Hi Colleen it depends on what you want to do. The T1.mgz probably isn't the correct volume to use in any case. The orig.mgz is close to the raw data (e.g. it has a skull in it and has not been bias corrected). If you want a skull-stripped, bias-corrected version you could use either the norm.mgz (gently bias corrected so it still shows subcortical boundaries) or the brain.mgz (aggressively bias corrected, may wash out e.g. thalamus and pallidum).
cheers Bruce On Mon, 30 Apr 2018, C.P.E. Rollins wrote: > External Email - Use Caution > > Dear Freesurfer developers, > > A collaborator shared with me Freesurfer outputs, but I would like to > some analyses requiring the scans in NIFTI format. I understand > mri_convert should do the trick for this, though I was wondering whether > I should use "orig.mgz" or "T1.mgz" to convert back to the original T1 > NIFTI files. > > Many thanks, > Colleen > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ 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.
