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
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