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Subject: [Freesurfer] Omitting aseg regions from segmentation
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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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<div>Hello Freesurfer team, <br>
<br>
I am currently working processing the volumetrics of exvivo brains, many of=
which do not have a brainstem/cerebellum.
<br>
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. <br>
<br>
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? <br>
<br>
Best,<br>
Kody Zalewski<br>
</div>
<br>
<p></p>
</div>
</body>
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