get_parcel_discon: Get parcel-based disconnection

In jdwor/LQT: Lesion Quantification Toolkit

Get parcel-based disconnection

Description

This function computes parcel-based direct disconnection measures using an MNI-registered lesion file and an MNI-registered brain parcellation.

Usage

get_parcel_discon(cfg, cores = 1)

Arguments

cfg	a pre-made cfg structure (as list object).
cores	an integer value that indicates how many parallel cores the function should be run on.

Value

An .RData file with the suffix .disconnectivity.RData. This contains the structural disconnection matrix (disconnectivity); an .RData file with the suffix .network_measures.RData, which contains various graph measures for the SC matrix; an .RData file with the suffix _percent_parcel_mats.RData. This file contains a disconnection adjacency matrix (pct_sdc_matrix) and a spared connection adjacency matrix (pct_spared_sc_matrix); a .txt file with the suffix .connectogram.txt. This file contains a connectogram that can be viewed on http://mkweb.bcgsc.ca/tableviewer/visualize/ by checking the two size options in step 2A (col with row size, row with col size); a .node file with the suffix _percent_parcel_SDC.node. This file contains the node information for external connectome viewers (e.g. MRIcroGL). Node sizes are proportional to the number of affected connections. Node colors can be pre-assigned in the .cfg file (cfg.node_color), but if not, they will be proportional to the amount of disconnection sustained analogous to node size; a .edge file with the suffix _percent_parcel_SDC.edge. This file contains the percent SDC matrix in a format that can be loaded into external viewers (e.g. MRICroGL); a .node file with the suffix _percent_parcel_spared_SC.node. This is analogous to (7), but for the spared SC matrix; a .edge file with the suffix _percent_parcel_spared_SC.edge. This is analogous to (8), but for the spared SC matrix; a .tdi.nii.gz file named the same way as the .trk.gz file. This contains a nifti image volume with track density imaging (TDI) values from the .trk.gz file at each voxel. It is essentially a way of converting the .trk.gz file into voxel space. Higher values indicate higher streamline densities at each grid element (voxel); a .nii file with the suffix _percent_tdi.nii.gz. For each voxel, values correspond the

jdwor/LQT documentation built on Nov. 21, 2023, 4:34 p.m.