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> 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
Log file for gtmseg Mon Dec 2 18:49:27 CET 2019 setenv SUBJECTS_DIR /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects cd /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects /usr/local/freesurfer/bin/gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz freesurfer-linux-centos6_x86_64-dev-20180911-69aa645 $Id: gtmseg,v 1.19 2016/03/24 17:32:23 greve Exp $ Linux linuxrechner2 4.15.0-65-generic #74~16.04.1-Ubuntu SMP Wed Sep 18 09:51:44 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux mri_gtmseg --s 0120test --usf 2 --o gtmseg+subcort_BN.mgz --apas apas+head+subcort_BN.mgz --no-subseg-wm --no-keep-cc --no-keep-hypo --ctab subcort_BN_LUT.txt $Id: mri_gtmseg.c,v 1.10 2016/08/02 21:07:24 greve Exp $ cwd /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects cmdline mri_gtmseg --s 0120test --usf 2 --o gtmseg+subcort_BN.mgz --apas apas+head+subcort_BN.mgz --no-subseg-wm --no-keep-cc --no-keep-hypo --ctab subcort_BN_LUT.txt sysname Linux hostname linuxrechner2 machine x86_64 user demenzbild subject 0120test USF 2 OutputUSF 2 apasfile apas+head+subcort_BN.mgz wmannotfile NULL ctxannotfile aparc.annot ctxlhbase 1000 ctxrhbase 2000 SubSegWM 0 KeepHypo 0 KeepCC 0 dmax 5.000000 nlist 0 lhmin 1000 lhmax 1900 rhmin 2000 rhmax 2900 Merging CTAB master with merge ctab Starting MRIgtmSeg() Starting MRIgtmSeg() USF=2 Loading /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/0120test/mri/apas+head+subcort_BN.mgz Loading surfaces t = 3.0110 Loading annotations t = 8.2580 Not segmenting WM Relabeling any unlateralized hypointenities as lateralized hypointenities MRIrelabelHypoHemi(): looping over volume nthreads = 1 Relabeling CC as WM Relabeling any hypointensities as WM MRIunsegmentWM(): looping over volume nthreads = 1 Upsampling segmentation USF = 2 t = 11.5600 MRIhiresSeg(): filling unknowns with 0 Beginning cortical segmentation using aparc.annot t = 102.6010 MRIannot2CorticalSeg(): looping over volume nthreads = 1 MRIannot2CorticalSeg(): found 0 unknown, filled with 0 Not subsegmenting WM Found 37 segs in the final list MRIgtmSeg() done, t = 124.5940 Computing colortable WARNING: segid 211 mAmygL tissue type is not set WARNING: segid 212 mAmygR tissue type is not set WARNING: segid 213 lAmygL tissue type is not set WARNING: segid 214 lAmygR tissue type is not set WARNING: segid 215 rHippL tissue type is not set WARNING: segid 216 rHippR tissue type is not set WARNING: segid 217 cHippL tissue type is not set WARNING: segid 218 cHippR tissue type is not set WARNING: segid 219 vCaL tissue type is not set WARNING: segid 220 vCaR tissue type is not set WARNING: segid 221 GPL tissue type is not set WARNING: segid 222 GPR tissue type is not set WARNING: segid 223 NACL tissue type is not set WARNING: segid 224 NACR tissue type is not set WARNING: segid 225 vmPuL tissue type is not set WARNING: segid 226 vmPuR tissue type is not set WARNING: segid 227 dCaL tissue type is not set WARNING: segid 228 dCaR tissue type is not set WARNING: segid 229 dlPuL tissue type is not set WARNING: segid 230 dlPuR tissue type is not set WARNING: segid 231 mPFthaL tissue type is not set WARNING: segid 232 mPFthaR tissue type is not set WARNING: segid 233 mPMthaL tissue type is not set WARNING: segid 234 mPMthaR tissue type is not set WARNING: segid 235 SthaL tissue type is not set WARNING: segid 236 SthaR tissue type is not set WARNING: segid 237 rTthaL tissue type is not set WARNING: segid 238 rTthaR tissue type is not set WARNING: segid 239 PPthaL tissue type is not set WARNING: segid 240 PPthaR tissue type is not set WARNING: segid 241 OthaL tissue type is not set WARNING: segid 242 OthaR tissue type is not set WARNING: segid 243 cTthaL tissue type is not set WARNING: segid 244 cTthaR tissue type is not set WARNING: segid 245 lPFthaL tissue type is not set WARNING: segid 246 lPFthaR tissue type is not set Writing output file to /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/0120test/mri/gtmseg+subcort_BN.mgz Writing colortable to /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/0120test/mri/gtmseg+subcort_BN.ctab Writing lta file to /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/0120test/mri/gtmseg+subcort_BN.lta mri_gtmseg finished in 2.23177 minutes mri_gtmseg done $Id: mri_segstats.c,v 1.122 2017/01/23 18:23:14 greve Exp $ cwd cmdline mri_segstats --seg /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/0120test/mri/gtmseg+subcort_BN.mgz --ctab /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/0120test/mri/gtmseg+subcort_BN.ctab --sum /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/0120test/stats/gtmseg+subcort_BN.stats --excludeid 0 --etiv --subject 0120test sysname Linux hostname linuxrechner2 machine x86_64 user demenzbild whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1439176 mm^3 (det: 1.353625 ) Loading /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/0120test/mri/gtmseg+subcort_BN.mgz Voxel Volume is 0.125 mm^3 Generating list of segmentation ids Found 38 segmentations Computing statistics for each segmentation Reporting on 37 segmentations Using PrintSegStat mri_segstats done Started at Mon Dec 2 18:49:27 CET 2019 Ended at Mon Dec 2 18:54:09 CET 2019 Gtmseg-Run-Time-Sec 282 Gtmseg-Run-Time-Hours 0.08 To check run: tkmeditfv 0120test nu.mgz -seg gtmseg+subcort_BN.mgz gtmseg+subcort_BN.ctab -opacity 1 gtmseg Done
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