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On 05/03/12 14:22, Ramón Casero Cañas wrote:

Seg3D 1.x expected s.data to be a 4D array and s.axis a 4-vector, with a
dummy dimension as the first dimension, if I'm not wrong. Has this
changed in Seg3D 2? Maybe that's why my .mat data is not loaded correctly.

Hi Peter, Ayla,

I looked a bit more into this problem.

Yes, Seg3D2 expects the scirunnrrd struct in the .mat file to have 3 dimensions, while Seg3D 1.x expected 4 dimensions (the first dimension being a dummy dimension).

I have updated scinrrd_save() in Gerardus so that it creates .mat files that can be read by Seg3D2.

Peter, if you want to write an image to a .mat file to read it in Seg3D2, you can do from Matlab

   nrrd = scinrrd_im2nrrd(im, res, offset);
   scinrrd_save('im.mat', nrrd);

After downloading the toolbox from here and adding it to your Matlab path

http://code.google.com/p/gerardus/source/checkout

Best regards,

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://www.cs.ox.ac.uk/people/Ramon.CaseroCanas
photos  http://www.flickr.com/photos/rcasero/

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• [Seg3D] Re: Re: Matlab files: Spacing, Ayla Khan, 03/02/2012
  • [Seg3D] Re: Re: Re: Matlab files: Spacing, Ramón Casero Cañas, 03/05/2012
    • [Seg3D] Re: Re: Re: Matlab files: Spacing, Ramón Casero Cañas, 03/16/2012

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