Mouse Scan Preprocessing

Mouse Scan Preprocessing

Assumptions

You have minc files from scans acquired here at the CIC, and have already generated them from DICOM format output by the Bruker computer. For conversion to minc, please see Mouse DICOM to MINC Conversion

mouse-preprocessing-v4.sh

Having the modules minc-toolkit, ANTs , qbatch and minc-toolkit-extras loaded is required to start.

mouse-preprocessing-v4.sh <filename to preprocess> <filename to save preprocessed minc>

To process multiple files, use a for-loop the run script itself over multiple files. For example:

for file in /path/to/converted/scans/*.mnc; do 
	echo mouse-preprocessing-v4.sh $file /path/to/save/preprocessed/$(basename $file) | qbatch -N mouse-preprocessing --ppj 4 -
done

This one script/new tool does the following in one step:

• fixes axis orientation (two axis are differently listed vs our atlases)
• flips right/left (our scans come out with right-left unfaithful)
• coordinate system reset (helps to align with atlases as our scans are in different space)
• denoising
• quick registration to an atlas to get a mask (may be used later in our pipelines when we figure out how to do that)
• bias field calculation and correction (corrects intensity difference due to magnetic field inhomogeneities)