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BrainVISA
| Date added: 3.2.2012 | Hot Hits: 46 |
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| Version: 4.1.1 mature | Submitter: Frederic Cervenansky This e-mail address is being protected from spambots. You need JavaScript enabled to view it | License: CeCILL-B v2 |
Supported platform:
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Target user group: Clinicians; Researchers; Students | Software technology type: Library |
| Website | Tags: Brain, fMRI, segmentation, Anatomist | Categories: Development environments/platforms |
Main Features: BrainVISA is distributed with a toolbox of building blocks dedicated to the segmentation of T1-weighted MR images. The product of the main assembly line made up from this toolbox is the following: grey/white classification for Voxel Based Morphometry, Meshes of each hemisphere surface for visualization purpose, Spherical meshes of each hemisphere white matter surface, a graph of the cortical folds, a labeling of the cortical folds according to a nomenclature of the main sulci.
Author(s):
Publication(s): M. Perrot, D. Rivière, and J.-F. Mangin. Cortical sulci recognition and spatial normalization. Medical Image Analysis, 15(4):529-550, 2011
Requirements:
You need about 1.5 Gb free disk space to install the BrainVISA pack 4.1.
Need Qt library
Installation method:
Since 4.1 version, there's no setup step anymore. Each package is a file .tar.bz2 (or .zip for windows). You just have to uncompress this file and the package is ready to use.
Here are the commands to uncompress the package:
On Linux and MacOS:
tar jxvf .tar.bz2
On Windows: unzip the zip file using whatever unzip tool you like (windows XP has one builtin in the system).
Data formats supported: DICOM, Ecat
Documentation: http://brainvisa.info/documentation.html
Constraints:
The package consists of two main programs, anatomist and brainvisa, and a suite of utility programs. All are located in the 'bin' directory of the package. It may be dangerous in a few cases to permanently add this directory to your path, because this can create conflicts with other programs on your system (e.g. python). We suggest two possibilities.
To start a program, type the full path along with the name of the program, e.g.:
~//bin/anatomist
(or create symbolic links to 'anatomist' and 'brainvisa' in a directory listed in your path (maybe /home/yourlogin/bin)
If you often launch anatomist, brainvisa or the accompanying programs, you can run a small shell script that modifies the path before each working session. Depending on your shell (bash, csh...; use 'echo $SHELL' to determine which shell is running), you need to run:
for sh or bash:
PATH=/home/yourlogin//bin:$PATH
export PATH
for csh or tcsh:
setenv PATH /home/yourlogin//bin:$PATH
If you really wish to add it permanently in your personal config file, you may have better keep the standard /usr/bin directory first, and before the path to the binary package, for more safety. If you don't have several BrainVISA packs installed, you may just append it at the end of the PATH list rather than at the beginning:
sh/bash example:
PATH=$PATH:/home/yourlogin//bin
export PATH
You can more safely add these lines in you ~/.profile or ~/.bashrc config file
csh/tcsh example:
setenv PATH ${PATH}:/home/yourlogin//bin
Similarly, you may add this line in your ~/.cshrc config file.
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