The nifti qform should be that of the scanner. doug octavian lie wrote: > 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. > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
