External Email - Use Caution Dear Doug,
thank you for your effort. Let me know if you have any updates on this. Best, Boris On Fri, Dec 6, 2019 at 5:45 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Hi Boris, I'll try to get to it today. Unfortunately, I think this is > going to require a fair amount of effort on my part. When I wrote this part > of PETsurfer, I just did not make it super flexible. > doug > > > On 12/5/2019 10:17 PM, Boris Rauchmann wrote: > > External Email - Use Caution > Did you already have the time to look at the logfile? Do you have any > suggestions how to proceed? > > Thank you! > > Am 02.12.2019 um 19:18 schrieb Boris Rauchmann <boris.rauchm...@gmail.com> > <boris.rauchm...@gmail.com>: > > > 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> 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> 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>> 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 >> >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://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 > > <gtmseg+subcort_BN.mgz.log> > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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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