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