This is the git repository contains the files of the Pig WM atlas and Connectivity Blueprint Preprint
Files in this repository provide the code and template files to recreate the figures in the paper.
The raw and perprocessd diffusion data is available on Zenodo
To recreate the contents of figures 4 and 5 use the scripts found in the IDW_scripts folder.
To recreate the contents of figures 6-9 run the associated notebook after creating the environment using the following commands
- conda create --name pigBP --file requirements.txt
- conda activate pigBP
To create a Cross Species Browser run the notebook.
Prior to running any of the associated notebooks please ensure your environment is configured with the packages isted in the requirements.txt
The contents of each folder are as follows
- IDW_scripts
- scripts to perform cross-species spatial prediction with Inverse Distance Weighted Interpolation as demonstrated in figures 4 and 5.
- For the manuscript regions were defined from the pig's Saikali atlas
- For the human the Harvard/Oxford atlas was used. ROIs we're generated/saved in standard space in FSLeye's
- ROIs were projected to the surface using the fsl command surf_proj before being passed to the scripts included in this folder.
- The Calculate KL matlab script comes from the original connectivity blueprint paper and it's associated github repo which can be found here
- PNI50_surfaces_FSICO5
- The Freesurfer compatible average surfaces in Icosahedron 5 space.
- this is not the space of the final blueprint but can be used for spherical registration. The figures use the AP corrected surfaces.
- T1_templatePNI50
- The pig T1 weighted full and brain extracted template as well and segmentation priors.
- Atlases
- The WM and adapted Saikali et al. Atlases.
- for use in FSLeyes add this folder as is to $FSLDIR/data/atlases
- The WM and adapted Saikali et al. Atlases.
- blueprints
- .mat files corresponding to the connectivity blueprints of each species.
- All human blueprints were sourced from Mars et al, 2018
- Pig blueprints were generated as shown in figure 1.
- data_driven_tracts
- Left and Right results of the data-driven tractography.
- These components were used to guide the definition of tractography protocols
- Raw files refer to minimal processing of the ICAs where as gmm file have had a threshold applied via gaussian mixture modeling
- see: https://www.sciencedirect.com/science/article/pii/S1053811917304044
- Protocols
- Contains the tractography protocols as defined in PNI50 space for use with the Xtract package.
- Tract Projections
- Tractograms showing each tracts termination points on the cortical surface.
- To visualize load the human and pig tract projection spec files
- Tracts
- Individual Nifti files of the tracts in the WM atlas
- Surfaces
- Surfaces used in the generation of the connectivity blueprint.
- Human surfaces are from the original Mars et al. blueprint paper
- Native pig surfaces to the PNI50 are in the pig_surfaces/Surf_Volume_geometry folder
- The pig surfaces called in the notebooks and spec files have been oriented with a corrected anterior-posterior and inferior-superior labelling.
- Cross_species_browser
- To use the cross species browser you need to run the Create_XspeciesBrowser.ipynb notebook.
- Doing so will create the dense connectome files using HCP workbench command and add them to the empty ?.CrossSpeciesBrowser.spec files
- Alternatively the cifti files can be downloaded from Zenodo
- Once Downloaded open them from wb_view after loading the associated empty spec file.
- You will be able to click on a vertex in one species and find the vertex in the other species which is the closest in the connecotpic space
- To use the cross species browser you need to run the Create_XspeciesBrowser.ipynb notebook.