Scripts and pipelines that are specific to the Mouse Imaging Centre lab. These programs are not very likely to be applicable to other centres.

Contains:

• script to crop brains for the large field of view in-vivo scans
• script to convert CT images to MINC (adding scan information to the header)
• MEMRI / saddle coil reconstruction script
• distortion correction script (ex-vivo, saddle coil, Bruker cryo coil)

Prerequisites

Python3

Installation

The perl code:

./autogen.sh
./configure
make
make install

Python scripts:

python3 setup.py install