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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 Content-Type: text/plain; charset="iso-8859-1"
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:
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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