I am new to Nipype, working on setting up a preprocessing pipeline. Things are running smoothly except I would like to add some preprocessing steps that are not part of the spm interface.
I’ve tried calling the relevant Matlab function from python but I don’t know how to pass the image files to it. My code looks like this right now:
mlab = matlab.MatlabCommand() mlab.inputs.paths = '/Documents/MATLAB/spm12/toolbox/biasCorrect' bcPath = '/Documents/MATLAB/spm12/toolbox/biasCorrect/' bcScr = os.path.join(bcPath, 'bcorrectNP.m') mlab.inputs.script = bcScr res = mlab.run()
It runs but doesn’t what it’s supposed to.
I’ve been looking at the following examples but it hasn’t helped: