Hi Octavian

not sure what eT2W FLAIR sense is. The T2_SPACE flair is the only one that we have routinely used that has about 1mm isotropic resolution, and yes we will take care of the registration. Whatever FLAIR you use just point FreeSurfer at it (nifti or dicom)

cheers Bruce

On Tue, 4 Jun 2013, octavian lie wrote:

Dear All,   Among T2 FLAIR, eT2W FLAIR sense, T2, which sequence should be preferably used as auxiliary for pial definition? Does Freesurfer take care of coregistration between these and the MPRAGE? What would be the command line (Linux Ubuntu) if I want to use SPM generated nifti DICOM concatenations for the T2 or FLAIR, instead of native DICOMs? Thank you,   Octavian