In this example tried it with only the subcortical segmentations from my atlas. Please find the logfile attached. It gives me back: "tissue type is not set" but I set it to 2 in the LUT.txt

In principle look the following commands right to you?

xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca

gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz

Ideally I would have a gtmseg with both, the subcortical and the cortical structures, but only the subcortical would also be fine as long as I can get  mri_gtmpvc running on it. 

Thanks,

Boris

On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:

Can you send the log file for each of the gtmseg runs?

On 11/26/2019 1:09 PM, Boris Rauchmann wrote:

        External Email - Use Caution        

Thank you! I have a gca for subcortical  and two gcs (lh/rh) for cortical structures. 

I created an annot (rh/lh) and a mgz using mris_ca_label and mri_ca_label for parcellation/segmentation stats. 

For the PET analysis I have the following problem:

If I use this command: gtmseg --s test --o test.mgz --ctab /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' 

It gives me the right regions for subcortical structures but it looks like it uses the standard FS parcellation with my labels for the cortical parcellations (only 93 cortical regions instead of 210). 

If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' --no-xcerseg I get all my 210 cortical parcellations but the standard FS subcortical segmentations. 

How can I use both in one gtmseg so that I can proceed with it doing my PET analysis in PETSurfer? It is not totally clear for me what to merge using xcerebralseg.

Thanks a lot!

On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:

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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<gtmseg+subcort_BN.mgz.log>