| Deletions are marked like this. | Additions are marked like this. |
| Line 3: | Line 3: |
|
= Software Project Template = '''edit as needed''' |
= Filtering Streamlines = |
| Line 6: | Line 5: |
| <<TableOfContents>> |
This tool filter streamlines from a *.trk that are: (1) outside a mask, (2) shorter than a length threshold, (3) u-shape fibers based on a segmentation file. |
| Line 8: | Line 8: |
|
== Introduction == This document describes the high level design of the software. |
= Usage = |
| Line 11: | Line 10: |
|
== Use Case Analysis == A use case analysis merely addresses the most obvious of questions: who needs the software, and what are they going to do with it. |
streamlineFilter -i streamlines -o streamlines -l maxLength -r refImage -m mask/segmentation -nu (filter ushape fibers) -s subsample |
| Line 14: | Line 12: |
|
=== Actors (Users) === In UML terminology, the persons (or software agents) external to a software component are called the actors. ==== Research ==== === Scenarios (Use Cases) === These establish the framework for test cases. They also bring out the vocabulary of the system. This vocabulary is defined in the Terms section following these scenarios. ==== Use Case #1 ==== ==== Use Case #2 ==== ==== Use Case #3 ==== ==== Use Case #4 ==== === Terms === The following is a list of some of the vocabulary used in the preceding scenarios, plus terms that are common across the system in which the software is used. == Requirements == === General Requirements === === Specific Requirements === == Implementation == === API === === System Architecture and Primary Components === === Classes === === Collaboration and Sequence Diagrams === UML diagrams describing the time-course of the objects composing the executable. === Properties === Here are listed the configurable properties of the executable. These can be configurables read from a configuration file, or configurables hard-coded into the source code. == Test Plan == === Introduction === Tests should cover the following categories of testing. ==== Functional ==== This type of test ascertains whether the software executes its basic functionality under optimal conditions. ==== Boundary ==== This type of test determines the breaking points of the software, and whether the software gracefully handles input near and beyond these boundaries. ==== Stability ==== This type of test determines long-term behavior of the software: whether is has a memory leak, or prone to crashes which are not repeatable in any single run of any of the other tests. ==== Performance ==== These tests produce benchmarks on the performance of the software. == References == |
where -i input streamline.trk file -o output streamline.trk file -l threshold length. Streamlines shorter than a threshold will be removed. -r reference image -m mask image. All streamlines outside the mask will be removed. This input doesn't need to be binary, streamlines passing through voxels with intensity larger than zero will be kept. -nu no ushape fibers. This flag will remove every streamline that starts and ends with the same segmentation label. (-m flag should input a segmentation file for this). -s subsampling number. It will randomly pick a subset of the streamlines in the file. |
Filtering Streamlines
This tool filter streamlines from a *.trk that are: (1) outside a mask, (2) shorter than a length threshold, (3) u-shape fibers based on a segmentation file.
Usage
streamlineFilter -i streamlines -o streamlines -l maxLength -r refImage -m mask/segmentation -nu (filter ushape fibers) -s subsample
where -i input streamline.trk file -o output streamline.trk file -l threshold length. Streamlines shorter than a threshold will be removed. -r reference image -m mask image. All streamlines outside the mask will be removed. This input doesn't need to be binary, streamlines passing through voxels with intensity larger than zero will be kept. -nu no ushape fibers. This flag will remove every streamline that starts and ends with the same segmentation label. (-m flag should input a segmentation file for this). -s subsampling number. It will randomly pick a subset of the streamlines in the file.