Provide at least reading capability for AFNI's (BRIK/HEAD) format

[yarikoptic]

AFNI is quite widely used, and ATM I know no library to load those volumetric files in Python. It would be really great if at least reading, even if limited (e.g. for a specific subbrick) capabilities were introduced.

[matthew-brett]

Yo - do you have some files in this format you can share?

[ghost]

Hi! I'm also interested in this feature and would be happy to (privately) share data files.

[ghost]

AFNI is open source, but I don't know what license it has; it is likely less permissive than NiBabel's, so just translating its C code into Python is shady. It would not be a violation of AFNI's copyright if one programmer were to read their source and document the file format in order for a second programmer to write a python implementation.

I would happy to be either of these two programmers!

[yarikoptic]

On Tue, 22 Sep 2015, Eamon Caddigan wrote:

AFNI is open source, but I don't know what license it has; it is likely less

FWIW AFNI core developments since 2000 is a product of NIH, ie.
USA goverment, so can't be copyrighted, thus public domain see
http://neuro.debian.net/debian/extracts/afni/copyright so depending on
which piece you are talking about it might be even more permissive than
nibabel ;)

Yaroslav O. Halchenko
Center for Open Neuroscience http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419
WWW: http://www.linkedin.com/in/yarik

[effigies]

Might also be worth noting that there are publicly available .BRIK/.HEAD files in http://afni.nimh.nih.gov/pub/dist/src/

[bcipolli]

Just received some BRIK/HEAD files to work with. Has anybody looked at code snippets to make this happen, or should I find them myself?

[bcipolli]

I was able to load my file using a MATLAB implementation here:
http://afni.nimh.nih.gov/pub/dist/src/matlab/BrikLoad.m

Perhaps we can port this to Python? Does anybody know reliable tools to convert code to get a head start?

[yarikoptic]

On Sun, 20 Dec 2015, Ben Cipollini wrote:

I was able to load my file using a MATLAB implementation here:
[1]http://afni.nimh.nih.gov/pub/dist/src/matlab/BrikLoad.m

Perhaps we can port this to Python? Does anybody know reliable tools to convert
code to get a head start?

FWIW, whenever last time I had to convert some matlab code over to
python I just did interactive replacement of () with [] and 1 with 0 for
a good head start and then just going through code. If it was old
enough many repmat's (or whatever it was) were adopted as numpy
broadcastings ;) overall wasn't too painful, just quite a bit of work

the question here would also be what would be the best way to fit this
beast within nibabel hierarchy. those multi-brik BRIKs and extensions
of all kinds (like provenance logs) -- in the long run ideally nibabel's
API should be able to expose them all

[bcipolli]

Agreed. To start with, I hope a PR for the most simple case (reading single BRIK/HEAD pairs) would be acceptable, as that's all the time I'll really have for.

[njmei-brown]

This is actually a project that I played around with a bit when I was first learning python some years back... there is absolutely no guarantee that this code still works or that it worked properly in the first place! So, user beware!

https://github.com/njmei/AFNI-Python-IO/blob/master/AFNIPyIO.py

To my knowledge though, most people use the native AFNI functions to convert the .BRIK and .HEAD files to .nifti and load into python with nibabel that way...

[bcipolli]

Nice. I will give that a try in the next couple of weeks!

[yarikoptic]

Was I dreaming that there was already a PR with BRIKs support?

[effigies]

Closed by #561.