Neurotica is an open-source Neuroscience library for Mathematica.
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README.md

Neurotica

Neurotica is an open-source Neuroscience library for Mathematica. This library is currently in development and is intended to replace the now depricated MmaSurfer library.

Contents

This repository contains a single Mathematica package, Neurotica; this package provides several basic functionalities:

  • Cortical Surface Meshes - Neurotica contains several methods for representing the cortical surface mesh and computing over it. The mesh data themselves are treated simultaneously as Mathematica BoundaryMeshRegion objects, Graph objects, and support properties and options.
  • MR Images - The Neurotica library includes code for handling and representing 3D MR images; the interface is based on that for Image3D.
  • FreeSurfer Interoperability - The ability to communicate between FreeSurfer and Mathematica is one of the main goals of this library. Import and Export functions for most FreeSurfer file formats (including MGH/MGZ as well as surface, w, and label files) are supported, and FreeSurfer subjects can be queried much like data structures.
  • NifTI Support - Neurotica supports NifTI-1, NifTI-2, CifTI, and GifTI file format importing.
  • Visual Cortex - Neurotica contains a small set of functions for examining fMRI data specifically relating to the occipital pole.
  • Registration - Neurotica includes its own registration library, which is designed for the registration of cortical surface-data to ideal 2D models.

Notes

This library is currently undergoing many rapid changes; please be patient and expect the contents to change over the next couple of months.

The notebook Tutorial.nb, included in the root directory of this repository, is the best place to start learning the library. It includes many examples and documents all currently supported public functions.

Installation

To install Neurotica, you will need to make sure that Mathematica can find a copy of it in its library directories. On Linux/Unix systems, the local library directory is "~/.Mathematica/Applications"; on Mac OSX, it is "~/Library/Mathematica/Applications"; and in Windows it is "C:\Users<username>\AppData\Roaming\Mathematica\Applications". To obtain the library's code itself, you can download the library from GitHub: https://github.com/noahbenson/Neurotica. Note that, in order to use the registration library, you will additionally need to initialize Neurotica's github submodules (shown in the block below). The recommended installation method is to clone this github repository then to make a symbolic link to Mathematica's library directory for the file src/Neurotica.m and the directory src/Neurotica. The following code demonstrates how this installation occurs on Mac OSX from the Terminal:

~$ cd Code
~/Code$ git clone https://github.com/noahbenson/Neurotica
Cloning into 'Neurotica'...
remote: Counting objects : 726, done.
remote: Compressing objects : 100% (14/14), done.
remote: Total 726 (delta 4), reused 0 (delta 0), pack - reused 712
Receiving objects : 100% (726/726), 422.29 KiB | 0 bytes/s, done.
Resolving deltas : 100% (427/427), done.
Checking connectivity ... done.
~/Code$ cd Neurotica
~/Code$ git submodule init
Submodule 'src/Neurotica/lib/nben' (https://github.com/noahbenson/nben) registered for path 'src/Neurotica/lib/nben'
~/Code$ git submodule update
Cloning into 'src/Neurotica/lib/nben'...
remote: Counting objects: 270, done.
remote: Compressing objects: 100% (94/94), done.
remote: Total 270 (delta 38), reused 0 (delta 0), pack-reused 151
Receiving objects: 100% (270/270), 1.41 MiB, done.
Resolving deltas: 100% (85/85), done.
Submodule path 'src/Neurotica/lib/nben': checked out 'cd129f7d626d42df1cc1d4d3d6e574f017059e43'
~/Code/Neurotica$ ls
LICENSE     README.md   Tutorial.nb src
~/Code/Neurotica$ cd src
~/Code/Neurotica/src$ 
Neurotica   Neurotica.m
~/Code/Neurotica/src$ cd ~/Library/Mathematica/Applications
~/Library/Mathematica/Applications$ ln -s ~/Code/Neurotica/Neurotica.m .
~/Library/Mathematica/Applications$ ln -s ~/Code/Neurotica/Neurotica/ .
~/Library/Mathematica/Applications$ ls Neurotica/
Coordinates.m  Global.m       Mesh.m         Registration.m VisualCortex.m
FreeSurfer.m   MRImage.m      NifTI.m        Util.m

# After this installation is complete, you can include the entire Neurotica library
# into Mathematica by using the typical <<Neurotica` syntax. Additionally, you can
# upgrade the library by typing 'git pull' from the ~/Code/Neurotica directory.

JLink

Mathematica interacts with Java libraries through an interface it calls JLink. The JLink interface boots up an instance of the Java Virtual Machine (JVM) whenever the JLink package is loaded (via <<JLink`). By default, Mathematica only allows the JVM to use a small amount of RAM, and this can cause Neurotica to encounter problems when interfacing with the nben library (https://github.com/noahbenson/nben), which Neurotica uses to perform mesh registration, due to the moderate memory requirements of keeping coordinate matrices and meta-data in memory. There are multiple ways to fix this listed here in the order of the Neurotica Author's preference:

  1. Edit your init file to include the following lines:

    Needs["Jlink`"];
    SetOptions[InstallJava, JVMArguments->"-Xmx2g"];
    SetOptions[ReinstallJava, JVMArguments->"-Xmx2g"];
    ReinstallJava[];

    (Note that this will allow the JVM to take up at most 2 GB of RAM; for a different amount you can edit the JVMArguments). Neurotica provides a function that will make this edit for you: NeuroticaFixJLinkMemoryPermanent[amount] where amount is a string that contains the memory allocation, e.g., "2g" for 2 gigabytes. This makes a permanent edit to the beginning of your init.m file.

  2. In a notebook, load JLink first, setup the memory, then load Neurotica. This fix is quick and easy; in the cell of your notebook in which you load Neurotica, include these lines, ending with your inclusion of Neurotica:

    Needs["Jlink`"];
    SetOptions[InstallJava, JVMArguments->"-Xmx2g"];
    SetOptions[ReinstallJava, JVMArguments->"-Xmx2g"];
    ReinstallJava[];
    Needs["Neurotica`"];
  3. Reinstall Java yourself, then reload Neurotica. This can be done with the following code:

    ReinstallJava[JVMArguments->"Xmx2g"];
    NeuroticaReload[];

    Neurotica provides a function that will perform this fix for you, which is identical to the NeuroticaFixJLinkMemoryPermanent[amount] function except that it provides only a temporary fix: NeuroticaFixJLinkMemory[amount], e.g. NeuroticaFixJLinkMemory["2g"] to allocate JLink a max of 2 GB of RAM. The downsides of this method are that it interrupts existing JLink connections (if you have any) and causes Neurotica to forget certain cached data, the latter of which is not usually noticeable. As long as you run this function early in your initialization, such as immediately after loading Neurotica, there shouldn't be any problems.

FreeSurfer

Neurotica needs to be able to find your FreeSurfer Subjects' directory ($SUBJECTS_DIR). You don't need to have FreeSurfer installed to use Neurotica, but in order to execute the examples in the tutorial, you'll need to have a subjects directory containing, at the least, the fsaverage, fsaverage_sym, and bert subjects. (The subject 'bert' is an example subject that is distributed with FreeSurfer). If you do not have FreeSurfer or FreeSurfer's default subject directory, please visit http://freesurfer.net/ to obtain these.

License

This README file is part of the Neurotica library.

The Neurotica library is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.