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Hi Bruce,

In response to your previous email, in v6.0 it doesn't look like recon-all has a "-no-cerebellum" flag (or any cerebellum-related flags), I did verify that the recon-all script in the bin folder had hemisphere-specific flags available however.

Is there any documentation on this? It still seems as if I'm missing something here, was it maybe included in previous versions of freesurfer and removed?

Best,
Kody Zalewski

Date: Mon, 4 Mar 2019 15:07:26 -0500 (EST)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Omitting aseg regions from segmentation
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <alpine.LRH.2.20.1903041505530.3767@gate.nmr.mgh.harvard.edu>
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Hi Kody

yes, there are some hidden options to recon-all for this. Take a look at
the script for things like -no-cerebellum, -rh-only, and see if they are
sufficient for what you are trying to do

cheers
Bruce

On Mon, 4 Mar 2019, zalewk wrote:

>
> ????????External Email - Use Caution????????
>
> Hello Freesurfer team,
>
> I am currently working processing the volumetrics of exvivo brains, many of which do not have a
> brainstem/cerebellum.
> It seems this often results in a subcortical alignment that isn't optimal, and fails to create the
> pial/wm surface where freesurfer attempts to label more ventral non-zero voxels as
> brainstem/cerebellum. Currently, I have to manually edit the aseg.auto_noCCseg.label_intensities.mgz
> and aseg.presurf.mgz to fix this.
>
> Is there a way to omit aseg labels (like the brainstem/cerebellum) from the processing stream that
> I've overlooked? If not, would there be a potential alternate solution such as creating a second
> atlas from the original sans these ROIs and have the cross-sectional stream still run normally?
>
> Best,
> Kody Zalewski