https://github.com/jennydaman/bigbrain-arterial-registration-datalad

Registration of cerebrovascular data to BigBrain
https://github.com/jennydaman/bigbrain-arterial-registration-datalad

bigbrainproject datalad-dataset

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Registration of cerebrovascular data to BigBrain

• Host: GitHub
• URL: https://github.com/jennydaman/bigbrain-arterial-registration-datalad
• Owner: jennydaman
• Created: 2023-07-29T09:24:43.000Z (over 1 year ago)
• Default Branch: master
• Last Pushed: 2023-07-29T11:32:22.000Z (over 1 year ago)
• Last Synced: 2024-04-24T04:41:59.416Z (8 months ago)
• Topics: bigbrainproject, datalad-dataset
• Language: Python
• Homepage:
• Size: 130 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# Overlay Cerebrovasculature Data on BigBrain

This is a [Datalad](https://www.datalad.org/) repository in which we registered

the dataset from https://zenodo.org/record/3707179 to the [BigBrain](https://bigbrainproject.org/).

This work was started during **HIBALL Hackathon 2023**.

See https://github.com/FZJ-INM1-BDA/HIBALL-Hackathon-2023/issues/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](https://github.com/caseypaquola/BigBrainWarp) (but don't think I did anything useful)

   --> `2_warp/`

## Getting the Data

First, install [Datalad](https://handbook.datalad.org/en/latest/intro/installation.html#installation-and-configuration).

My recommendation is to use [Micromamba](https://mamba.readthedocs.io/en/latest/installation.html#micromamba-standalone-executable).

Next, run

```shell

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](https://docs.docker.com/engine/install/#server) is used to run some other

programs, see [Other References](#Other-References).

There are also some Python dependencies:

```shell

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](https://nerc.mghpcc.org/)