Recommendations for Processing Head CT Data

We will focus on aspects of quantitatively analyzing the CT data and getting the data into a format familiar to most MRI neuroimaging researchers. Therefore, we will not go into detail of DICOM reading tools or imaging suites for radiologists, which are generally proprietary and quite costly. Moreover, we will be focussing specifically on non-contrast head CT data, though many of the recommendations and software is applicable to images of other areas of the body.

Software

Converting DICOM to NIfTI

• https://github.com/rordenlab/dcm2niix

Registration

• https://github.com/neurolabusc/Clinical
• https://github.com/ANTsX/ANTsRCore

Getting Data

• https://cran.r-project.org/package=TCIApathfinder