Re: [Freesurfer] Advantage of having skull for longitudinal processing?

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