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 "DICOM to minc conversion".

##mouse-preprocessing-v2.sh Having the modules minc-toolkit and minc-toolkit-extras loaded is required to start. Put simply, the preprocessing pipeline is now summed up in a single script/tool (mouse-preprocessing-v2.sh). Point it at a minc and tell it where to stick the new one. This takes care of the rest of the preprocessing and outputs a new minc along with a mask for each subject.

>mouse-preprocessing-v2.sh /path/to/converted/scan/scan.mnc /path/to/save/preprocessed/scan.mnc

To do in parallel, for-loop the script itself over multiple files. For example:

>for file in /path/to/converted/scans/*.mnc; do mouse-preprocessing-v2.sh $file /path/to/save/preprocessed/$(basename $file); 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 (makes it look pretty) -quick registration to an atlas to get a mask (may be used later in our pipelines when we figure out how to do that) -biasfield calculation and correction (corrects intensity difference due to magnetic field inhomogeneities)