The tmi_viewer package contains two programs:
Displays multimodal neuroimaging data (surfaces and volumes) in the same space from a TMI file (although TMI files are not required).
Features:
- Multiple surfaces with vertex painting can be easily viewed with voxel images.
- Voxel images can be viewed as: (1) surfaces using a marching cube algorithm, (2) voxel contour, (3) and voxel scalar field.
- The default settings are optimized for viewing neuroimages.
- tmi_viewer is highly optimized for speed.
- Many autothresholding algorithms available including: Otsu et al., Li et al., Yen et al., and Z threholding.
- Extremely fast algorithm for applying Lapacian or Taubin (low-pass) smooth. e.g., ~1000 passes takes around one minute.
- Easy export of background transparent images for creating figures.
- Many new look-up tables (LUTs) that are specifically designed for visualising neuroimaging statistics (as well as the LUTs included with matplotlib).
Outputs a web-page with whole brain slices from voxel-based neuroimages in native coordinates with optional overlaps.
Features:
- Great for making figures: Creates a web-page displaying overlapping any number of voxel-based images, and they can be at any resolution.
- Many autothresholding algorithms available including: Otsu et al., Li et al., Yen et al., and Z threholding.
- Import images, binarize them at any threshold, and paint the image outline.
- Specify number of slices, size of slices, transparency, etc.
For Ubuntu:
sudo apt-get install vtk6 python-vtk python-qt4
For OSX:
brew install vtk
Using PIP (Recommended):
sudo -H pip install -U tmi_viewer
From source:
sudo python setup.py install
- Additional requirement: mayavi
Note: this example uses python 3.5
Create and source virtual environment
virtualenv -p python3.5 python3env
source python3env/bin/activate
Install TFCE_mediation
pip install -U tfce-mediation
Download and install SIP and PyQT4
a. Download and unzip SIP and PyQT4
b. Install SIP (not version may be different)
cd sip-4.19.7
python configure.py
make
make install
c. Install PyQT4
cd ../PyQt-x11-gpl-4.12.1
python configure-ng.py
Accepted the user agreement then run:
make
make install
pip install vtk
pip install vtk
pip install tmi_viewer
pip install -U tmi_viewer
These programs relies on Mayavi, and setting can changed using the Mayavi interactive session. If you use them please cite:
Ramachandran, P. and Varoquaux, G., Mayavi. 3D Visualization of Scientific Data. IEEE Computing in Science & Engineering, 13 (2), pp. 40-51 (2011).