Dear All,

 

I am using a pipeline for electrode coregistration including freesurfer for pial surface generation, run by default recon-all -all and mris_volmask with --save_distance option. The FS files ?h.dpial.ribbon.mgz are the sole FS output. They are converted in the pipeline to nii.gz files using the mri_convert with no specific flags. Question, what coordinate system is used in the converted nii.gz file: a native/scan system, FS system, talairach system (after several recon-all steps of talairach transformation), or NIFTI system? Is there a way to call a command to confirm the exact system used?

Thank you,

 

 

Octavian.