README.md

Overlay Cerebrovasculature Data on BigBrain

This is a Datalad repository in which we registered the dataset from https://zenodo.org/record/3707179 to the BigBrain.

This work was started during HIBALL Hackathon 2023. See FZJ-INM1-BDA/HIBALL-Hackathon-2023#8

Summary

1. Data were downloaded and unzipped inside Zenodo_3707179/
2. ActualBrain/ImageBasedModel/BrainHemispheres/Polygon.ply was converted into various other formats such as MNI .obj and Wavefront .obj --> 0_mesh_formats/
3. ActualBrain.obj was transformed to fit within the bounding box of ICBM 152 --> transforms/center_rotate.xfm
4. ActualBrain.obj was converted to a volumetric mask then linearly registered to ICBM 152 (Talairach space) --> transforms/ActualBrain_to_tal.xfm
5. Ran BigBrainWarp (but don't think I did anything useful) --> 2_warp/

Getting the Data

First, install Datalad. My recommendation is to use Micromamba.

Next, run

datalad clone https://github.com/jennydaman/bigbrain-arterial-registration-datalad.git
cd bigbrain-arterial-registration-datalad
datalad get 1_to_icbm 2_warp mesh_formats transforms Zenodo_3707179/ActualBrain

Installation of Dependencies

CIVET-2.1.0 and BigBrainWarp should be installed to your environment. Docker is used to run some other programs, see Other References.

There are also some Python dependencies:

pip install vtk numpy

Other References

• AFNI https://afni.nimh.nih.gov/pub/dist/doc/program_help/ConvertSurface.html
• MIRTK https://mirtk.github.io/commands/convert-pointset.html

Acknowledgements

• Data are hosted on the NERC OpenStack Swift