Hi Kasper,
The -3T flag uses a special 3T atlas for Talairach alignment, as well as enabling the 3T-specific NU intensity correction parameters that are turned on using the -nuintensitycor3t flag. The -nuintensitycor3t flag only changes the NU intensity correction parameters, without using the 3T atlas in the earlier Talairach stage.
Best, Lee
On Fri, 6 Nov 2015, Kasper Jessen wrote:
Dear freesurfer, To clear up som confusion i would like to ask if there is a difference between adding a -3T or -nuintensitycor3t flag?
Best regards, Kasper
-- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kasper_j@cnsr.dk eller kasper.jessen@regionh.dk