facerecognition_proc-tsss_meg.json and softwarefi…

23fc1e4

…lters

moved _proc-tsss_meg.fif to derivatives

af1b45a

fixed derivatives filenames

f4d401b

added onset and duration columns to beh events

ace6af5

added MEGCoordinatesUnits and LandmarkCoordinateUnits to _fid.json

70b1de6

Fixes after running BIDS validator

fd5e4ef

updated _fid.json files

eb93dbc

added .pos files

ba7c6cf

added commas to sub-01_ses-meg_task-facerecognition_fid.json

6ed3d24

changed AnatomicalMRICoordinateSystem value to NIfTi

d670137

made several changes to _meg.json files

c135183

Fixes

0411afc

removed OnlineFilters from _meg.json

9db41e8

Merge branch 'master' into bep008_meg

7035e5a

guiomar and others added 13 commits March 5, 2018 16:37

fid.json --> coordsystem.json

d225cb7

fid.json --> coordsystem.json

*_coordsystem.json are session specific

a252ac4

Coodsystem, Headshape, Photo, don't need to include *_task-label in t…

a550f56

…he name Coodsystem, Headshape and Photo, files don't need to include *_task-label in the name. They are session specific

Remove MRI coordinates

821e654

Head coils.

d55b2d1

update ds00246 and ds00247

3e18f4f

channels.tsv replace 0 by n/a

d176ed9

remove anatomical coordinates

addcffc

HeadCoildFrequency

4c00b9a

Merge pull request #58 from guiomar/bep008_meg

2543278

Merge remote-tracking branch 'guiomar/bep008_meg' into bep008_meg

update ds000117 from Rik

312d5b7

updating

4d7d515

ENH simpler bidsignore

3a1c35f

jasmainak reviewed Mar 23, 2018

View reviewed changes

FIX ds000248 issue with maxfilter

9de08fa

agramfort and others added 2 commits March 25, 2018 22:21

fix ds000248

1e12320

Merge pull request #67 from agramfort/bep008_meg

68c60b8

fix ds000248

replace Neuromag/Elekta by Elekta/Neuromag

e9ee914

Remove derivatives folder

7b0eeed

jasmainak merged commit 4647512 into master Mar 26, 2018

sappelhoff deleted the bep008_meg branch December 5, 2018 08:01

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MEG examples#45

MEG examples#45
jasmainak merged 59 commits intomasterfrom
bep008_meg

chrisgorgo commented Jan 29, 2018

Uh oh!

jasmainak Mar 23, 2018

Uh oh!

chrisgorgo Mar 23, 2018

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jasmainak commented Mar 23, 2018

Uh oh!

chrisgorgo commented Mar 23, 2018

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jasmainak commented Mar 26, 2018

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jasmainak commented Mar 26, 2018

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guiomar commented Mar 26, 2018

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jasmainak commented Mar 26, 2018

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jasmainak commented Mar 26, 2018

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chrisgorgo commented Jan 29, 2018

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jasmainak commented Mar 26, 2018

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guiomar commented Mar 26, 2018

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