How to save in .mat format

akmal871026 · August 1, 2022, 4:16pm

Dear all,

Does anyone know how to save labeling images in slicer?

Let’s say labeled a tumor in the liver. then I want to save it in a logical/categorical data set (.mat)

because currently just have .nrrd format, then it cannot be open in matlab.

pieper · August 1, 2022, 5:03pm

I don’t use matlab myself but I understand there is code available to open nrrd files in matlab. It should be pretty trivial.

lassoan · August 2, 2022, 10:19am

You can use this Matlab nrrd reader to read segmentations (.seg.nrrd files) saved by Slicer:

github.com

PerkLab/SlicerMatlabBridge/blob/master/MatlabCommander/commandserver/nrrdread.m

function img = nrrdread(filename)
% Read image and metadata from a NRRD file (see http://teem.sourceforge.net/nrrd/format.html)
%   img = cli_imageread(filename) reads the image volume and associated metadata
%
%   img.pixelData: pixel data array
%   img.ijkToLpsTransform: pixel (IJK) to physical (LPS, assuming 'space' is 'left-posterior-superior')
%     coordinate system transformation, the origin of the IJK coordinate system is (1,1,1) to match Matlab matrix indexing
%   img.metaData: contains all the descriptive information in the image header
%   img.metaDataFieldNames: Contains full names of metadata fields that cannot be used as Matlab field names because they contains
%     special characters (space, dot, etc). Special characters in field names are replaced by underscore by default when the NRRD
%     file is read. Full field names are used when writing the image to NRRD file.
%
%  Supports reading of 3D and 4D volumes.
%
%   Current limitations/caveats:
%   * Block datatype is not supported.
%   * Only tested with "gzip" and "raw" file encodings.
%
% Partly based on the nrrdread.m function with copyright 2012 The MathWorks, Inc.

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How to save in .mat format

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