[Nipy-devel] Are libraries to read and write afni, nifit and dicom images needed?

[John Ollinger]

I have been following developments on this list and am wondering if some 
software that I have developed would be useful to the effort.   Here are 
the most useful capabilities:

AFNI: Read in native python, write using python to wrap to3d.

nifti: read and write in native python. Supports quaternion transformation 
only.

dicom: read only in native python.  Assumes uninformative file names and 
sorts based on slice position, slice acquisition time, and image type 
(magnitude, phase, real, imaginary).  Uses Dave Clunies dicom tools which 
are wrapped using swig into a python shareable object libary.

A single function named "readfile" determines the file type, reads it, and 
returns a dictionary containing basic parameters common to all file 
types.  One element is a dictionary containing the entire header (or a 
larger fraction of it in the case of dicom), and a transformation matrix 
that defines the rotation and translation required to get the data into a 
coordinate system where the voxel at (0,0,0) is at (-xmax,-ymax,-zmax) and 
corresponds to the right, anterior, inferior corner of the image.

Would this be useful or a duplication of effort?   I have tried to find 
software to do this on the web but the code I have found is either 
incomplete or unworkable.

John


---------------------------------------

John M. Ollinger
Associate Scientist
University of Wisconsin
Waisman Center for Brain Imaging
T-231 Waisman Center
1500 Highland Ave.
Madison, WI 53705

608-265-6619 (voice)