I would like to report the center of mass coordinates from ROIs I made from the Juelich 50% probability atlas from FSL, which is in MNI space. The orientation is RPI. Is there a way to use 3dCM to report MNI coordinates instead of dicom coordinates? And do I need to be careful with the signs of the coordinates given that the ROIs are in RPI orientation?
Thanks very much,
3dCM output is by default in RAI order, that is from right to left, anterior to posterior and inferior to superior. The order is not dependent on the storage orientation of the dataset. The space of the dataset is a completely separate issue. If the dataset is in MNI space, the coordinates will refer to the MNI space in the RAI order. If you would like LPI order, you can reverse the signs of the x and y coordinate.