9.3. FATCAT Visualization

This visualiztion ties in with the current FATCAT Demo, which has a number of data sets and commented scripts. If you don’t have it already (?!?!), then please check out the Demo installation instructions?.

At some point you should read the README file under FATCAT_Demo, and go over the comments in each of the scripts that provide context to the different commands used. Scripts Do_*_VIS* are meant to illustrate interactive visualization of the results. The scripts will open results in AFNI and SUMA and a prompt window will guide throuh basic viewing steps. See also the quick tour for tract viewing. You should be able to create images such as the ones shown above. Fun times!

9.3.1. Do_06_VISdti_SUMA_visual_ex1.tcsh

Results visualized by script Do_06_VISdti_SUMA_visual_ex1.tcsh

../../_images/Do_06_vis1.jpg

Tracts going though an interactively positioned mask in the midbrain area. Slice transparency set to 8. (link)

../../_images/Do_06_vis2.jpg

Tracts going though one ROI, with volume rendering turned on. (link)

../../_images/blank2.jpg

9.3.2. Do_09_VISdti_SUMA_visual_ex2.tcsh

Results visualized by script Do_09_VISdti_SUMA_visual_ex2.tcsh

../../_images/Do_09_vis2.1.jpg

Surfaces with surface contour (see IsoSurface) of ROI in color, slices, and tracts barely visible. ref:(link)<media/Do_06_vis2.1.jpg>

../../_images/Do_09_vis2.2.jpg

Surfaces hidden to reveal deterministic tracts through ROIs of the DMN. ref:(link)<media/Do_09_vis2.2.jpg>

../../_images/Do_09_vis2.3.jpg

Connection is maintained with AFNI which is displaying intersection of surfaces with the volume. Clicking anywhere in SUMA will cause AFNI to jump to the corresponding location. (link)

../../_images/blank2.jpg

Comparison of deterministic to mini-probabilistic results.

../../_images/blank2.jpg

Composite display of connectivity matrices

../../_images/Do_09_vis3.1.jpg

(link) ..

9.3.3. Do_09_VISdti_SUMA_visual_ex3.tcsh

Script Do_09_VISdti_SUMA_visual_ex3.tcsh can be used to demonstrate simultaneous, interactive, functional and anatomical connectivity. Just follow the directions that come up on the screen when you launch the script.

9.3.4. Connectoming

Results of script Do_11_RUNdti_Connectome_Examp.tcsh which finds connections between a large number of ROIs.

../../_images/Connectoming.jpg

The tracts here are colored depending on which pair of ROIs they join. (link). To launch suma with the results displayed here, use:

suma -tract CONNECTOMING/o.OME8_000.niml.tract