[1.04051699267085 0.0305758332141335 -0.00587607061245411 -0.408180698522639;-0.0131651244706705 1.01355036349809 0.178869026671064 5.525713070727;0.00858069949657015 -0.189210095956333 1.13290591179485 -8.67816311115488;0 0 0 1] [1.04051699267085 0.0305758332141335 -0.00587607061245411 -0.408180698522639;-0.0131651244706705 1.01355036349809 0.178869026671064 5.525713070727;0.00858069949657015 -0.189210095956333 1.13290591179485 -8.67816311115488;0 0 0 1] [1 2 3 3 4 4 4 5 5 5 5 6 6] [118.821915461309 166.067718616957 37.0765566631329 73.529670730711 63.3796942611871 15.5908912363791 32.3722241951649 144.389385460814 250.257093894795 226.59305442346 126.841407864575 17.1097458755349 7.25889361626901] [310.44025762708;60.9235770026175;209.068202999092;316.992548141832;436.633903613316;30.9102133470668;116.16481842308;1680.31967213104;4358.33398027832;3832.07472155377;569.740487163623;49.4279367697549;7.15620799989234] -4.87962293624878 [-0.408180698522639 5.525713070727 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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 20 0.590852646657678 15 0.0646372139453888 0.0660819485783577 [1.09999847412109 1 1] [1.09999847412109 1 1] 1.03440750240073 0 [5 35.6653060913086 110.836112976074 164.335021972656] [0.03042565099895 0.2170280367136 0.674452185630798 1] T1 [14.6200441040509 19.9846240297872 18.1118435523278 10.0019078034757] [0.0917566269636154 0.125425174832344 0.113671451807022 0.0627728179097176] 55.1777267456055 0.335763663053513 0.157928630709648 0.397481560707092 [2.19999694824219 2 2] 2.06881500480146 0.5 [8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 3.04687833786011 2.59817171096802 1.4456387758255 1.91836734693878 1.14771316166442 1.75 1.29274427890778 1.32163894176483 2.42756566522097 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 20220703-105415 1639 1639 20 0.590852646657678 15 0.0646372139453888 0.0660819485783577 20 0.590852646657678 [233.407735832902 705.488481763533 534.324150961334 0 0] 0.685747676206103 0.000465475288586612 1911.75674012959 1473.22036855777 [0.158433687732271 0.478875052789408 0.362691259478321 0 0] [2.583206710235 0.61258390140708] [2.57696843147278 0.772415111543245 1] [1.9927539268601 0.258719704293834 0.296400559136445;2.60334901466242 0.174498881635943 0.437634283347571;3.24857483896867 0.279732670333097 0.265965157515985] [0.9298979444502 0.336801026728512 0.533004258614015;4.26107226317411 0.359738288560022 0.466995741385985] 1.12666708143127 [0.695288931973254 6.45034218371782 4.3637079647687 0.5 0.5] 1.04654752885866 8.61490291626733 5.30325352729605 [0.177501600159228 25 5 10109.5414764023 0.470827992235438] [false] [0.0346088260412216 0.0382147058844566 0.0650840103626251] [false] [835.984199568027 489.611425926418 406.765083985183 814.912288013922 2012.53874984619 8428.87786109263] [738.723801150872 461.775360618053 225.677295968059 601.07705797191 1080.46599101978 9183.81199034535] [43.2831001281738 114.652099609375 166.355606079102] [0 0 5.26031732559204 43.2831001281738 114.652099609375 166.355606079102 227.891860961914 777.310852050781] [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 [0.0206808242946863 0.0744524598121643 0.0819738358259201 0 0] [0.0822564010955945 0 0.0822564010955945 0;0.192396111276542 0.00990043310414986 0.202296544380692 2111.24755859375;0.192396111276542 0.00990043310414986 0.202296544380692 2111.24755859375] [0.043033093214035 0.0981637835502625 0.107783608138561] [0.0301897618919611 0.0417909286916256 0.0511855781078339] 0.107783608138561

0.0819738358259201

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 [0.00979558937251568 0.0364138968288898 0.0513677373528481 0.0590662956237793 0.0635235160589218 0.0710013285279274] [0.0833825800126597 0 0.0833825800126597 0;0.218431181318681 0.0137304029304029 0.232161584249084 7028.25;0.19481603405251 0.0163525764581006 0.211168610510611 11769.1455078125;0.174575559320839 0.0177465259519398 0.192322085272779 19135.58203125;0.161226411278913 0.0183140924101654 0.179540503689078 32037.8125;0.161226411278913 0.0183140924101654 0.179540503689078 32037.8125] [0.0116866994649172 0.0434165298938751 0.0640946105122566 0.0873158201575279 0.106710143387318 0.111061997711658] [0.00326705607585609 0.012643032707274 0.0271051116287708 0.0456980317831039 0.061322346329689 0.0652812942862511] 0.111061997711658

