Operating system: Windows 10 Slicer version: 4.6.2 Expected behavior: Matrix in ijk coordinates Actual behavior: Matrix in unknown reference system Hi guys, I’m a beginner in Slicer and I’m in trouble saving the transformation matrix. I obtained this matrix with the Fiducial registration module…

Thank you @lassoan for your answer. Yes, the question is the same, but I’m sorry I didn’t understand what I should do to obtain the transformation matrix in xyz coordinates.

What anatomical axes your xyz axes correspond to: LPS or RAS?

Do you process your images in Matlab?

Maybe I was not clear in the question, I’m sorry but I was a little bit confused. I didn’t understand how to deal with the matrix in the txt file, so w.r.t. LPS axes (e.g.I have to do its inverse, to pre or post multiply it for a certain matrix ,…) to obtain the matrix that appears in Slicer. How i…

Here is the conversion done by Slicer’s MatlabBridge extension: PerkLab/SlicerMatlabBridge/blob/f7d4511ffe9424e827362942beccb29c7007b526/MatlabCommander/commandserver/cli_lineartransformread.m#L25-L30 if (strcmpi(transformType,'itk')) transform=transform_lps; elseif (strcmpi(transformT…

This is full python code to get the transform matix same in Slicer The important thing in python We can not use transfrom_itk = np.reshape(transform_raw, (3,4)) or transfrom_itk = np.reshape(transform_raw, (3,4), order='F') reader = pd.read_table("Your path\\LinearTransform_3.txt", header=None…

Saving Linear Transformation Matrix

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lassoan (Andras Lasso) October 7, 2017, 4:53am 2

I think this topic should answer your questions: Displayed transform vs .tfm content

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Saving Linear Transformation Matrix

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