ROAST_lesion
Ainslie Johnstone
Jan 2021


The ROAST_lesion folder contains code needed for running two modified version of ROAST 2.7 (https://www.parralab.org/roast/)

- roast_seg 
This is a truncated version of ROAST which just runs segmentation and then stops. It outputs all the files needed to run ROAST from stage 3 onwards. This is useful because you can modify the ROAST segmented files as needed, e.g. adding another tissue type, cleaning up lesion segmentation etc. 
 
- roast7 
This is a version of ROAST which allows for a 7th tissue type. You must input all the files that are output from roast_seg, either with or without your own edits. 
The filenames for additional scripts edited from the original roast pipeline end with the number '7'. 

N.B. zeropadding, resampling and RAS reorienting are all turned off in roast_seg and roast7. You should make sure your inputs are already correctly oriented before you run these scripts. A function (PrepForROAST.m) to perform this is included here also. 


Also here is an example of the code (lesion_example_solarSystemAJ.m) I used to make the artificial lesions, and run roast7 in my own brain.