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MEG examples (#45)
* 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
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‎README.md‎

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‎ds000117/.bidsignore‎

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run-*_echo-*_FLASH.json
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**/sub-*_ses-mri_run-*_echo-*_FLASH.nii.gz

‎ds000117/CHANGES‎

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Revision history for OpenfMRI dataset ds000117
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1.0.0 2017-11-08
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- Converted to BIDS format
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- Changed subject order (see README)
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0.1.1 2016-09-17
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- Replaced ds117_R0.1.0/sub004/MEG/run_02_sss.fif and ds117_R0.1.0/sub006/MEG/run_03_sss.fif since the original versions were corrupted
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0.1.0 2014-11-03
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- Initial Release

‎ds000117/README‎

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This dataset was obtained from the OpenfMRI project (http://www.openfmri.org).
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Accession #: ds000117
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Description: Multi-subject, multi-modal (sMRI+fMRI+MEG+EEG) neuroimaging dataset on face recognition
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Please cite the following references if you use these data:
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A multi-subject, multi-modal human neuroimaging dataset
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Wakeman, D.G. & Henson, R.N. (2015). A multi-subject, multi-modal human neuroimaging dataset. Sci. Data 2:150001 doi: 10.1038/sdata.2015.1
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Multi-subject, multi-modal (sMRI+fMRI+MEG+EEG) neuroimaging dataset on face recognition
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==================================================================================
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Please note that the subject ordering has changed since version 0.1.x (non-BIDS) of this
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dataset. Additionally, three subjects have been left out. The mapping is as follows:
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0.1.x: 02 03 05 14 08 09 10 11 12 15 16 17 18 23 24 25
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current: 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16
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func/
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-----
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The experiment began at the third nifti volume (corresponding to 5 ignored scans: 3 forced siemens dummies (no files) and 2 included in the data).
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meg/
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----
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Three anatomical fiducials were digitized for aligning the MEG with the MRI: the nasion
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(lowest depression between the eyes) and the left and right ears (lowest depression
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between the tragus and the helix, above the tragus). This procedure is illustrated here:
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http://neuroimage.usc.edu/brainstorm/CoordinateSystems#Subject_Coordinate_System_.28SCS_.2F_CTF.29
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and in task-facerecognition_fidinfo.pdf
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The following triggers are included in the .fif files and are also used in the “trigger” column of the meg and bold events files:
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Trigger Label Simplified Label
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5 Initial Famous Face FAMOUS
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6 Immediate Repeat Famous Face FAMOUS
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7 Delayed Repeat Famous Face FAMOUS
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13 Initial Unfamiliar Face UNFAMILIAR
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14 Immediate Repeat Unfamiliar Face UNFAMILIAR
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15 Delayed Repeat Unfamiliar Face UNFAMILIAR
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17 Initial Scrambled Face SCRAMBLED
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18 Immediate Repeat Scrambled Face SCRAMBLED
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19 Delayed Repeat Scrambled Face SCRAMBLED
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stimuli/meg/
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------------
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The .bmp files correspond to those described in the text. There are 6 additional images in this directory, which were used in the practice experiment to familiarize participants with the task.
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stimuli/mri/
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------------
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The .bmp files correspond to those described in the text.
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If you wish to publish any of these data, please acknowledge Daniel Wakeman and Richard Henson. The data has been published so far in:
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Wakeman, D.G. & Henson, R.N. (2015). A multi-subject, multi-modal human neuroimaging dataset. Sci. Data 2:150001 doi: 10.1038/sdata.2015.1
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Henson, R.N., Wakeman, D.G., Litvak, V. & Friston, K.J. (2011). A Parametric Empirical Bayesian framework for the EEG/MEG inverse problem: generative models for multisubject and multimodal integration. Frontiers in Human Neuroscience, 5, 76, 1-16.
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Henson, R.N., Wakeman, D.G., Phillips, C. & Rowe, J. (2012). Effective Connectivity between OFA and FFA during face perception: DCM of evoked MEG, EEG and fMRI responses. HBM2012 Abstract.
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### Comments added by Openfmri Curators ###
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===========================================
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General Comments
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----------------
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Defacing
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--------
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Defacing was performed by the submitter
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Quality Control
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---------------
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Mriqc was run on the dataset. Results are located in derivatives/mriqc. Learn more about it here: https://mriqc.readthedocs.io/en/latest/
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Where to discuss the dataset
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----------------------------
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1) www.openfmri.org/dataset/ds000117/ See the comments section at the bottom of the dataset
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page.
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2) www.neurostars.org Please tag any discussion topics with the tags openfmri and ds000117.
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3) Send an email to submissions@openfmri.org. Please include the accession number in
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your email.
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Known Issues
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------------
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N/A
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‎ds000117/acq-epi_T1w.json‎

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{
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"RepetitionTime": 2,
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"EchoTime": 0.095,
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"FlipAngle": 90,
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"Manufacturer": "Siemens",
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"ManufacturersModelName": "TIM TRIO",
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"MagneticFieldStrength": 3,
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"PulseSequenceType": "EPI"
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}

‎ds000117/acq-mprage_T1w.json‎

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{
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"RepetitionTime": 2.25,
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"EchoTime": 0.00298,
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"InversionTime": 0.9,
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"FlipAngle": 9,
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"Manufacturer": "Siemens",
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"ManufacturersModelName": "TIM TRIO",
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"MagneticFieldStrength": 3,
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"PulseSequenceType": "MPRAGE"
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}

‎ds000117/dataset_description.json‎

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{
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"BIDSVersion": "1.0.2",
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"License": "CC0",
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"Name": "A multi-subject, multi-modal human neuroimaging dataset",
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"Authors": ["Wakeman, DG", "Henson, RN"],
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"Acknowledgements": "This work was supported by the UK Medical Research Council (MC_A060_5PR10) and Elekta Ltd. We would also like to acknowledge the contribution of Andre van der Kouwe and the A.A. Martinos Center for Biomedical Imaging (MGH) for providing the Multi-Echo FLASH sequences used in this work.",
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"HowToAcknowledge": "Cite this paper: https://www.ncbi.nlm.nih.gov/pubmed/25977808 and consider including the following message: 'This data was obtained from the OpenfMRI database. Its accession number is ds000117'",
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"ReferencesAndLinks": ["https://www.ncbi.nlm.nih.gov/pubmed/25977808", "https://openfmri.org/dataset/ds000117/"],
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"Funding": ["UK Medical Research Council (MC_A060_5PR10)","Elekta Ltd."]
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}
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‎ds000117/participants.tsv‎

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participant_id age sex first_ses
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sub-01 31 M meg
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sub-02 25 M meg
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sub-03 30 M meg
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sub-04 26 F meg
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sub-05 23 F meg
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sub-06 26 M meg
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sub-07 31 F meg
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sub-08 26 M meg
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sub-09 29 M meg
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sub-10 23 M meg
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sub-11 24 F meg
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sub-12 24 F meg
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sub-13 25 F meg
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sub-14 24 F mri
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sub-15 30 M mri
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sub-16 25 M mri
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sub-emptyroom n/a n/a n/a

‎ds000117/run-1_echo-1_FLASH.json‎

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{
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"RepetitionTime": 0.020,
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"FlipAngle": 5,
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"EchoTime": 0.00185
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}

‎ds000117/run-1_echo-2_FLASH.json‎

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{
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"RepetitionTime": 0.020,
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"FlipAngle": 5,
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"EchoTime": 0.00415
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}

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