CBICA Toolkit

This project houses the common classes and functions that are used throughout CaPTk and other C++ projects under the CBICA umbrella (including collaborators). All functions/classes are cross-platform.

Dependencies

• ITK
• OpenCV

Changes to dependencies should be discussed in the group so that any downstream effects can be rectified.

Documentation

https://cbica.github.io/CBICA_Toolkit/

Functionality Overview

• Command line parsing
• Safe Image I/O (NIfTI, DICOM)
• Image Utilities and wrappers to ITK filters
  • CreateMaskIndeces
  • GetPixelValuesFromIndeces
  • Preprocessing: histogram matching, smoothing, image comparison, orientation fix, skull stripping, resize, resample
  • Image sanity checking
  • Distance calculations: image and world coordinates
  • Create new image based on existing image
• Generic functionalities: file/directory check, sym-link creation, sub-directories, filename splitting, create/delete/copy directory, file/folder size, normalize path, get current working and/or executable directory, get/set environment variables, CSV parsing, confusion matrix, ROC, randn,
• First order statistics using a standard vector

Full Function List

https://cbica.github.io/CBICA_Toolkit/functions_func.html

Full Class List

https://cbica.github.io/CBICA_Toolkit/annotated.html

Usage

Add this repo as a git submodule (see this page for details on how to do this).

Root CMakeLists File:

# for projects within CaPTk/src/applications
ADD_SUBDIRECTORY( ${PROJECT_SOURCE_DIR}/../../cbica_toolkit ) 

# for projects that add CBICA_Toolkit as a sub-module
ADD_SUBDIRECTORY( ${MAIN_PROJECT_SOURCE_DIR}/src/CBICA_Toolkit ) 

INCLUDE_DIRECTORIES( ${CACHED_INCLUDE_DIRS} )
TARGET_LINK_LIBRARIES( ${PROJECT_NAME} CBICA_Basic CBICA_)

Source code:

#include "cbicaUtilities.h" // or the relevant header file

int main()
{
  // use functions as needed
}