NewSegment of /media/bonilha/AllenProj/MasterSet/harvestOutput/controls/BONC0001/T1_BONC0001_session.nii ------------------------------------------------------------------------ 12-Jul-2022 17:36:19 - Running job #1 ------------------------------------------------------------------------ 12-Jul-2022 17:36:19 - Running 'Segment' SPM12: spm_preproc_run (v7670) 17:36:19 - 12/07/2022 ======================================================================== Segment /media/bonilha/AllenProj/MasterSet/harvestOutput/controls/BONC0001/T1_BONC0001_session.nii Completed : 17:37:26 - 12/07/2022 12-Jul-2022 17:37:26 - Done 'Segment' 12-Jul-2022 17:37:26 - Done Brain extraction of /media/bonilha/AllenProj/MasterSet/harvestOutput/controls/BONC0001/T1_BONC0001_session.nii Warping /media/bonilha/AllenProj/MasterSet/harvestOutput/controls/BONC0001/bT1_BONC0001_session.nii based on NewSegment of /media/bonilha/AllenProj/MasterSet/harvestOutput/controls/BONC0001/T1_BONC0001_session.nii ------------------------------------------------------------------------ 12-Jul-2022 17:37:26 - Running job #1 ------------------------------------------------------------------------ 12-Jul-2022 17:37:26 - Running 'Normalise: Write' 12-Jul-2022 17:37:28 - Done 'Normalise: Write' 12-Jul-2022 17:37:28 - Done Saving T1 in /media/bonilha/AllenProj/MasterSet/harvestOutput/controls/BONC0001/T1_BONC0001_session_lime.mat Stage T1 required 69.2958 seconds Item opts: No field(s) named biasstr accstr Item 'Dartel Template', field 'val': Value must be either empty, a cellstr or a cfg_dep object. Item extopts: No field(s) named segmentation Item atlases: No field(s) named aal3 mori anatomy3 julichbrain Schaefer2018_100Parcels_17Networks_order Schaefer2018_200Parcels_17Networks_order Schaefer2018_400Parcels_17Networks_order Schaefer2018_600Parcels_17Networks_order Item GM: No field(s) named warped Item WM: No field(s) named warped Item output: No field(s) named WMHC ------------------------------------------------------------------------ 12-Jul-2022 17:37:29 - Running job #1 ------------------------------------------------------------------------ 12-Jul-2022 17:37:29 - Running 'CAT12: Segmentation' External diary log is written to "/media/bonilha/AllenProj/MasterSet/harvestOutput/controls/BONC0001/T1_BONC0001_session_lime.mat.log.txt". ------------------------------------------------------------------------ CAT12.8.1 r2000: 1/1: ./controls/BONC0001/T1_BONC0001_session.nii ------------------------------------------------------------------------ SANLM denoising (medium): 10s APP: Rough bias correction: Initialize 2s Estimate background 1s Initial correction 2s Refine background 1s Final correction 2s Final scaling 2s 12s Correct center-of-mass 2s Affine registration 7s SPM preprocessing 1 (estimate 1 - TPM registration): 30s SPM preprocessing 1 (estimate 2): 29s SPM preprocessing 2 (write): Write Segmentation 7s Update Segmentation 7s Update Skull-Stripping 12s Update probability maps 1s 27s Global intensity correction: 5s SANLM denoising after intensity normalization (medium): 4s Fast Optimized Shooting registration Dartel registration with 1.50 mm on a 1.50 mm Template: Template: "/home/bonilha/Documents/GitHub/Bonilha/Toolbox/imaging/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii" 1 | 0.2601 | 828246 0 828246 832.598 2 | 0.1860 | 592373 33575 625948 396.870 3 | 0.1626 | 517843 32738 550581 263.502 4 | 0.1498 | 476995 17591 494585 282.184 5 | 0.1351 | 430146 33570 463716 238.981 6 | 0.1304 | 415221 34715 449937 164.647 7 | 0.1295 | 412312 17733 430044 204.541 8 | 0.1204 | 383489 30582 414071 178.114 9 | 0.1182 | 376314 32106 408420 136.888 10 | 0.1176 | 374409 16581 390990 159.487 11 | 0.1098 | 349673 29562 379235 114.156 12 | 0.1082 | 344445 31448 375893 105.358 13 | 0.1081 | 344130 16417 360547 111.915 14 | 0.1013 | 322448 27719 350167 80.893 15 | 0.0996 | 317121 29958 347079 71.118 16 | 0.0992 | 315787 31479 347266 55.915 17 | 0.0984 | 313200 32327 345527 53.020 18 | 0.0978 | 311529 32941 344470 51.344  132s 134s Local adaptive segmentation (LASstr=0.50): Prepare maps 2s Prepare partitions 1s Prepare segments (LASmod = 1.00) 5s Estimate local tissue thresholds (WM) 7s Estimate local tissue thresholds (GM) 11s Intensity transformation 0s SANLM denoising