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

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