Bilateral beamformer

[woolrich]

Added bilateral beamformer
Changed bem_display to show bilateral pairs
Changed bem_display to be a pass through call to coreg_display
Changed Beamformer report to include a bem_display
Some docs might need additional updating to make folks aware of existence of bilateral beamformer

Example run using Wakeman Henson:

import os.path as op

from osl_ephys import utils, source_recon, preprocessing
from osl_ephys.source_recon import beamforming, parcellation

setup dirs

data_dir = '/Users/woolrich/yale_workshop/3.SourceRecon/wake_hen'
recon_dir = op.join(data_dir, "recon")
out_dir = op.join(data_dir, "recon", "glm")

sub_name = "sub{sub_num}"
smri_files_path = op.join(data_dir, sub_name, "anatomy", "highres001.nii.gz")
smri_files = utils.Study(smri_files_path).get()

fif files

subject = "{subject}"
preproc_fif_files_path = op.join(data_dir, subject + "_meg", subject + "_meg_preproc_raw.fif")
preproc_fif_files = utils.Study(preproc_fif_files_path)
subjects = preproc_fif_files.fields['subject']
preproc_fif_files = preproc_fif_files.get()

config = """
source_recon:
- extract_polhemus_from_info: {}
- compute_surfaces:
include_nose: false
- coregister:
use_nose: false
use_headshape: false
- forward_model:
model: Single Layer
gridstep: 10
- beamform_and_parcellate:
freq_range: [3, 20]
chantypes: [mag, grad]
rank: {meg: 55}
use_bilateral_pairs: True
bilateral_tol: 5
parcellation_file: Glasser52_binary_space-MNI152NLin6_res-8x8x8.nii.gz
method: spatial_basis
orthogonalisation: None
"""

Run source batch

source_recon.run_src_batch(
config,
outdir=recon_dir,
subjects=subjects,
preproc_files=preproc_fif_files,
smri_files=smri_files,
)

[matsvanes]

Looking good so far @woolrich. Can you add an example or FAQ to guide the user regarding parameter settings? Do you have some minimal code for us to test the functions?

[woolrich]

Looking good so far @woolrich. Can you add an example or FAQ to guide the user regarding parameter settings? Do you have some minimal code for us to test the functions?

I pasted some example code in the first comment above.
Have a go at running and let me know.

Wrt "an example", where would you recommend putting that?

[woolrich]

Added patch beamformer

Example call:

config = """
source_recon:
- beamform_and_parcellate:
freq_range: [3, 20]
chantypes: [mag, grad]
rank: {meg: 55}
dipole_patches_file: Glasser52_binary_space-MNI152NLin6_res-8x8x8.nii.gz
group_patches: True
parcellation_file: Glasser52_binary_space-MNI152NLin6_res-8x8x8.nii.gz
method: spatial_basis
orthogonalisation: None
"""
source_recon.run_src_batch(
config,
outdir=recon_dir,
subjects=subjects,
preproc_files=preproc_fif_files,
smri_files=smri_files,
)