ENIGMA MEG data upload

Converting Data to BIDS

1. Fieldtrip
   1. data2bids.m
2. Brainstorm
   1. https://neuroimage.usc.edu/brainstorm/ExportBids
   2. Add fiducials to MRI json: https://github.com/jstout211/meg_fiducials_extract
3. SPM
   1. SPM currently does not export to BIDS - use the following scripts to make the bids files
   2. https://github.com/jstout211/meg_fiducials_extract
4. Biscuit
   1. GUI driven BIDS conversion for KIT and Elekta data
   2. https://macquarie-meg-research.github.io/Biscuit/

Steps prior to data upload

(if data is already anonymized+bids format skip this section)

1. Anonymize MEG data
2. Anonymize and deface MRI (options below)
   1. Freesurfer: mri_deface : https://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface
   2. Pydeface: pydeface : https://github.com/poldracklab/pydeface
   3. SPM: spm_deface : https://www.fil.ion.ucl.ac.uk/spm/software/spm12/
   4. Brainstorm : MRI (right click) > Deface Volume : https://neuroimage.usc.edu/brainstorm/Introduction
   5. Fieldtrip: ft_defacevolume: https://www.fieldtriptoolbox.org/reference/ft_defacevolume
   6. Afni: @afni_refacer_run : https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/refacer/refacer_run.html
   7. Brainvoyager:  : https://download.brainvoyager.com/bv/doc/UsersGuide/GettingStarted/AnonymizationAndDefacing.html
3. Confirm defacing algorithm prior to upload using an MR viewer (many options above)
4. Datasets for upload
   1. MEG resting state
   2. MEG emptyroom
   3. MEG/MRI Transformation matrix (or locations of head coils in MRI coordinates). Provided MRI must match transform or coil locations.
      1. MNE python (-trans.fif)
      2. Brainstorm
      3. SPM
      4. Fieldtrip
      5. Vendor transform (Still to be determined if this is acceptable)
   4. Coded subject list with age, gender, and other demographics (TBD)
5. Information on data acquisition
   1. EyesOpen/EyesClosed
   2. VerticalAcquisition/SupineAcquisition
   3. Scanner Vendor/Model
   4. If Vertical/Horizontal EOG and ECG - provide channel numbers

Consult the Pipeline FAQ if you run into any problems.

Globus Website

Data to be included in the Enigma MEG mega-analysis and data harmonization procedure will be uploaded using the Globus software. Globus is a secure, fault-tolerant, peer-to-peer software based on GridFTP. Secure control signals are communicated with the Globus website, but data transfer is only performed between endpoints (peer-to-peer).

An endpoint per lab will be created on NIH storage and given access credentials via email. Only users within your lab and the NIH MEG Core will be able to view and write data in the provided endpoint. Once you receive an email from globus connecting you to a globus endpoint, you will need to create an account on the globus website associated with your institution.

 The globus website will allow you to see the upload endpoint
 https://www.globus.org/

Required Software to see local data

 Globus connect personal is used to browse local data for upload.
 https://www.globus.org/globus-connect-personal

Data upload process

* DATA MUST BE ANONYMIZED BEFORE UPLOAD! *

• Log into the Globus website to view main menu

• Find remote endpoint - Click the search field

• Select Remote Endpoint provided over email - Go to the "Your Collections" or "Shared With You" tab

• Connected to Remote Endpoint - View Contents and select folder (It is possible that the folder is empty)

• Start Globus Connect Personal on your computer to interact with local files/folders.

If no collection available - see next section to create endpoint.

• Create a local endpoint (on your computer)

• Navigate Local Path. Select Data. Hit Start to initiate upload

• Visualize Ongoing Activity

• After completion: Globus upload details and email of successful transfer

Admin - Globus Endpoint Creation (Ignore)

Setup Endpoint Globus