Roi select
The Regions of Interest Selection Tool (roi_select) is a command-line program that, when provided with a collection of curves, selects and outputs only the subset that passes through a particular region (or regions) of interest.
Introduction
After we run DTI data through a pipeline (whether our in-house one or a third-party one, such as DTK), we are left with data for hundreds of thousands of streamlines. Often times, however, we are interested in only a small subset of that data. We may be working with a specific structure in the brain and would like to see a visualization of only that structure. Or we may be interested in a particular region and would like to compute statistics about the streamlines that pass through that region. Perhaps we want to see how many streamlines connect two distinct regions and what paths they take. The roi_select tool can help achieve these goals.
Installation
Dependencies
roi_select has two dependencies:
- libcurvecollection — for file I/O and in-memory data handling
- gg/args — for command-line argument processing
Both are located under $G. You will first need to set up your sandbox. (You may be able to do it automatically.)
To install libcurvecollection:
cd $G/common/libcurvecollection make all make install
To install gg_args:
cd $G/common/utility make all make install cd $G/common/gg make all make install
(see more information)
Installing roi_select
To install roi_select:
cd $G/project/brain/roi/select make all
This will create a subdirectory obj with executables for each of the compilers supported under $G. Unless you have a compelling reason against doing so, your best best is to stick with GCC4. Therefore, to execute, run ./obj/roi_select-gcc4.