[Pkg-exppsy-pynifti] [Nipy-devel] Image, design, usecases

[Souheil Inati]

Hi all,

I'd like to briefly chime in on this discussion from the perspective  
of one of the "physicists who are not python experts".

I use the nifti format to store the output of my MR image  
reconstruction and intermediate calculations.  It is VERY important to  
me that whatever simple image handling tools that come out of this  
discussion as a successor to pynifti maintain the full features of the  
NIFTI standard, including multi-dimensional arrays and a variety of  
numerical precisions. I routinely use 5-D complex for images  
reconstructed from pulse sequences that have multiple contrasts  
(echos) acquired with array coils.  I always use double precision for  
my calculations, but tend to write intermediate results as single  
precision (float or complex). I use the q-form to maintain scanner  
coordinate system information and registration for scans acquired  
within the same session but with different slice orientations and  
resolutions.  I sometimes use the s-form to store rigid body  
transformations into a subject's anatomical space across sessions.

I don't care if I have to do a bit of work to write a function to read  
a slice, or a time series, or a volume, or the whole data set.   
Whatever.  It's just a header with an n-dimensional array stored as   
block of data on disk.

The only real essentials are:
  - basic file handling: open, seek, read, write, close
  - proper handling of the header : some validation is nice. I don't  
really care about the extensible part of the header.

Memory mapping mapping as an numpy array would be great, but not a  
requirement.  Only supporting uncompressed versions is fine too.   
Anything that restricts you to 4D is bad from my perspective.

Just my $0.02.

Cheers,
Souheil

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

Souheil Inati, PhD
Research Associate Professor
Center for Neural Science and Department of Psychology
Chief Physicist, NYU Center for Brain Imaging
New York University
4 Washington Place, Room 809
New York, N.Y., 10003-6621
Office: (212) 998-3741
Fax:     (212) 995-4011
Email: souheil.inati at nyu.edu