A new release (v3)

I posted the last public jip version on the NITRC site almost 2 years ago (version 2.1). There have been some small but significant changes that have been incorporated into the newest version. The major changes in version 3 are listed here.


Display program:

  • On startup, the old display software didn’t work very well with very large volumes.  If the volume could not fit on the screen as a mosaic, it would try to use the tri-plane format, and then go to a single slice if the 3-plane format still was too large. Now, you get what you ask for.  If a large volume doesn’t fit onto your screen using a 1-to-1 pixel mapping, then it will be shown at lower resolution.
  •  A grayscale bar has been attached to the right side of the image window to facilitate windowing of images.


Alignment program

  • The old distortion fields used shifted cosine-squared spatial basis functions, which have an advantage of smooth variation. However, one cannot easily develop a diffeomorphic multi-scale algorithm with those bases, because distortion fields cannot be represented consistently at each spatial scale. The new algorithm uses a 1-2-1 weighting of nearest neighbors at the highest resolution for the basis functions, and then lower-resolution bases are constructed from higher-level bases using a mixing matrix. The upshot is that distortion fields are represented consistently at each spatial scale, and this prevents bad mappings from creeping into the final solution.
  • The target and source dimensions and resolutions now are stored in the output alignment file, so that one can use inverse transformations if desired.



We have been performing simultaneous PET/fMRI studies here, so I have created a GLM version of the common simplified reference tissue model (SRTM) for analysis of PET data using tracers that are amenable to this approach.

I'm sure there are things I am forgetting.  If I remember, I will update the list.  Additionally, I have created a few other programs, such as aligning histological slices into volumes using MRI as a template.  Other programs may be this added to this set at a later time.

A new website

Ok - I finally created a website to document jip functionality. It's incomplete, but it's a start!  I'd been looking for good web-creation software, and I choose Sandvox. It's pretty easy so far.

I plan to slowly add to this site to provide more and better documentation of what exists. New releases will be uploaded to the NITRC web site:

If you have comments, bug reports, suggestions, etc., please either post on the NITRC site or email

Joe Mandeville

Joseph B. Mandeville, Athinoula A. Martinos Center for Biomedical Imaging at MGH/MIT/Harvard