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../derivatives/CAT12.8.1_1980 0 64 human 1070 1 1.5 12 Template_T1 /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_T1_masked.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/brainmask.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/T1.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cat.nii 0.5 22 1 2 0 1 5 0 0.7 0.1 BCGWHw 2 1 1 1 0 2 10 1 1 /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/neuromorphometrics.nii 0 csf gm wm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/lpba40.nii 0 gm wm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cobra.nii 0 gm wm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/hammers.nii 0 csf gm wm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/thalamus.nii 0 gm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/suit.nii 0 gm wm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/ibsr.nii 0 csf gm wm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/aal3.nii 1 gm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/mori.nii 1 gm wm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/anatomy3.nii 1 gm wm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/julichbrain.nii 1 gm wm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii 1 gm wm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii 1 gm wm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii 1 gm wm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii 1 gm wm [false] Desikan /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_a2009s.freesurfer.annot 0 1 Destrieux /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_DK40.freesurfer.annot 0 1 HCP /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_HCP_MMP1.freesurfer.annot 0 0 Schaefer2018_100P_17N /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_100Parcels_17Networks_order.annot 1 0 Schaefer2018_200P_17N /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot 0 0 Schaefer2018_400P_17N /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_400Parcels_17Networks_order.annot 1 0 Schaefer2018_600P_17N /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_600Parcels_17Networks_order.annot 1 0 0 1 3 5 7 9 11 13 13 15 17 19 21 23 25 27 0 0 0 /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii 0.5 [1 0.3] 0 pbt2x /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_Dartel.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_Dartel.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_Dartel.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_5_Dartel.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_6_Dartel.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_GS.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_GS.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_GS.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_GS.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii 0 1 1639 6 0.0628218766688279 8.5 0.0574171617627144 0.0551595129072666 [0.999999993821372 1.00000001816488 1.00000000727884] [0.999999993163534 1.00000002385505 1.00000001013407] 1.0000000064217 0 [0 39161.63671875 202904.265625 396720.03125] [0 0.0987135395407677 0.511454582214355 1] T1 [1025.40666264445 37460.1868790541 51029.7614521108 36753.64263239] [0.00258471118286252 0.0944247394800186 0.128629148006439 0.0926437750458717] 133148.84375 0.335624217987061 0.124074056744576 0.311294674873352 [1.99999998764274 2.00000003632976 2.00000001455768] 2.00000001284339 0.5 [1.89584374427795 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 3.04896998405457 2.11217427253723 1.23188161849976 1.20408163265306 1.01570546916721 1.425 1.14834320545197 1.10319030284882 2.06140366235492 voxel dimensions RMS error of voxel size brain next to the image boundary mean within the tissue classes standard deviation within the tissue classes contrast between tissue classes contrast between tissue classes noise to contrast ratio inhomogeneity to contrast ratio average Euler number (characteristic) average area of topological defects average number of defects RMSE of the expected boundary intensity Ym of the IS, OS, and CS RMSE of the expected boundary position Ypp of the IS, OS, and CS Percentual area of self-intersections of the IS and OS. total intracranial volume (GM+WM+VT) relative