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https://github.com/noahbenson/Neurotica

Neurotica is an open-source Neuroscience library for Mathematica.
https://github.com/noahbenson/Neurotica

Last synced: 7 months ago
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Neurotica is an open-source Neuroscience library for Mathematica.

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README 

        
# 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\\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 <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/](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 .