Getting started

Requirements

The requirements to use PaCER are:

• MATLAB, including the Image Processing Toolbox
• post-operative CT image in nifti file format.

A CT slice-thickness <= 1 mm is recommended, however, PaCER will work on lower resolution data too by falling back to a less sophisticated contact detection method (yielding lower accuracy). Nifti input files are supported in compressed form (.nii.gz) as well as non-compressed (.nii).

Examples

The easiest way to learn about PaCER is to run the example files. We recommend to add the PaCER directory and all its subdirectories to your MATLAB path first. This can be archived by running the file SETUP_PACER.m in MATLAB (once). The examples include a call to SETUP_PACER.

The following examples require only a post op CT dataset - they should work out of the box for most CT scan protocols as long as the slice thickness is not toooo bad :-) Easy conversion from DICOM to NIFTI is possible dcm2nii which is included in MRIcron. Advanced example demonstrating further use-cases (e.g. visualisation of segmentations and atlas data, simple volume of tissue activated model etc.) can be found in the examples/advanced/ directory. However these examples require appropriate co-registered image modalities (e.g. atlases, segmentation). We are in the process to provide a full example dataset in the future.

• EXAMPLE_1.m - Basic PaCER call and electrode plot. Start here!
  • EXAMPLE_1_1.m - Continues EXAMPLE_1 by adding an MPR view of the CT image and demonstrating some plot customisations