Module 3

Purpose: Assign electrodes to brain regions of interest (ROIs)

Description

Module 3 assigns electrodes in the pre-implant MRI space to a specific brain region of interest (ROI). The brain can be subdivided into contiguous regions of interest (ROIs) based on the structural or functional similarity within each region. Users can input any brain atlas (e.g. AAL atlas, Lausanne Atlas, DKT Atlas) to Module 3, and recieve the ROI assignment for each electrode as an output.

  • Input Files:

    • Pre-implant MRI: anat/sub-XXXX_ses-YYYY_acq-3D_space-T00mri_T1w.nii.gz

    • Post-implant CT: ct/sub-XXXX_ses-YYYY_acq-3D_space-T01ct_ct.nii.gz

    • Electrode coords in CT space: ieeg/sub-XXXX_ses-YYYY_space-T01ct_ desc-vox_electrodes.txt

  • Output Files (in sub-xxx/derivatives/ieeg_recon/module3/)

    • sub-xxxx_ses-yy_space-T00mri_atlas-ZZZZ_radius-#_desc-vox_coordinates.csv

    • sub-xxxx_ses-yy_space-T00mri_atlas-ZZZZ_radius-#_desc-vox_coordinates.json

    • sub-xxxx_ses-yy_space-T00mri_atlas-ZZZZ_radius-#_desc-vox_coordinates.txt

    • sub-xxxx_ses-yy_space-T00mri_atlas-ZZZZ_radius-#_sampling_mask.nii.gz

    • sub-xxxx_ses-yy_space-T00mri_atlas-ZZZZ.nii.gz

    • MNI/

      • greedy_afine_fsl.mat

      • greedy_afine.mat

      • sub-xxxx_ses-yy_acq-3D_space-MNI152NLin2009cAsym_T1w_electrode_spheres.nii.gz

      • sub-xxxx_ses-yy_acq-3D_space-MNI152NLin2009cAsym_T1w.nii.gz

      • sub-xxxx_ses-yy_space-MNI152NLin2009cAsym_desc-vox_electrodes.txt

      • sub-xxxx_ses-yy_T00mri_MNI_registration.svg

Running Module 3

If running from the iEEG-recon Application, follow the Running the App instructions.

If running from the command line, make sure your input patient data is organized according to the pseudo-BIDS structure outlined in Data Setup. You can also run the tutorial with our example data. You can run Module 3 using the AntSpyNet atlas (default) or by specifying any Freesurfer Atlas.

The code below demonstrates how to run Module 3 from the command line.

Run using AntSpyNet atlas

$ docker run -v absolute/path/to/exampleData:/source_data lucasalf11/ieeg_recon -s sub-RID0922 -m 3 -cs ses-clinical101 -rs ses-clinical01 -d /source_data -r 2 -apn

| Arguments:
| -s: subject ID
| -m: Module number
| -cs: name of session with CT scan
| -rs: name of session with reference MRI scan
| -d: path to BIDS directory
| -r: radius
| -apn: run AntsPyNet DKT and Atropos segmentation

Run specifying any Freesurfer atlas

  • Replace -apn with the following to specify a particular freesurfer atlas and parcellation labels:

    • -a /path/to/NIFTI

    • -an /path/to/atlas/segmentation

    • -lut /path/to/roi_csv (e.g. DKTatlas+aseg+VEP_lut.csv)

  • If ROI labels and coordinates are separate, you can further replace -lut with:

    • -ri /path/to/ROI indices (e.g. DKTatlas+aseg+VEP_indices.txt)

    • -rl /path/to/ROI_labels (e.g. DKTatlas+aseg+VEP_labels.txt)

Note

For the atlas lookup tables, all of the regions that the atlas has need to be included. Having more regions than those found for any given subject is okay, but having less regions is not okay.

For example, if you want to use the DKT atlas, make sure the atlas lookup table you provide has all of the DKT atlas labels - even if you want to ignore certain labels, this is not where this should be done. Removing brain regions should be done in post-processing.

Optional Arguments

  • -mni run an additional MNI registration for visualization purposes

Example for running Module 3 using Greedy, running AntsPyNet DKT segmentation, generating MNI ROI assignments, and using a radius of 2 mm.

$ docker run -v absolute/path/to/exampleData:/source_data lucasalf11/ieeg_recon -s sub-RID0922 -m 3 -cs ses-clinical01 -rs ses-clinical01 -r 2 -apn -mri -d /source_data

| Arguments:
| -s: subject ID
| -m: Module number
| -cs: name of session with CT scan
| -rs: name of session with reference MRI scan
| -d: path to BIDS directory
| -r: radius
| -apn: use atropos atlas from AntsPyNet
| -mni: (optional) perform MNI registration

Module 3 Outputs

Example output of atropos atlas in MRI (T00) space, obtained by using the -apm flag for sub-XXX_ses-YYYY_space-T00mri_atlas-atropos.nii.gz:

Single contact selected

Example output of atropos atlas mask` in MRI (T00) space using radius = 2 (sub-RID050-ses-research3T_space-T00mri_atlas-atropos_radius-2_sampling_mask.nii.gz). Voxels in brain regions that contain electrodes have a value of 1. Electrode spheres from the output of Module 2 are also shown in the image below:

Single contact selected