Difference between revisions of "ENIGMA MEG data upload"

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(Data anonymization added)
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=Steps prior to data upload=
'''---DATA MUST BE ANONYMIZED BEFORE UPLOAD!---'''
 
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#Anonymize MEG data
<br><br>
 
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#Anonymize MRI, deface, confirm correct defacing (options below)
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## Freesurfer: mri_deface : https://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface
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## Pydeface: pydeface : https://github.com/poldracklab/pydeface
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## SPM: spm_deface : https://www.fil.ion.ucl.ac.uk/spm/software/spm12/
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## Brainstorm : MRI (right click) > Deface Volume : https://neuroimage.usc.edu/brainstorm/Introduction
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## Fieldtrip: ft_defacevolume: https://www.fieldtriptoolbox.org/reference/ft_defacevolume
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## Afni: @afni_refacer_run : https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/refacer/refacer_run.html
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## Brainvoyager: : https://download.brainvoyager.com/bv/doc/UsersGuide/GettingStarted/AnonymizationAndDefacing.html
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#Confirm defacing algorithm prior to upload using an MR viewer (many options above)
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=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).
 
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.
 
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.
   
=Globus Website=
 
 
The globus website will allow you to see the upload endpoint
 
The globus website will allow you to see the upload endpoint
 
https://www.globus.org/
 
https://www.globus.org/
   
==Required Software to see local data==
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=Required Software to see local data=
 
Globus connect personal is used to browse local data for upload.
 
Globus connect personal is used to browse local data for upload.
 
https://www.globus.org/globus-connect-personal
 
https://www.globus.org/globus-connect-personal
   
==Data upload process==
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=Data upload process=
 
'''---DATA MUST BE ANONYMIZED BEFORE UPLOAD!---'''
<br>
 
 
<br><br>
 
'''*Log into the Globus website to view main menu'''
 
'''*Log into the Globus website to view main menu'''
 
<br>
 
<br>

Revision as of 22:06, 25 February 2021

Steps prior to data upload

  1. Anonymize MEG data
  2. Anonymize MRI, deface, confirm correct defacing (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)


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