after LAS (medium) 9s 34s ROI segmentation (partitioning): Atlas -> subject space 3s Major structures 2s Ventricle detection 7s Blood vessel detection 4s WMH detection (WMHCstr=0.50 > WMHCstr'=0.06) 13s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 2s Final corrections 1s 33s Blood vessel correction (BVCstr=0.50): 0s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 15s AMAP peaks: [CSF,GM,WM] = [0.36±0.06,0.68±0.08,0.98±0.04] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 2s Level 1 cleanup (brain masking) 1s Level 2 cleanup (CSF correction) 0s Level 3 cleanup (CSF/WM PVE) 0s 3s Dartel registration with 1.50 mm on a 1.50 mm Template: Template: "/home/bonilha/Documents/GitHub/Bonilha/Toolbox/imaging/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii" 1 | 0.1767 | 463762 0 463762 334.780 2 | 0.1433 | 376044 15571 391614 139.346 3 | 0.1381 | 362469 18879 381348 52.479 4 | 0.1359 | 356499 10496 366994 151.747 5 | 0.1278 | 335313 23429 358743 54.043 6 | 0.1269 | 332989 24619 357608 33.651 7 | 0.1269 | 332980 12763 345743 129.635 8 | 0.1182 | 310289 26876 337165 46.618 9 | 0.1175 | 308453 27719 336172 27.447 10 | 0.1178 | 309008 14406 323414 116.660 11 | 0.1081 | 283721 29933 313654 46.406 12 | 0.1071 | 281108 31106 312214 28.423 13 | 0.1075 | 282060 16337 298397 98.508 14 | 0.0986 | 258618 30254 288872 42.515 15 | 0.0973 | 255424 31876 287300 27.403 16 | 0.0971 | 254903 33460 288362 32.735 17 | 0.0966 | 253491 34078 287569 23.761 18 | 0.0963 | 252586 34693 287278 21.475 111s Jacobian determinant (RMS): 0.110450 Template Matching: 0.096259 Write result maps: 4s Surface and thickness estimation: lh: Thickness estimation (0.50 mm³): WM distance: 26s CSF distance: 10s PBT2x thickness: 32s 73s Create initial surface 44s Topology correction: 66s Surface refinement: 44s Reduction of surface collisions with optimization: 35s Spherical mapping with areal smoothing 61s Spherical registration 174s rh: Thickness estimation (0.50 mm³): WM distance: 27s CSF distance: 10s PBT2x thickness: 32s 73s Create initial surface 44s Topology correction: 71s Surface refinement: 67s Reduction of surface collisions with optimization: 35s Spherical mapping with areal smoothing 60s Spherical registration 187s Final surface processing results: Average thickness: 2.4786 ± 0.6107 mm Euler characteristic / defect size: 36 / 1.10% Display thickness: /media/bonilha/AllenProj/MasterSet/harvestOutput/controls/BONC0001/surf/lh.thickness.T1_BONC0001_session Display thickness: /media/bonilha/AllenProj/MasterSet/harvestOutput/controls/BONC0001/surf/rh.thickness.T1_BONC0001_session Show surfaces in orthview: /media/bonilha/AllenProj/MasterSet/harvestOutput/controls/BONC0001/T1_BONC0001_session.nii Surface ROI estimation: 5s Surface and thickness estimation takes: 1091s ROI estimation: ROI estimation of 'cobra' atlas 1s ROI estimation of 'neuromorphometrics' atlas 4s ROI estimation of 'lpba40' atlas 1s ROI estimation of 'hammers' atlas 3s ROI estimation of 'thalamus' atlas 0s ROI estimation of 'ibsr' atlas 1s ROI estimation of 'AICHA' atlas 0s ROI estimation of 'aal' atlas ------------------------------------------------------------------------ WARNING 01: cat_main1639:cat_main_roi Error in cat_main_roi. ------------------------------------------------------------------------ Quality check: 4s Print 'Graphics' figure to: /media/bonilha/AllenProj/MasterSet/harvestOutput/controls/BONC0001/report/catreport_T1_BONC0001_session.pdf ------------------------------------------------------------------------ CAT preprocessing takes 26 minute(s) and 38 second(s). Image Quality Rating (IQR): 74.15% (C) Segmentations are saved in /media/bonilha/AllenProj/MasterSet/harvestOutput/controls/BONC0001/mri Reports are saved in /media/bonilha/AllenProj/MasterSet/harvestOutput/controls/BONC0001/report Labels are saved in /media/bonilha/AllenProj/MasterSet/harvestOutput/controls/BONC0001/label ------------------------------------------------------------------------ Already done: skipping normalization of /media/bonilha/AllenProj/MasterSet/harvestOutput/controls/BONC0001/T1_BONC0001_session.nii Skipping VBM (already done) /media/bonilha/AllenProj/MasterSet/harvestOutput/controls/BONC0001/T1_BONC0001_session.nii Saving postscript file ~/Desktop/MasterNormalized