Team2021Group19

h1. Plastimatch Installation

h2. Software description

An open source software for image computation. 

h2. Use in Onko

Plastimatch is used in the pyradiomics pipeline for two reasons. 

First, Pyradiomics, the library required for the analysis and computation of features from the patient images, uses SimpleITK for the processes of image loading and handling. As a result, the input has to be in a format that SimpleITK recognizes. The files input to Onko are of the DICOM format, a format not recognized by SimpleITK. This is where Plastimatch is used, to essentially convert the data/images from the format that they are input in to a format that can be recognized by SimpleITK (and in turn, Pyradiomics). The converted file is of the nrrd format (an alternative can be nii.gz, either of the two work in the same manner and yield the same results) and is saved to a new folder called “nrrd” inside the respective patient folder. The original image data is not altered in any way in the process. 

Second, Pyradiomics does not support DICOM-RT struct as a direct input. Much like the patient data, the DICOM-RT struct file, containing the Region-of-interest/segmentation masks must also be converted to the nrrd format (again, using Plastimatch). Each region-of-interest is saved as a separate nrrd file inside the “structures” folder. The “structures” folder can be found inside the “nrrd” folder mentioned earlier. 

h3. Installation

1.  Open the terminal

2.  Type (or copy and paste) the command “sudo apt-get install plastimatch” in the terminal

3.  Press “Enter”

4.  Enter your password when asked

5.  When asked "Do you want to continue", type “y” or "Y"

6.  Press “Enter”