Re: [Freesurfer] (no subject)

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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> 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:

...

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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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