There is no cut off for the minimum size. As it gets smaller, the PVC
noise amplification will become bigger (it also depends on the shape as
well).

I think the --no-xcerseg is the right way to go now

On 8/13/19 11:00 AM, Boris Rauchmann wrote:
>
>         External Email - Use Caution
>
> Thank you for your prompt answer - the command worked. This is the
> atlas mentioned: http://atlas.brainnetome.org/brainnetome.html
> What is approximately the smallest possible segment when using PVC?
> Also, does the exclusion of extracerebral structures harm? I used that
> flag because it complained:
>
> gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
> ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok
> but you must indicate whether to use what is there (--no-xcerseg)
> or create a new one and overwrite what is there (--xcerseg)
> or specify your own headseg (--head)
>
> and did not want to override my apas+head.mgz
>
> Thanks,
> Boris
>
> On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D.
> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote:
>
>     I don't know what the Brainnetome is, but it looks like you have
>     it in
>     annotation form. I think that command should work. Why are you using
>     --no-xcerseg? This will cause it to not include extracerebral
>     structures. Also note that you cannot use arbitrarily small segments
>     when doing PVC.
>
>     On 8/13/19 10:26 AM, Boris Rauchmann wrote:
>     >
>     >         External Email - Use Caution
>     >
>     > Dear all,
>     >
>     > my intention is to use the Brainnetome Atlas
>     parcellation/segmentation
>     > in PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I
>     used:
>     >
>     > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
>     > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg
>     >
>     > Is this the right approach to obtain a high resolution
>     segmentation to
>     > run PVC methods?
>     >
>     > Thanks,
>     > Boris
>     >
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