To define jip executables, source this script:
source /usr/pubsw/packages/jip/define-jip.tcsh (with a Linux tcsh shell)
or
source /usr/pubsw/packages/jip/define-jip.bash (with a Linux bash shell)
This script does two things:
- 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).
- 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
Resources
Quite a few MRI templates, with associated resources like regions of interest, can be found at
/space/aspartate/3/users/jbm/atlases-MGH
Resources include
- 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.
- 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.
- 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.