Update BIDS dataset for OMEGA tutorial

[ftadel]

There are many issues with the current dataset that we use for the OMEGA tutorial.

Changes to the BIDS dataset

• /derivatives/freesurfer:
  • Move the FreeSurfer folders to follow this recommendation: https://surfer.nmr.mgh.harvard.edu/fswiki/BIDS
  • Add a dataset_description.json, participants.json, participants.tsv
  • Include the full FreeSurfer segmentation
• /dataset_description.json
  • Add field: DatasetType, 'raw'
• /CHANGES:
  • Add the documentation of all these changes
• /sub-0002/ses-01/sub-0002_ses-01_scans.tsv
  • Should document the anatomical scans as well
• /sub-0002/ses-01/anat/sub-0002_ses-01_T1w.json
  • File is missing and should be added: This is how are set the fiducials, for matching them with the ones defined in the MEG
• sub-0002/ses-01/meg/sub-0002 ses-01 meg sub-0002_ses-01_coordsystem.json
  • IntendedFor: The link was not updated with the new session names (still using ses-0001)
  • The coils should be named NAS/LPA/RPA for more clarity
  • Should include the AnatomicalLandmarks as well, not only the coil positions (computed as the average of the two positions in the .pos file)

Example of updated meta-data files, with empty data files:
sample_omega_sub0002_empty.zip

The new dataset should pass the online validator:
https://bids-standard.github.io/bids-validator/

Actions to be taken

• Update OpenNeuro dataset:

  • https://openneuro.org/datasets/ds000247
  • It was previously not being downloaded correctly: I posted a bug report and got this fixed by the OpenNeuro developers

• Update BIDS-example repository:

  • https://github.com/bids-standard/bids-examples/tree/master/ds000247
  • Update the same files as on OpenNeuro, but with empty datafiles (see function empty_files.zip)

• Update OMEGA Brainstorm tutorial:

  • https://neuroimage.usc.edu/brainstorm/Tutorials/RestingOmega
  • End of section "Import the dataset" must be edited: https://neuroimage.usc.edu/brainstorm/Tutorials/RestingOmega#Import_the_dataset
  • Paths must be edited throughout the page after posting the changes in the dataset on OpenNeuro

[ftadel]

We need to reprocess the T1 MRI of the 5 subjects with FreeSurfer 7.3.2.

• Install FreeSurfer 7.3.2:
  • https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads
  • https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer
• Download all the MRI volumes:
  • https://openneuro.org/crn/datasets/ds000247/snapshots/1.0.1/files/sub-0002:ses-01:anat:sub-0002_ses-01_T1w.nii.gz
  • https://openneuro.org/crn/datasets/ds000247/snapshots/1.0.1/files/sub-0003:ses-01:anat:sub-0003_ses-01_T1w.nii.gz
  • https://openneuro.org/crn/datasets/ds000247/snapshots/1.0.1/files/sub-0004:ses-01:anat:sub-0004_ses-01_T1w.nii.gz
  • https://openneuro.org/crn/datasets/ds000247/snapshots/1.0.1/files/sub-0006:ses-01:anat:sub-0006_ses-01_T1w.nii.gz
  • https://openneuro.org/crn/datasets/ds000247/snapshots/1.0.1/files/sub-0007:ses-01:anat:sub-0007_ses-01_T1w.nii.gz
• Run recon-all including the contralateral registration on each of them:
  • recon-all -i sub-0002_ses-01_T1w.nii.gz -subjid sub-0002_ses-01
  • recon-all -all -contrasurfreg -subjid sub-0002_ses-01
• Zip the folder of each subject separately (to make it easier to transfer):
  • tar zcvf sub-0002.tgz $SUBJECTS_DIR/sub-0002_ses-01
• Upload the 5 archives somewhere easily accessible across the ocean (e.g. McGill OneDrive)