Thank you. Can you please clarify, documentation for mri_convert states default for resampling is -interpolate, does this mean trilinear? Also, which method is preferable for bbregister (I am applying it for intrasubject uni and multimodal registration), trilinear or cubic interpolation? I assume trilinear if that is the default, but cubic is listed in recon-all dev table in the -T2pial (multimodal) step, see below. Thank you again, Octavian

bbregister --s <subjid> --mov mri/orig/T2raw.mgz --lta mri/transforms/T2raw.lta --init-fsl --T2	transforms/T2raw.lta
orig/T2raw.mgz	mri_convert -odt short -at mri/transforms/T2raw.lta -rt cubic -ns 1 -rl mri/orig.mgz mri/orig/T2raw.mgz mri/T2.prenorm.mgz

On Thu, Apr 30, 2020 at 1:16 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

It will but, it will always be resampled with trilinear interpolation.

On 4/30/2020 12:55 PM, Octavian Lie wrote:
External Email - Use Caution

Dear All,

I have seen bbregister command lines using --o option to get the final output (say a .nii vol), and others where bbregister is used to get an lta transform, which is used in a follow-up step (mri_convert with -ns 1 (no scale), and -rl orig.mgz (reslice-like)

Are these options equivalent? meaning

when using bbregister with '--o x.nii' option, is the output volume x.nii resliced to orig.mgz, and without rescale?

Thanks,

Octavian
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