Poistats Overview

The goal of the POIStats (Path-of-Interest Statistics) algorithm is to calculate the highest probability path between two user-defined seed regions from magnetic resonance diffusion tensor data. The best path is determined by minimizing the energy of the entire path through randomization of the position of the control points of a spline curve drawn through the data and of the position of the endpoints. The energy of each point in the path is given by the negative natural logarithm of the scaled orientation density function at that point. The magnitude of the perturbation is time-step dependent the magnitude is decreased exponentially with time step number. A set of replicates are used to explore the path parameter space and minimization of the path energy is achieved using a Metropolis algorithm with a constant percentage reduction of the temperature. The Metropolis algorithm accepts a path if its energy is less than that of the current lowest energy path; otherwise it accepts the path with a probability based on the difference in energy between the current path and the current best path normalized by the current temperature. Replicates can be exchanged between temperature baths and the exchange is determined also using a Metropolis algorithm.

Creating seed regions

dmri_poistat is constrained to the start and end points -- be careful
poistats needs these two sees at least
use intermediate regions which will be used to initialize the path. Poistats will not be constrained to be in these intermediate regions though
using Tkmedit to create seed regions
start tkmedit loading the fa as the initial volume. For example:

tkmedit -f fa.nii

load dti with "File->DTI->Load DTI Volumes..."
In the "Load DTI Volume" window, you'll browse for the two volume with the "Browse..." button. In "Load DTI Vector Volume," load the eigenvec1 volume and in the "Load DTI FA Volume" browse for the fa volume. Click "OK" when you've found the volumes. The DTI volumes will be loaded and this could take a moment.
Create a new segmentation "File->New Segmentation"
You can either use the default "FreeSurferColorLUT.txt" file, use another one, or create your own. Click "Browse..." to locate the file and "OK" to creat the new segmentation. The benefit of creating your own or using the other one is that we've used distinct colors and it's easier to determine a region from another.
Navigate Tkmedit to where the starting region is.
Label the first region going to "Tools->Configure Segmentation Brush..." This opens the "Segmentation Brush Info" window.
In the "Segmentation Brush Info" window under "Color," select the first label. If you'd like, keep this window open, since you'll be changing the segmentation brush again to label other regions.
Change to the segmentation brush by clicking on the "Edit Segmentation Tool" button.
Annotate the seed region by moving the mouse cursor over the pixel that should be included in the region and clicking with the middle button. You may want to move through various slices and validate your selectiong by turning the DTI overlay on and off with Ctrl D or "View->DTI Overlay."
Annotate another region by selecting another label from the "Segmentation Brush Info" window and repeating the previous step for as many regions as you'd like.
Save the seed regions by going to "File->Save Segmentation As." Enter a name for the volume and click "OK."

Additional Information

1. Run poistats with dmri_poistats. Run without any parameters for help documentation on the inputs and outputs.

1. Visualize results with tkmedit or scuba2 (see scuba2 directions)