Hi Adam,

the longitudinal registration should not care, but the regular stream would like to have the skull in the image. This will help for a couple steps (full head talairach registration -> eTIV etc).

Best, Martin

On 5. Jun 2019, at 03:57, Adam Martersteck acmarter@gmail.com wrote:

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Hi Freesurfer team,

I'm thinking of pre-skullstrip'ing my brains prior to being input into FreeSurfer.

My fear was this information in the skull might be useful during mri_robust_register or mri_robust_template for longitudinal analyses:

Martin discusses this in his Freesurfer workshop talk at 9 minutes in (youtube: http://www.youtube.com/watch?v=vxJODPBLd3M&t=9m21s http://www.youtube.com/watch?v=vxJODPBLd3M&t=9m21s) where the heatmap covers parts of the skull and the Freesurfer wiki which mentions that the Tukey biweight will deweight regions of noise like tongue/eye/neck differences.

But it appears the longitudinal stream registers everything on each cross-sectional's norm.mgz to create the fused norm -- which is skullstripped and missing neck/tongue/eyes/skull already.

Am I missing something? Is it alright if my T1.mgz, rawavg.mgz, orig.mgz, etc. do not have a skull for longitudinal processing?

Thanks, Adam _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer