DEPRECATED pydpiper: Running MBM.py on cross sectional data

MICe-build-model is a toolkit that allows you to perform image registration on mouse brains. This works by trying to fit two ore more images into an average. Differences between the average image and individual images allow us to calculate differences between 2 or more groups of mice. For detailed information on how the pipline works at every stage, please consult: https://wiki.mouseimaging.ca/display/MICePub/MiceBuildModelAlgorithm.

In order to run MICe-build-model, you will first create a run directory, ex: mbm_run_date.

First, you must create a .csv file with a list of absolute paths to all of your input files. The first file in the list will be the target file for your registration, as we will be using a bootstrapping option, so choose wisely. The first row of your .csv file should be "file", following by the list of scan paths.

Next, you'll create your run script, which will look something like this:

module load pydpiper
#or module load cobralab on niagara

MBM.py --verbose --pipeline-name=whateveryoulike \
--csv-file mbm_subjects.csv \
--resolution 0.070 \

MBM.py: the pipeline that will run the registrations. Running MBM.py --help in your terminal will give you a list of all the pipeline options.

--verbose: will print jobs to screen

--pipeline-name: whatever name makes sense to you

--csv-file: your input csv-file. You can also just use --files and point to a folder with your input files.

--resolution: voxel resolution of input data

Please note that as newer versions of the modules exist, they should be switched in for the modules listed in the script.

For information on QC and anaylsis, see:

• pydpiper: Running MBM.py without a target atlas
• pydpiper: Introduction to twolevel_model_building.py

Note: This SOP was based on https://github.com/CobraLab/documentation/wiki/pydpiper:-Running-MBM.py-without-a-target-atlas