Mouse Scan Preprocessing

Mouse Scan Preprocessing PV5

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 collected under PV5. For conversion to minc, please see Mouse DICOM to MINC Conversion

mouse-preprocessing-v6_pv5_dicom.sh

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

mouse-preprocessing-v6_pv5_dicom.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-v6_pv5_dicom.sh $file /path/to/save/preprocessed/$(basename $file) 
done | qbatch -N mouse-preprocessing --ppj 4 -

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)

Mouse Scan Preprocessing PV6

Preprocessing for PV6 depends upon if you are starting from the raw Bruker data or exported DICOMs. For PV6, DICOM export is not required, and so starting from the Bruker raw data is generally the way to go. The same modules apply.

For raw Bruker data, first convert to NIFTI using Brkraw (documentation on setting up a Brkraw environment and performing conversion). Then, use the NIFTIs as input for running the script mouse-preprocessing-v7_pv6_brkraw_nifti.sh. It will output MINC files.

For DICOMs, use mouse-preprocessing-v6_pv6_dicom.sh. It should take DICOMS as input and output MINC files. Note, this is seldom used if at all because DICOM export is not required for PV6. This has not been real-world tested in the lab yet.