tissue volume (CSF,GM,WM) relative WMH volume total surface area 1639 LINUX 7771 9.3 12.8.1 1980 /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_vol_qa.m /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_stat_marks.m cat12 20220711-191324 1639 1639 6 0.0628218766688279 8.5 0.0574171617627144 0.0551595129072666 6 0.0628218766688279 [311.785792779535 744.512530019408 529.76929673758 0 0] 0.737109823936052 0.000464740478184309 2002.49323762208 1586.06761953652 [0.19657786902594 0.469407811400227 0.334014319573833 0 0] [2.65572825396561 0.638470288019683] [2.64437794685364 0.779875265970239 1] [2.09676463694317 0.247902117150272 0.335166909012159;2.71328097295537 0.183611125137539 0.407189926677598;3.39416242194538 0.273688835298441 0.257643164310243] [0.945515395392195 0.386256033170216 0.594617807042657;4.3042123185825 0.304921660545206 0.405382192957343] 1.7817950256859 [1.38034965923025 6.28031270474546 3.84867671648406 0.5 0.5] 1.04647404781843 8.6215364234576 5.14848545866247 [0.696983664772727 2118 659 3839.82307397453 0.496378724336795] [false] [0 0 0.0907841175794601] [false] [920.863801474478 446.560090556661 533.690912530337 751.332192949678 1708.7000503173 9052.57757129164] [809.277151385782 423.732874250567 311.047098641831 972.868340141441 1347.45684835173 8807.65021954317] [49729.03125 231828.171875 410933.65625] [0 0 1051.23425292969 49729.03125 231828.171875 410933.65625 591536 1105798.375] [0 0.02 0.05 1 2 3 4 5] 16 1.5 3 0.5 [1 1 1 1 1] 0.015 [0.03 0.03 0.03 0.03 0.03;0.03 0.03 0.03 0.03 0.03;0.03 0.03 0.03 0.03 0.03;0.03 0.03 0.03 0.03 0.03;0.03 0.03 0.03 0.03 0.03] 15 0 2 1 Shooting_Template_0_GS_tr1.5_rr3.0-3.0_or1.5_regstr15.0 [0.0200188551098108 0.0734647810459137 0.0813822224736214 0 0] [0.0852860858698948 0 0.0852860858698948 0;0.202671541028521 0.0103928038195259 0.213064344848047 2216.24462890625;0.202671541028521 0.0103928038195259 0.213064344848047 2216.24462890625] [0.0433654636144638 0.0998614355921745 0.112856589257717] [0.0310502704232931 0.0526283346116543 0.0659764111042023] 0.112856589257717

0.0813822224736214

64 1.5 1.5 0.25 [1.66666666666667 1.5 1.33333333333333 1.16666666666667 1] 0.051 [0.0501 0.0501 0.0501 0.0501 0.0501;0.0501 0.0501 0.0501 0.0501 0.0501;0.0501 0.0501 0.0501 0.0501 0.0501;0.0501 0.0501 0.0501 0.0501 0.0501;0.0501 0.0501 0.0501 0.0501 0.0501] 0.5 0 2 1 Shooting_Template_0_GS_tr1.5_rr2.5-1.5_or1.5_regstr0.5 [0.00907475873827934 0.0327237658202648 0.047443650662899 0.0565108731389046 0.0633211880922318 0.0704898610711098] [0.0855339333320655 0 0.0855339333320655 0;0.223085485347985 0.0123827571733822 0.235468242521368 6338.423828125;0.201392362500556 0.0157381366174942 0.21713049911805 11326.92578125;0.181204901801215 0.0180322043916099 0.199237106192825 19443.62109375;0.163949721697107 0.0207974279455033 0.184747149642611 36382.04296875;0.163949721697107 0.0207974279455033 0.184747149642611 36382.04296875] [0.0104407723993063 0.0378784909844398 0.0589889474213123 0.0861159265041351 0.111298754811287 0.118558771908283] [0.0031620638910681 0.0129718128591776 0.0291583016514778 0.0511776022613049 0.0710096061229706 0.0780047625303268] 0.118558771908283

0.0704898610711098

------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./execute/dir_9674/ds/sub-sc016/sub-sc016_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 41s APP: Rough bias correction: Initialize 9s Estimate background 9s Initial correction 8s Refine background 4s Final correction 6s Final scaling 6s 52s Correct center-of-mass 3s Affine registration 13s SPM preprocessing 1 (estimate 1 - TPM registration): 105s SPM preprocessing 1 (estimate 2): 78s SPM preprocessing 2 (write): Write Segmentation 24s Update Segmentation 25s Update Skull-Stripping 57s Update probability maps 12s 118s Global intensity correction: 22s SANLM denoising after intensity normalization (medium): 13s Fast Optimized Shooting registration 44s Local adaptive segmentation (LASstr=0.50): Prepare maps 5s Prepare partitions 3s Prepare segments (LASmod = 1.08) 20s Estimate local tissue thresholds (WM) 26s Estimate local tissue thresholds (GM) 37s Intensity transformation 0s SANLM denoising after LAS (medium) 13s 108s ROI segmentation (partitioning): Atlas -> subject space 10s Major structures 5s Ventricle detection 