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

[Matthew Brett]

Hi,

> Where is that?  I don't see anything with that name here:
> http://git.debian.org/?p=pkg-exppsy/pynifti.git;a=tree;f=nifti;h=41f14be3faf382124ea616b8868d93af8e6f70fc;hb=HEAD

No, it's not the current master branch, I think you can't see it with
that interface.  Try:

git clone git://git.debian.org/pkg-exppsy/pynifti.git
cd pynifti/
git checkout -b souheil/brifti origin/mb/brifti

> BTW - Here's my thinking on numerical precision.   Scanners store data in
> single precision complex.  This is sufficient to represent analog signals
> which have bit digitized by a 16-bit digitizer (which gives you steps of
> about 3E-05).  The intrinsic MR signal to noise ratio is something almost
> always less than 1000, and definitely less than 10000, so I can safely say
> that the raw data from the device is good to 3 or maybe 4 digits.  If I save
> my intermediate results in single precision floating point (6 digits) and do
> all my calculations in double precision with algorithms that are accurate to
> 10 digits, I'm guaranteed to have done the best that I could have.   For a
> much nicer description of this point of view, see Lloyd Trefethen's
> manifesto: http://www.comlab.ox.ac.uk/nick.trefethen/ten_digit_algs.htm

Sold...

> The above is really only the most trivial of use cases.  One of the main
> reasons that I am excited about moving all of my matlab code to python is to
> take advantage of numpy's very good handling of very large data sets and
> cluster/multi-core machines.  Here's the current architecture of my code:
> 1) go through a giant (>10GB) raw data file and cut it up into little pieces
> corresponding to 1-slice (or 1 volume) worth of raw data
> 2) send each piece to a cluster node where it is turned into an image by
> launching matlab, running a series of calculations on the data.
> 3) stitch all the images back together
> This is horrendous.  The math part of the code is quite compact and
> readable.  The rest of it is glue to submit things to PBS, blah, blah blah.
>  Oh yeah, and I have to have as many copies of matlab running as I do
> compute nodes (96 in my case).  Ugh.  Anyway, I'm hoping to use ipcluster to
> make things suck less.

Yes, that's the thing that's waiting to happen...  If an example
script comes to you, then send it - that would help. For now, have a
look again at:

https://cirl.berkeley.edu/mb312/pyniftidocs/design.html

- I've tried to add something to describe your case at the end...

Matthew