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On 01/12/11 00:16, Ayla Khan wrote:

Hi Ramon,

For you, is the scirunnrrd structure the most useful structure for working in 
matlab?

Hi Ayla,

The scirunnrrd structure is something I depend on because:

* it provides a way of having the image but also the spacing, offset, etc all together

* I have already developed quite a lot of software in Geradus based on that structure, usually Matlab functions called scinrrd_*()

See e.g.

http://code.google.com/p/gerardus/source/browse/#svn%2Ftrunk%2Fmatlab%2FFileFormatToolbox

http://code.google.com/p/gerardus/source/browse/#svn%2Ftrunk%2Fmatlab%2FFiltersToolbox

etc

 * I have a lot of image processing results saved in that format

Apart from the Spline Tool not being available in Seg3D2, the scinrrd format is what currently keeps us tied up to the old Seg3D (which is a pain, as Seg3D has so much better 3D visualization).

On a related note, I got in touch with the NRRD folks, and they would actually like me to change the name from scinrrd to something else, e.g. scimat. Now I know that makes sense, as the scirunnrrd has nothing to do with NRRD, but when I started using Seg3D, that was not clear to me.

I'm busy writing a grant application before Christmas, but after that is done, I could think about renaming scinrrd to scimat.

However, it would also be interesting to know what you guys think on your end, what your plans are regarding that format.

If Seg3D is saving to a new Matlab structure, and it has some kind of flag to differentiate it from the old one, I could extend my

scinrrd_load.m
scinrrd_save.m

functions.


Cheers,

Ramon.


--
Dr. Ramón Casero Cañas

Computational Biology
Department of Computer Science
University of Oxford
Wolfson Building, Parks Rd
Oxford OX1 3QD

tlf     +44 (0) 1865 610737
web     http://web.comlab.ox.ac.uk/people/Ramon.CaseroCanas
photos  http://www.flickr.com/photos/rcasero/

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• [Seg3D] Re: Re: Re: Announcing Seg3D 2.1.2, Ramón Casero Cañas, 12/01/2011

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