Scripting MRI/CT coregistration pipeline

[Raymundo.Cassani]

Hi @mnichols,

@mnichols

I have yet to find the equivalent function of Register with default MRI->SPM: Register + reslice

The function you are looking for is:

mri_coregister(MriFileSrc, MriFileRef, Method, isReslice)

where MriFileSrc is the volume to register, MriFileRef is the reference volume,
and "SPM: Register + reslice" is obtained with using method = 'spm' and isReslice = 1

@mnichols

then export a .mat file.

There is nothing to do here, all files in Brainstorm database are saved as .mat
A function that may be useful is file_fullpath(fileName) this returns the absolute path, in case fileName is relative to the Brainstorm database directory. e.g, Subject01/subjectimage_MRI.mat

Tip: See this section of the tutorial Scripting to know how to find interactive callback functions
https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting#Find_interface_callback_functions

Best,
Raymundo