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.

This file has been truncated. show original

Topic		Replies	Views
Reading Matlab mat file into 3D Slicer Support matlab	5	3412	April 24, 2022
Comparing Label maps: nrrd, nii and .mat Support	2	1164	August 22, 2017
Nrrdwrite.m of 2d image Support	4	1163	February 10, 2018
Exporting MATLAB data for gel dosimetry Support gel-dosimetry	4	521	December 14, 2020
Exporting segmentation to another software Support	3	446	December 24, 2020

How to save in .mat format

Related topics