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[Seg3D] Re: Announcing Seg3D 2.1.2

Chronological Thread 
  • From: Ramón Casero Cañas <>
  • To:
  • Subject: [Seg3D] Re: Announcing Seg3D 2.1.2
  • Date: Thu, 29 Sep 2011 21:41:12 +0100

On 24/09/11 01:33, Jeroen Stinstra wrote:

Seg3D version 2.1.2 is now available for download at:

This new version has several bug fixes and a few new features:

* We upgraded Matlab support: files can now be exported as Matlab files.

Hi Jeroen,

Thanks for the last upgrade. I have compiled it, and I could read a volume, a segmentation mask, and save the segmentation mask to/from Matlab.

A couple of comments, though.

The format of the Matlab file seems to have changed. In Seg3D, it used to be a scirunnrrd struct, with the image data, and information about the axis (spacing, offset...).

The file I have created from a segmentation mask has a struct called mask_volume, that contains


ans =

    data: [512x512x135 int8]
    axis: []

This means that the image resolution, offset, etc, information is lost.

The way to save the mask is a bit confusing, as instead of providing the file name, you have to provide the directory, and then the file name is taken from the mask label.

In my modest opinion, this is quite inconvenient. It is much faster to see the list of files you have, and quite often double click on an existing file to overwrite it. This avoids having to type the name.

Or you could also click once on a file name, and then edit it and save.

With the new Seg3D2 way, it seems that we'll have to type a lot more.

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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