To define jip executables, source this script:

               source /usr/pubsw/packages/jip/define-jip.tcsh      (with a Linux tcsh shell)


               source /usr/pubsw/packages/jip/define-jip.bash     (with a Linux bash shell)

This script does two things:

  1. It defines executables for each program. Executables are located in a bin directory at a parallel level under subdirectories that are specific for 64-bit or 32-bit versions. Executables are selected based upon the user’s system, using `uname -s`-`uname -m` (for instance, to choose Linux-x86_64 for a 64-bit Linux OS).
  2. It defines the environment variable JIP_HOME, which is used to locate on-line documentation.

To define these things from a startup file like .cshrc, place any argument at the end to suppress output, so that you don’t see the output every time you log onto your computer:

               source /usr/pubsw/packages/jip/define-jip.tcsh quite


Quite a few MRI templates, with associated resources like regions of interest, can be found at


Resources include

  1. Templates for rat brain (Paxinos and Watson, 1998):
    • A low-resolution version of the atlas in coordinate space. This is appropriate for defining regions of interest by direct tracing using wire frames. Unfortunately, the atlas here is at a resolution lower than what is ideal, so it is helpful to have an atlas in hand for reference.
    • MRI templates were created from about 30 rats and include T2 contrast (RARE), pre-MION multi-shot EPI, and post-MION multi-shot EPI. The templates are provided at several resolutions (generally 250 microns in plane) and with numerous selections for the number of slices.
  2. Templates for mouse brain (Allen Mouse Brain):
    • The Allen Mouse Brain atlas was digitized and formatted into a single volume with 250 micron slice spacings. This can be used to define regions of interest.
    • A “fake mouse brain” was created by manually segmenting gray matter, white matter, and CSF. This can be used as a basis for alignment of mouse brain templates to the Allen Mouse Brain space.
    • Some (but not many) regions of interest have been defined from the atlas.
    • The LONI MDA mouse brain was downloaded and registered to the AMB space. As for the rat, templates are provided at numerous resolutions and with numerous slice numbers.
  3. Templates for monkey brain:
    • The WADRC average of 112 rhesus monkey brain MRIs (McLaren et al., 2007) was downloaded and is given at 500 micron resolution. This template is aligned to the Saleem-Logothetis atlas. It also have been resampled into a more useful (for fMRI) resolution of 1 cubic mm. Many regions have been manually created in this space by JBM.
    • The INIA19 atlas (Rohlfing et al., 2013) has been downloaded, and a transformation has been defined between this and the 112RM templates. The INIA19 resources provide a quite detailed segmentation of brain regions. jip command files have been created that will enable extraction of these regions, creation of overlays, and translation to the 112RM space.

© Joseph B. Mandeville 2013