Re: [Freesurfer] 3T or nuintensitycor3t

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

Re: [Freesurfer] 3T or nuintensitycor3t

Hi Lee, Do you recommend its use (i.e. both the -nuintensitycor3t flag and the 3T atlas for Talariach alignment)? Where can i find the documentation for the usage of -3T flag? Best, Kasper 2015-11-06 18:47 GMT+01:00 Lee Tirrell : > Hi Kasper, > > The -3T flag

[Freesurfer] 3T or nuintensitycor3t

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

Re: [Freesurfer] 3T or nuintensitycor3t

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