• PoistatsOverview

1. Introduction: blah blah blah

1. 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

1. load dti with "File->DTI->Load DTI Volumes..."

2. 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.

3. Create a new segmentation "File->New Segmentation"

4. 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.
5. Navigate Tkmedit to where the starting region is.

6. Label the first region going to "Tools->Configure Segmentation Brush..." This opens the "Segmentation Brush Info" window.

7. 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.
8. Change to the segmentation brush by clicking on the "Edit Segmentation Tool" button.

9. 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."

10. 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.

11. Save the seed regions by going to "File->Save Segmentation As." Enter a name for the volume and click "OK."

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)