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>> 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> > > 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
