A complete pipeline integrating multiple imaging analysis toolboxes into one. This package allows for the input of DICOM images, which will be automatically converted to Niftii files and ACPC-alligned.
Most of this project is based on the image processing pipeline created by Liberty Hamilton of the UCSF Chang Lab (see: https://github.com/ChangLabUcsf/img_pipe). It also incorporates a different method for electrode registraion, based on an edited version of the electrode-registration-app made by Falcon Dai (see: https://github.com/towle-lab/electrode-registration-app).
Package Requirements: This package has been tested on Ubuntu 16.04 LTS and requires the user to install the following packages:
-FreeSurfer https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki
-ACPC-detect https://www.nitrc.org/projects/art
-MATLAB (tested on 2017b/2018a)
-SPM 12 for MATLAB http://www.fil.ion.ucl.ac.uk/spm/software/spm12/
-dcm2niix (install via NeuroDebian, or compile yourself. Just make sure you can run it from terminal. See: http://neuro.debian.net/install_pkg.html?p=dcm2niix)
N.B.: Make sure ALL these packages are available to your terminal (i.e. correctly configure your .bashrc) or the pipeline will run into errors.