This is information on how to set up registration environments (quarantines) from 2007-2011. More current information can be found here:

Pydpiper on the SickKids HPF

PydPiper at MICe with quarantines

Running Pydpiper on SciNet

This paragraph applies only to people that run the MICe-build-model script at the Mouse Imaging Centre.

When you want to perform a registration, you should set your shell environment to a so called quarantine. A quarantine here means an environment where the version of all the tools used for the registration is stable, i.e., there are continuous changes made to the minc software and tools, and a quarantine provides a snapshot in time of the state of the tools at that time. The advantage of a quarantine is that if in a year or two years from now you want to reproduce the results you get now, you can use the same quarantine you used now (with the current software).

The quarantines can be found here:


Currently we have to following quarantines in historical order from the latest to the oldest (for new pipelines, use the newest version):


To set an environment you have to run a bash script that resides in each of the quarantine folders. The latest quarantine is the "toothless" quarantine, and this is how you can set its environment (note the space between the first dot and the path that follows after it):

> . /axiom2/projects/software/arch/linux64/quarantine_toothless/environment

If the environment is set correctly, you will see, in red letters, "TOOTHLESS" at the beginning of your shell line.

More information about the toothless quarantine can be found here: Toothless Quarantine

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