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


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    • Re: [Freesurfer] Omitting aseg regions from segmentation Bruce Fischl

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