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> 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 > > 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
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