Preprocess Rat brains

Your rat data may need preprocessing, therefore here are the preprocessing steps performed by the script mentioned here:

• flip
• reorder dimensions to standard MINC ordering
• center
• N4 bias field correct everything
• Otsu mask
• re-bias field correct with otsu mask
• register to rat template
• bias field correction with template mask

First, have your rat brains in MINC.

Preprocessing

Niagara

Load the modules:

> module load cobralab
> module load minc-toolkit ANTs minc-toolkit-extras

CIC

> module load minc-toolkit minc-toolkit-extras ANTs qbatch

The ways to use the script are either by file:

rat-preprocessing-v3.sh input output

Example: rat-preprocessing-v3.sh rat1_t1.mnc rat1_t1_preproc.mnc

Example: bash rat-preprocessing-v3.sh rat1_t1.mnc rat1_t1_preproc.mnc

Example: ./rat-preprocessing-v3.sh rat1_t1.mnc rat1_t1_preproc.mnc

Its best to submit this to a cluster to do the preprocessing, at the CIC:

for file in /path/to/input/*mnc; do
	echo rat-preprocessing-v3.sh $file /path/to/save/outputs/$(basename $file .mnc)_preproc.mnc
done | qbatch --ppj 4 -N rat-preproc -

On Niagara:

for file in /path/to/input/*mnc; do
	echo rat-preprocessing-v3.sh $file /path/to/save/outputs/$(basename $file .mnc)_preproc.mnc
done | qbatch -N rat-preproc -