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. > <dgr...@mgh.harvard.edu <mailto:dgr...@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. > > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu> > <mailto:dgr...@mgh.harvard.edu <mailto:dgr...@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 > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
