This repository contains the instructions & code to construct structural connectivity matrices and calculate network measures in the following manuscript:
Anatomical and network changes to the connectome following peri-insular hemispherotomy: A connectomic approach by Chari et al.
The structural imaging (3T T1 MPRAGE sequences) were organised in BIDS format and fed through Connectome Mapper 3. We chose the Lausanne Atlas at Scale 3 for this study.
Multi-shell multi-tissue diffusion imaging was preprocessed using standard preprocessing steps according to the script diffusion_preproc.sh. The multi-shell multi-tissue dicom files were stored in a folder called 'dwi' and the negative phase encoded series in a folder called 'negPE'. All tools were mrtrix in line with their recommended steps.
This was done by combining the parcellation scheme with the preprocessed diffusion imaging according to the script make_connectome.sh. Firstly the structural data was registered to diffusion space and the cortical target labels were amended according to Scale3_NewLabels.txt. For this, we fused the hippocampal subparcels into a single label, resulting in 253 cortical, subcortical and brainstem parcels per subject. The connectome used anatomically constrained tractography and the SIFT2 filtering step. The output is a 253x253 weighted, undirected structural connectivity matrix in .csv format.
The simulated PIH steps were performed on an adolescent atlas brain, available through the Open Science Framework page for this project under SimulatedCuts.zip. These were registered onto the individual subject brains and the diffusion was re-run exclusing the regions of interest for each cut from the streamlines, as per the script hemispherotomy.sh. The output connectomes are available either as csv files (Output.zip) or imported into a matlab structure (hemispherotomy.mat) at the Open Science Framework page for this project
The extracted connectomes were assembled as structures and analysed in Matlab v2020b using the scripts provided. The Matlab scripts are ordered and the intermediate output files are also provided. Graphical figures were generated in Matlab.
The network visualisations require dowloading SurfIce and exporting txt files of the structural connectivity matrices in the desired formats. For more information, please see the SurfIce Wiki on viewing a connectome network map.