Difference between revisions of "ENIGMA MEG data upload"

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=Converting Data to BIDS=
# Fieldtrip
## data2bids.m
# Brainstorm
## https://neuroimage.usc.edu/brainstorm/ExportBids
## Add fiducials to MRI json: https://github.com/jstout211/meg_fiducials_extract
# SPM
## SPM currently does not export to BIDS - use the following scripts to make the bids files
## https://github.com/jstout211/meg_fiducials_extract

=Steps prior to data upload=
=Steps prior to data upload=
(if data is already anonymized+bids format skip this section) <br>
(if data is already anonymized+bids format skip this section) <br>
Line 20: Line 30:
###Fieldtrip
###Fieldtrip
###Vendor transform (Still to be determined if this is acceptable)
###Vendor transform (Still to be determined if this is acceptable)
##Subject list with age, gender, and other demographics (TBD)
##Coded subject list with age, gender, and other demographics (TBD)
#Information on data acquisition
##EyesOpen/EyesClosed
##VerticalAcquisition/SupineAcquisition
##Scanner Vendor/Model
##If Vertical/Horizontal EOG and ECG - provide channel numbers


=Globus Website=
=Globus Website=
Line 35: Line 50:


=Data upload process=
=Data upload process=
'''---DATA MUST BE ANONYMIZED BEFORE UPLOAD!---'''
<big>'''* DATA MUST BE ANONYMIZED BEFORE UPLOAD! *'''</big>
<br><br>
<br><br>
'''*Log into the Globus website to view main menu'''
*'''Log into the Globus website to view main menu'''
<br>
<br>
[[File:GlobusMainMenu.png| 900px | Alt text]]
[[File:GlobusMainMenu.png| 900px | Alt text]]
<br><br>
<br><br>


'''*Find remote endpoint - Click the search field'''
*'''Find remote endpoint - Click the search field'''
<br>
<br>
[[File:GlobusSearch.png| 900px | Alt text]]
[[File:GlobusSearch.png| 900px | Alt text]]
<br><br>
<br><br>


'''*Select Remote Endpoint provided over email - Go to the "Your Collections" or "Shared With You" tab'''
*'''Select Remote Endpoint provided over email - Go to the "Your Collections" or "Shared With You" tab'''
<br>
<br>
[[File:GlobusSelectEndpoint.png | 900px | Alt text]]
[[File:GlobusSelectEndpoint.png | 900px | Alt text]]
<br><br>
<br><br>


'''*Connected to Remote Endpoint - View Contents and select folder (It is possible that the folder is empty) '''
*'''Connected to Remote Endpoint - View Contents and select folder (It is possible that the folder is empty) '''
<br>
<br>
[[File:GlobusConnectRemote.png | 900px | Alt text]]
[[File:GlobusConnectRemote.png | 900px | Alt text]]
<br><br>
<br><br>


'''*Start Globus Connect Personal on your computer to interact with local files/folders.
*'''Start Globus Connect Personal on your computer to interact with local files/folders.'''
<br>If no collection available - see next section to create endpoint'''
''If no collection available - see next section to create endpoint.''
<br>
<br>
[[File:GlobusConnectLocalContent.png |900px | Alt text]]
[[File:GlobusConnectLocalContent.png |900px | Alt text]]
<br><br>
<br><br>


'''*Create a local endpoint (on your computer)'''
*'''Create a local endpoint (on your computer)'''
<br>
<br>
[[File:GlobusCreateLocalEndpoint.png |900px | Alt text]]
[[File:GlobusCreateLocalEndpoint.png |900px | Alt text]]
<br><br>
<br><br>


'''*Navigate Local Path. Select Data. Hit Start to initiate upload'''
*'''Navigate Local Path. Select Data. Hit Start to initiate upload'''
<br>
<br>
[[File:GlobusLocalDataSearchForUpload.png |900px | Alt text]]
[[File:GlobusLocalDataSearchForUpload.png |900px | Alt text]]
<br><br>
<br><br>


'''*Visualize Ongoing Activity '''
*'''Visualize Ongoing Activity '''
<br>
<br>
[[File:GlobusVisualizeOngoingActivity.png |900px | Alt text]]
[[File:GlobusVisualizeOngoingActivity.png |900px | Alt text]]
<br><br>
<br><br>


'''*After completion: Globus upload details and email of successful transfer'''
*'''After completion: Globus upload details and email of successful transfer'''
<br>
<br>
[[File:GlobusUploadConfirmation.png |900px | Alt text]]
[[File:GlobusUploadConfirmation.png |900px | Alt text]]
<br><br>
<br><br>


==Admin - Globus Endpoint Creation (Ignore)==
Setup Endpoint [https://megcore.nih.gov/index.php?title=Administer_globus_endpoint Globus]

Revision as of 11:52, 31 May 2022

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

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

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


Alt text

  • Find remote endpoint - Click the search field


Alt text

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


Alt text

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


Alt text

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

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

  • Create a local endpoint (on your computer)


Alt text

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


Alt text

  • Visualize Ongoing Activity


Alt text

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


Alt text


Admin - Globus Endpoint Creation (Ignore)

Setup Endpoint Globus

Retrieved from "https://megcore.nih.gov/index.php?title=ENIGMA_MEG_data_upload&oldid=5192"