What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with your subcortical ROIs added? If so, you can try merging it with the aparc, eg,
mri_aparc2aseg --s subject --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg, and then run gtmseg as you have done below. Let me know if that works doug On 12/2/19 1:18 PM, Boris Rauchmann wrote: > > External Email - Use Caution > > 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. > <dgr...@mgh.harvard.edu <mailto:dgr...@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. >> <dgr...@mgh.harvard.edu <mailto:dgr...@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. >> > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu> >> <mailto: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 >> <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>> >> > <mailto: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>> >> > > <mailto: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>> >> > <mailto: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> >> <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 <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
