Installation
Voxalign runs on a separate computer, not the scanner console
Use voxalign on Tess (mac mini behind scanner operator) <RECOMMENDED>
*Make sure you log in as mrfuser*
A voxalign environment is already created, so all you have to do is open a terminal window and type
source ~/Desktop/voxalign/bin/activate
Set up on your own computer:
I recommend installing in a python virtual environment:
create an environment named voxalign:
python3 -m venv voxalign
activate it:
source /path/to/env/voxalign/bin/activate
install voxalign:
pip install
https://github.com/brown-bnc/voxalign/archive/master.zip
You'll also need to install FSL on your computer.
Now that your environment is activated, you can:
Calculate a voxel prescription that exactly matches a prescription from an earlier scan session on the same participant: run-voxalign
Calculate a voxel position(s) that matches an MNI coordinate(s) of your choice: mni-lookup
Calculate the dice coefficient (a measure of overlap) to assess how well-aligned your session 1 and session 2 voxels ended up: dice-coef
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