Hi,
I have a problem registering SEEG contacts with MRI. I have a combined MRI (3D volume +mask) that I combined in MATLAB using niftiwrite. It resulted in an MRI file with MRI coordinate. I can put the fiducial points manually and convert the MRI to obtain SCS and MNI coordinate as well. However, my SEEG contacts were obtained from world coordinate (EEG: ASCII, Name,XYZ_World). Is there a way to convert the MRI to world coordinate as well (or maybe Stereo contact)?
Thank you,
Kind regards,
Jacob
Also when I register my image (from niftiwrite) it can register with default MRI (raw file) but when I displayed the register+reslice on MRIviewer the left and right side are oriented wrongly (before registration it does not)
Thank you.
Kind regards,
Jacob
Is there a way to convert the MRI to world coordinate as well (or maybe Stereo contact)?
You can export the contact positions to a large number of file formats and coordinates systems (right-click > File > Export to file).
You can use cs_convert to convert between coordinate systems:
https://neuroimage.usc.edu/brainstorm/CoordinateSystems#Converting_between_coordinate_systems
Also when I register my image (from niftiwrite) it can register with default MRI (raw file) but when I displayed the register+reslice on MRIviewer the left and right side are oriented wrongly (before registration it does not)
Unfortunately it is difficult to guide you with this little information, especially because it appears that most of the processing (volume coregistration, definition of the contacts positions, ...)
First, I recommend you follow these two tutorials, using the example datasets provided:
Then, please provide a more detailed step-by-step explanation of what you are doing (all the interface interactions), with screen captures to illustrate each step.