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[Seg3D] Re: Re: Re: Matlab files: Spacing

Chronological Thread 
  • From: Ramón Casero Cañas <>
  • To:
  • Subject: [Seg3D] Re: Re: Re: Matlab files: Spacing
  • Date: Fri, 16 Mar 2012 19:41:17 +0000

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

Seg3D 1.x expected 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

Best regards,


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

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