Loading transformation from Matlab .mat file

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1

Hi,

I tried to load a FSL generated .mat transformation matrix as a transform but the system crashed. The simple goal is to use the .mat matrix to transform vtk objects into a different imaging space; using 3d Slicer, I envision dragging the vtk objects onto the transform node and hardening the transformation and saving the transformed vtk objects.

Thanks for your help.

2

Instead of saving transform in proprietary Matlab mat file format, could you save the transform into ITK transform file format? Slicer can directly read/write ITK transform files.

You can use Slicer’s MatlabBridge extension to run Matlab functions directly from Slicer. See more information here: https://www.slicer.org/wiki/Documentation/Nightly/Extensions/MatlabBridge

You can also use this Matlab function that writes a linear transformation matrix to an ITK transformation file: https://github.com/PerkLab/SlicerMatlabBridge/blob/master/MatlabCommander/commandserver/cli_lineartransformwrite.m

3

Thanks Andras. I believe ITK stores the matrix in LPS format but from what I see in the cli_lineartransformationwrite.m function, there is the option to save transformation matrix in RAS. My images are in RAS so I’m guessing that I’d have to set the transformType to ‘slicer’?

4

ITK transform is always stored as LPS. The flag controls if you work in RAS or LPS, so that it converts to/from LPS transforms files accordingly.

1 Like
5

Hi,

I tried to load the FSL generated .mat transformation matrix into Matlab and got the following error message:

>> a = load('affine_ct_mr.mat')
Error using load
Unable to read MAT-file C:\Users\Vinit\Documents\MATLAB\affine_ct_mr.mat. Not a binary MAT-file. Try load -ASCII to read as text.

So, I had converted the .mat array into a .txt file using FSL and was able to read this into Matlab as a 4x4 array:

>> b = load('affine_ct_mr.txt')

b =

    0.9892    0.0481    0.1165  -13.8786
   -0.0145    0.9642   -0.2878   13.6338
   -0.1213    0.2732    0.9450   12.4001
         0         0         0    1.0000

When I attempt to run the cli_lineartransformwrite.m function, I get the following error message:

>> cli_lineartransformwrite('affine_ct_mr_slicer', b, 'slicer')
Undefined function or variable 'cli_transformwrite'.

Error in cli_lineartransformwrite (line 31)
cli_transformwrite(outputfilename, allTransforms);
6

Matlab requires all necessary .m files to be in the current working directory or in the path. Either change the working directory to .../MatlabCommander/commandserver or add this folder to the path in Matlab.

As it seems that you are very new to Matlab, I would advise to spend minimum necessary time with it, and instead focus your efforts on learning Python, which is a much more versatile language, with many more libraries, much larger community, and it is completely open-source and free.

1 Like
7

Actually, I’m modifying my workflow to include doing intermodality registrations directly in 3d Slicer based on our convos. This way transformations can be directly calculated without requiring an intermediary Matlab step. I fully agree with what you are saying about Python and open-source. I’ve been doing my neuroimaging work in Nipy precisely for the reasons of versatility and support; the very same reasons why I’m using 3d Slicer. Appreciate all your help.

1 Like