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