Hi Lee,

To be absolutely sure that i understand it correctly. By adding the -3T flag, it used both the 3T atlas for Talairach alignment and the 3T-specific NU intensity correction parameters. So, all i need to pass in the command line (recon-all) is the -3T flag. I do not need to add additional flags in the command line to get both of the above.

Is this correct?

Best, kasper

2015-11-06 18:47 GMT+01:00 Lee Tirrell ltirrell@nmr.mgh.harvard.edu:

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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