> For the complete documentation index, see [llms.txt](https://docs.ccv.brown.edu/bnc-user-manual/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.ccv.brown.edu/bnc-user-manual/standalone-tools/voxalign-automated-mr-spectroscopy-voxel-placement/installation.md).

# Installation

{% hint style="info" %}
Voxalign is available on github at <https://github.com/brown-bnc/voxalign>
{% endhint %}

## 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:

{% hint style="info" %}
voxalign has so far only been tested on macOS
{% endhint %}

I recommend installing in a python virtual environment:

1. create an environment named voxalign: `python3 -m venv voxalign`
2. activate it: `source /path/to/env/voxalign/bin/activate`
3. install voxalign:\
   `pip install` [`https://github.com/brown-bnc/voxalign/archive/master.zip`](https://github.com/brown-bnc/voxalign/archive/master.zip)

You'll also need to [install FSL](https://fsl.fmrib.ox.ac.uk/fsl/docs/#/install/index) 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**](/bnc-user-manual/standalone-tools/voxalign-automated-mr-spectroscopy-voxel-placement/multi-session-alignment.md)
* Calculate a voxel position(s) that matches an MNI coordinate(s) of your choice: [**mni-lookup**](/bnc-user-manual/standalone-tools/voxalign-automated-mr-spectroscopy-voxel-placement/center-on-mni-coordinate.md)
* Calculate the dice coefficient (a measure of overlap) to assess how well-aligned your session 1 and session 2 voxels ended up: [**dice-coef**](/bnc-user-manual/standalone-tools/voxalign-automated-mr-spectroscopy-voxel-placement/quantify-voxel-overlap.md)

***

<details>

<summary>Use of voxalign is governed by the following license</summary>

Copyright 2025, Brown University, Providence, RI.

All Rights Reserved

Permission to use, copy, modify, and distribute this software and\
its documentation for any purpose other than its incorporation into a\
commercial product or service is hereby granted without fee, provided\
that the above copyright notice appear in all copies and that both\
that copyright notice and this permission notice appear in supporting\
documentation, and that the name of Brown University not be used in\
advertising or publicity pertaining to distribution of the software\
without specific, written prior permission.

BROWN UNIVERSITY DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,\
INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR ANY\
PARTICULAR PURPOSE. IN NO EVENT SHALL BROWN UNIVERSITY BE LIABLE FOR\
ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES\
WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN\
ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF\
OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.

</details>


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://docs.ccv.brown.edu/bnc-user-manual/standalone-tools/voxalign-automated-mr-spectroscopy-voxel-placement/installation.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.