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

[Martin Reuter]

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  wrote:
> 
> External Email - Use Caution
> 
> 
> 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=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

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Advantage of having skull for longitudinal processing?

[Adam Martersteck]

External Email - Use Caution

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=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