15s Blood vessel detection 14s WMH detection (WMHCstr=0.50 > WMHCstr'=0.15) 31s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 5s Final corrections 6s 87s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 40s AMAP peaks: [CSF,GM,WM] = [0.36 0.07,0.68 0.07,0.98 0.04] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 6s Level 1 cleanup (brain masking) 4s Level 2 cleanup (CSF correction) 2s Level 3 cleanup (CSF/WM PVE) 3s 14s Optimized Shooting registration with 2.50:-0.25:1.50 mm (regstr=0.50): Template: "/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii" 1 | 2.50 | 0.0855 0.0000 0.0855 | 32.0000 2 | 2.50 | 0.0831 0.0011 0.0843 | 29.4886 3 | 2.50 | 0.0825 0.0017 0.0841 | 26.9772 4 | 2.50 | 0.0821 0.0019 0.0840 | 24.6107 5 | 2.50 | 0.0819 0.0020 0.0838 | 22.6548 6 | 2.50 | 0.0816 0.0021 0.0837 | 20.6989 7 | 2.50 | 0.0814 0.0021 0.0835 | 18.9688 8 | 2.50 | 0.0811 0.0022 0.0833 | 17.4455 9 | 2.50 | 0.0809 0.0023 0.0831 | 15.9223 10 | 2.50 | 0.0806 0.0024 0.0830 | 14.6627 11 | 2.50 | 0.0803 0.0024 0.0827 | 13.4764 12 | 2.50 | 0.0800 0.0025 0.0825 | 12.3015 13 | 2.50 | 0.0797 0.0026 0.0823 | 11.3776 14 | 2.50 | 0.0794 0.0026 0.0821 | 10.4537 15 | 2.25 | 0.0773 0.0027 0.0800 | 9.5920 16 | 2.25 | 0.0744 0.0041 0.0785 | 8.8725 29 | 2.00 | 0.0749 0.0018 0.0767 | 3.3283 30 | 2.00 | 0.0690 0.0043 0.0733 | 3.1221 31 | 2.00 | 0.0671 0.0052 0.0724 | 2.9160 43 | 1.75 | 0.0659 0.0030 0.0689 | 1.5785 44 | 1.75 | 0.0617 0.0053 0.0670 | 1.5194 45 | 1.75 | 0.0604 0.0060 0.0664 | 1.4626 57 | 1.50 | 0.0586 0.0043 0.0629 | 1.0900 58 | 1.50 | 0.0556 0.0063 0.0619 | 1.0730 59 | 1.50 | 0.0546 0.0069 0.0616 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 207s Prepare output 14s 221s Jacobian determinant (RMS): 0.010 0.038 0.059 0.086 0.111 | 0.118559 Template Matching: 0.086 0.223 0.201 0.181 0.164 | 0.163950 Write result maps: 68s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 55s CSF distance: 23s PBT2x thickness: 68s 155s Create initial surface 117s Topology correction: 119s Surface refinement: 132s Reduction of surface collisions with optimization: 89s Spherical mapping with areal smoothing 116s Spherical registration 338s rh: Thickness estimation (0.50 mm ): WM distance: 44s CSF distance: 22s PBT2x thickness: 62s 136s Create initial surface 158s Topology correction: 133s Surface refinement: 157s Reduction of surface collisions with optimization: 82s Spherical mapping with areal smoothing 103s Spherical registration 339s Final surface processing results: Average thickness (FS): 2.6557 0.6384 mm Surface intensity / position RMSE: 0.0574 / 0.0552 Euler number / defect number / defect size: 6.0 / 8.5 / 0.06% Display thickness: /var/lib/condor/execute/dir_9674/ds/sub-sc016/surf/lh.thickness.sub-sc016_T1w Display thickness: /var/lib/condor/execute/dir_9674/ds/sub-sc016/surf/rh.thickness.sub-sc016_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_9674/ds/sub-sc016/sub-sc016_T1w.nii Surface ROI estimation: 119s Surface and thickness estimation takes: 2489s ROI estimation in native space: ROI estimation of 'cobra' atlas 14s ROI estimation of 'neuromorphometrics' atlas 48s ROI estimation of 'lpba40' atlas 15s ROI estimation of 'hammers' atlas 36s ROI estimation of 'thalamus' atlas 3s ROI estimation of 'ibsr' atlas 13s ROI estimation of 'aal3' atlas 22s ROI estimation of 'mori' atlas 32s ROI estimation of 'anatomy3' atlas 46s ROI estimation of 'julichbrain' atlas 58s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 24s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 43s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 95s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 136s Write results 137s 585s Quality check: 7s Print 'Graphics' figure to: /var/lib/condor/execute/dir_9674/ds/sub-sc016/report/catreport_sub-sc016_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 70 minute(s) and 18 second(s). Image Quality Rating (IQR): 84.39% (B) GM volume (GMV): 46.94% (744.51 / 1586.07 ml) GM thickness (GMT): 2.66 0.64 mm Segmentations are saved in /var/lib/condor/execute/dir_9674/ds/sub-sc016/mri Reports are saved in /var/lib/condor/execute/dir_9674/ds/sub-sc016/report Labels are saved in /var/lib/condor/execute/dir_9674/ds/sub-sc016/label ------------------------------------------------------------------------