It gets the subcortical from apas+head.mgz which gets created along the
way by xcerebralseg. You can create your own with xcerebralseg by
specifying your volume as the mergevol. I think this will work, but I'm
not sure. I'm assuming you've used the GCA to create your own
subcortical seg for the given subject

On 11/5/19 1:06 PM, Boris Rauchmann wrote:
>
>         External Email - Use Caution
>
> I just realized that the above mentioned command (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)
> gives me only the cortical segmentation. Is there any way to also
> include the subcortical segmentation based on my individual atlas? I
> also have an Atlas_subcortex.gca file available.
>
> Best,
> Boris
>
> On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D.
> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote:
>
>     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>
>     <mailto: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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