FreeROI is a versatile image processing software developed for neuroimaging data. Its goal is to provide a user-friendly interface for neuroimaging researchers to visualize and analyze their data, especially in defining region of interest (ROI) for ROI analysis.

Easy installation

The easiest way to configure your local python environment to support FreeROI is to use the Anaconda python distribution. Download and install anaconda2 (We recommend anaconda-4.1.1), then run the following command to install all required and related packages. (If your anaconda forcely installs PyQt5, you have to execute conda uninstall pyqt=5 before install PyQt4)

$ conda install numpy scipy nose scikit-image pyqt=4 mayavi

In addition, one non-standard package (nibabel) for reading and writing neuroimaging data should be installed:

$ pip install nibabel

Finally, download FreeROI source code to <your_directory> by clicking here or executing $ git clone http://github.com/BNUCNL/FreeROI <your_directory>. Then:

$ cd <your_directory>
$ python setup.py install

This should work on most platform (i.e., Mac or Linux PCs). You can also skip Anaconda and customize your python environment, please see next section.

For Windows users, an exectable version is available. Unzip the package, and store the directory in a place which path has no Chinese characters. Double click freeroi.exe to run the program.

DIY on your environment

Currently supports the following systems:

• ubuntu/debian
• centos/redhat/fedora
• mac osx
• windows

Dependency

• Python 2.7
• pip >= 1.4.1
• Qt4 >= 4.7

Install Qt4

• On Ubuntu/Debian

  $ apt-get install libqt4-dev 
  

• On CentOS/Fedora/Fedora

  $ yum install qt4 qt4-devel
  

• On Mac OSX

  $ brew install qt --build-from-source
  

If you cannot install Qt4 with above methods, you may need to install it manually. The source code of Qt4.8 could be downloaded from the homepage of Qt.

Install SIP and PyQt4

• On Ubuntu/Debian

  $ apt-get install python-qt4 python-qt4-dev
  

If you cannot install SIP and PyQt4 with above methods, you may need to install it manually. The source codes can be downloaded from SIP and PyQt4. Untar these packages, and install them like this

# install SIP
$ cd SIP
$ python configure.py
$ make
$ make install
# install PyQt4
$ cd ../PyQt
$ python configure.py
$ make
$ make install

Install VTK

• On Ubuntu/Debian

  $ apt-get install python-vtk
  

• On any 64-bit platform $ pip install VTK-5.10.1+qt486-cp27-none-win_amd64.whl

• On any 32-bit platform $ pip install VTK-5.10.1+qt486-cp27-none-win32.whl

Install related python module

Then, several python modules should be installed. Here we provide a script quick_start.sh to install them automatically.

Install FreeROI

After download the source code of FreeROI, you only to execute:

python setup.py install

Documentation

Please find more complete documentation for FreeROI at this page. The documentation for FreeROI is currently incomplete, but will be imporoved in the coming days, weeks, or months.

License

FreeROI is under Revised BSD License. See the LICENSE file for the full license text.