0.0710013285279274

------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./condor/execute/dir_3859/ds/sub-53/sub-53_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 112s APP: Rough bias correction: Initialize 6s Estimate background 9s Initial correction 7s Refine background 4s Final correction 6s Final scaling 7s 46s Correct center-of-mass 4s Affine registration 9s SPM preprocessing 1 (estimate 1 - TPM registration): 71s SPM preprocessing 1 (estimate 2): 49s SPM preprocessing 2 (write): Write Segmentation 16s Update Segmentation 18s Update Skull-Stripping 39s Update probability maps 9s 83s Global intensity correction: 16s SANLM denoising after intensity normalization (medium): 17s Fast Optimized Shooting registration 33s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 2s Prepare segments (LASmod = 1.00) 13s Estimate local tissue thresholds (WM) 20s Estimate local tissue thresholds (GM) 27s Intensity transformation 0s SANLM denoising after LAS (medium) 35s 105s ROI segmentation (partitioning): Atlas -> subject space 7s Major structures 3s Ventricle detection 11s Blood vessel detection 9s WMH detection (WMHCstr=0.48 > WMHCstr'=0.00) 25s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 3s Final corrections 4s 64s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 32s AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.05] Final cleanup (gcutstr=0.24): Level 1 cleanup (ROI estimation) 4s Level 1 cleanup (brain masking) 3s Level 2 cleanup (CSF correction) 1s Level 3 cleanup (CSF/WM PVE) 3s 11s 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 | 0.0834 0.0000 0.0834 | 32.0000 2 | 2.50 | 0.0809 0.0011 0.0820 | 29.4886 3 | 2.50 | 0.0801 0.0017 0.0819 | 26.9772 4 | 2.50 | 0.0798 0.0019 0.0817 | 24.6107 5 | 2.50 | 0.0795 0.0021 0.0816 | 22.6548 6 | 2.50 | 0.0792 0.0022 0.0814 | 20.6989 7 | 2.50 | 0.0789 0.0023 0.0812 | 18.9688 8 | 2.50 | 0.0786 0.0024 0.0810 | 17.4455 9 | 2.50 | 0.0783 0.0025 0.0808 | 15.9223 10 | 2.50 | 0.0780 0.0026 0.0806 | 14.6627 11 | 2.50 | 0.0777 0.0027 0.0804 | 13.4764 12 | 2.50 | 0.0774 0.0028 0.0802 | 12.3015 13 | 2.50 | 0.0771 0.0029 0.0800 | 11.3776 14 | 2.50 | 0.0767 0.0030 0.0797 | 10.4537 15 | 2.25 | 0.0760 0.0031 0.0790 | 9.5920 16 | 2.25 | 0.0728 0.0046 0.0774 | 8.8725 29 | 2.00 | 0.0734 0.0021 0.0755 | 3.3283 30 | 2.00 | 0.0672 0.0045 0.0716 | 3.1221 31 | 2.00 | 0.0649 0.0055 0.0704 | 2.9160 43 | 1.75 | 0.0635 0.0032 0.0667 | 1.5785 44 | 1.75 | 0.0595 0.0052 0.0647 | 1.5194 45 | 1.75 | 0.0582 0.0059 0.0641 | 1.4626 57 | 1.50 | 0.0566 0.0043 0.0609 | 1.0900 58 | 1.50 | 0.0537 0.0061 0.0598 | 1.0730 Shooting registration with 2.50:-0.25:1.50 mm takes: 142s Prepare output 10s 152s Jacobian determinant (RMS): 0.012 0.043 0.064 0.087 0.107 | 0.111062 Template Matching: 0.083 0.218 0.195 0.175 0.161 | 0.161226 Write result maps: 24s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 28s CSF distance: 14s PBT2x thickness: 44s 93s Create initial surface 86s Topology correction: 92s Surface refinement: 98s Reduction of surface collisions with optimization: 67s Spherical mapping with areal smoothing 80s Spherical registration 313s rh: Thickness estimation (0.50 mm ): WM distance: 35s CSF distance: 15s PBT2x thickness: 46s 103s Create initial surface 86s Topology correction: 94s Surface refinement: 74s Reduction of surface collisions with optimization: 69s Spherical mapping with areal smoothing 88s Spherical registration 302s Final surface processing results: Average thickness (FS): 2.5832 0.6126 mm Surface intensity / position RMSE: 0.0646 / 0.0661 Euler number / defect number / defect size: 20.0 / 15.0 / 0.59% Display thickness: /var/lib/condor/execute/dir_3859/ds/sub-53/surf/lh.thickness.sub-53_T1w Display thickness: /var/lib/condor/execute/dir_3859/ds/sub-53/surf/rh.thickness.sub-53_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_3859/ds/sub-53/sub-53_T1w.nii Surface ROI estimation: 7s Surface and thickness estimation takes: 1737s ROI estimation in native space: ROI estimation of 'cobra' atlas 7s ROI estimation of 'neuromorphometrics' atlas 27s ROI estimation of 'lpba40' atlas 8s ROI estimation of 'hammers' atlas 19s ROI estimation of 'thalamus' atlas 1s ROI estimation of 'ibsr' atlas 7s ROI estimation of 'aal3' atlas 11s ROI estimation of 'mori' atlas 16s ROI estimation of 'anatomy3' atlas 24s ROI estimation of 'julichbrain' atlas 31s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 22s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 50s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 75s Write results 76s 312s Quality check: 4s Print 'Graphics' figure to: /var/lib/condor/execute/dir_3859/ds/sub-53/report/catreport_sub-53_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 49 minute(s) and 25 second(s). Image Quality Rating (IQR): 80.72% (B-) GM volume (GMV): 47.89% (705.49 / 1473.22 ml) GM thickness (GMT): 2.58 0.61 mm Segmentations are saved in /var/lib/condor/execute/dir_3859/ds/sub-53/mri Reports are saved in /var/lib/condor/execute/dir_3859/ds/sub-53/report Labels are saved in /var/lib/condor/execute/dir_3859/ds/sub-53/label ------------------------------------------------------------------------