[1.09588769549117 0.05124412470592 0.0223967930836912 2.62804990112222;-0.0568450804455436 1.03317322837426 0.134317841502073 -23.7028270470435;-0.0170153137534749 -0.143336123022875 1.14082842752725 -19.7566430499054;0 0 0 1] [1.09588769549117 0.05124412470592 0.0223967930836912 2.62804990112222;-0.0568450804455436 1.03317322837426 0.134317841502073 -23.7028270470435;-0.0170153137534749 -0.143336123022875 1.14082842752725 -19.7566430499054;0 0 0 1] [1 2 3 3 4 4 4 5 5 5 5 6 6] [409592.080189248 532222.702216353 193491.243389923 281451.771046039 116216.963634539 25394.8376512256 59180.284882002 224463.45003844 407283.710624904 340892.048904772 116918.361124692 36102.6747257932 13083.5191335529] [2485476739.40448;264613431.229865;1581067001.82721;1669632042.63263;1452797164.16195;110593150.742878;435993662.047501;2386672537.18178;16161146069.0587;1738976967.92964;1621014218.48465;208860666.111183;40203519.0446996] -12.5106868743896 [2.62804990112222 -23.7028270470435 -19.7566430499054] 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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 8 0.112083598270889 10 0.0638725608587265 0.0619441121816635 [0.999999992470947 1.00000002277828 0.999999993117216] [0.999999992657692 1.0000000209194 0.999999995784783] 1.00000000278881 0 [0 163823.09375 366844.3125 539447.9375] [0 0.303686589002609 0.680036544799805 1] T1 [52356.4116053336 66251.8187933688 55925.0430425563 31985.8656226189] [0.0970555394887924 0.122814111411572 0.103670880198479 0.0592937022447586] 172603.625 0.319963455200195 0.1038708537817 0.245894312858582 [1.99999998494189 2.00000004555656 1.99999998623443] 2.00000000557763 0.5 [1.89584374427795 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 3.28388142585754 1.82214832305908 1.06967830657959 1.30612244897959 1.02802089956772 1.5 1.27745127677917 1.23888230323792 1.92526109087571 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 20220711-171632 1639 1639 8 0.112083598270889 10 0.0638725608587265 0.0619441121816635 8 0.112083598270889 [178.254966374684 669.716994505104 532.673189300548 0 0] 1.24685099206503 0.000903093015538544 1868.46076576807 1380.64515018034 [0.129109906590698 0.485075397119693 0.385814696289609 0 0] [2.55896762678714 0.600921759465605] [2.57391953468323 0.743648553441797 1] [1.9623240038968 0.241195025136102 0.281084738636588;2.5783569836082 0.169126864082225 0.430177176605068;3.17709418734057 0.258072745842501 0.288738084758345] [0.905754077272692 0.334656207831203 0.53760193295077;4.17091154984703 0.390316077184255 0.46239806704923] 1.00891986621979 [0.5 6.56169894252322 4.77899957416683 0.5 0.5] 1.09030930155385 8.60771106142368 5.41728055784116 [0.628134822845459 6033 2060 3899.28903262317 0.371735636570603] [false] [0 0 0.340682506561279] [false] [804.592450669753 470.105294597148 243.523076789638 474.288682871606 1948.64624961554 7082.39292120647] [727.425602888502 445.466925739035 151.704840635929 364.745007336268 1158.05757554748 7638.41260092166] [180317.5 395905.28125 533075.875] [0 18062.125 5507.0634765625 180317.5 395905.28125 533075.875 709455.0625 955643.5] [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 [0.0188598856329918 0.066305972635746 0.0722232162952423 0 0] [0.077758782956542 0 0.077758782956542 0;0.183968808470654 0.00895516669192091 0.192923975162575 1909.67138671875;0.183968808470654 0.00895516669192091 0.192923975162575 1909.67138671875] [0.0394815616309643 0.0858323350548744 0.0951557978987694] [0.028048999607563 0.0402311310172081 0.049341905862093] 0.0951557978987694

0.0722232162952423

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 [0.00868695043027401 0.0314060300588608 0.0439322516322136 0.0512632355093956 0.0556380338966846 0.0622355937957764] [0.0789408210132447 0 0.0789408210132447 0;0.207275778388278 0.011601066468254 0.218876844856532 5938.2958984375;0.186534726737917 0.0148377357670499 0.201372462504967 10678.896484375;0.167223924019171 0.016823238796658 0.184047162815829 18140.02734375;0.153891467302483 0.0175368809568452 0.171428348259328 30678.1953125;0.153891467302483 0.0175368809568452 0.171428348259328 30678.1953125] [0.0101915635168552 0.0367209427058697 0.055375799536705 0.078936792910099 0.1009341776371 0.105667911469936] [0.00316912122070789 0.0123578039929271 0.0269382949918509 0.0459286831319332 0.0624048374593258 0.066411942243576] 0.105667911469936

0.0622355937957764

------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./execute/dir_32266/ds/sub-sc026/sub-sc026_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 27s APP: Rough bias correction: Initialize 6s Estimate background 6s Initial correction 6s Refine background 3s Final correction 5s Final scaling 5s 37s Correct center-of-mass 6s Affine registration 10s SPM preprocessing 1 (estimate 1 - TPM registration): 5s Use initial fine affine registration. 64s SPM preprocessing 1 (estimate 2): 59s SPM preprocessing 2 (write): Write Segmentation 15s Update Segmentation 18s Update Skull-Stripping 38s Update probability maps 8s 80s Global intensity correction: 15s SANLM denoising after intensity normalization (medium): 18s Fast Optimized Shooting registration 32s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 3s Prepare segments (LASmod = 1.20) 14s Estimate local tissue thresholds (WM) 18s Estimate local tissue thresholds (GM) 22s Intensity transformation 0s SANLM denoising after LAS (medium) 23s 88s ROI segmentation (partitioning): Atlas -> subject space 8s Major structures 4s Ventricle detection 13s Blood vessel detection 9s WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 27s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 3s Final corrections 4s 71s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 31s AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.07,0.98 0.04] Final cleanup (gcutstr=0.25): 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 | 0.0789 0.0000 0.0789 | 32.0000 2 | 2.50 | 0.0769 0.0010 0.0779 | 29.4886 3 | 2.50 | 0.0763 0.0015 0.0778 | 26.9772 4 | 2.50 | 0.0760 0.0017 0.0777 | 24.6107 5 | 2.50 | 0.0758 0.0018 0.0776 | 22.6548 6 | 2.50 | 0.0756 0.0019 0.0774 | 20.6989 7 | 2.50 | 0.0754 0.0019 0.0773 | 18.9688 8 | 2.50 | 0.0751 0.0020 0.0772 | 17.4455 9 | 2.50 | 0.0749 0.0021 0.0770 | 15.9223 10 | 2.50 | 0.0747 0.0022 0.0769 | 14.6627 11 | 2.50 | 0.0744 0.0023 0.0767 | 13.4764 12 | 2.50 | 0.0742 0.0023 0.0765 | 12.3015 13 | 2.50 | 0.0739 0.0024 0.0763 | 11.3776 14 | 2.50 | 0.0737 0.0025 0.0761 | 10.4537 15 | 2.25 | 0.0718 0.0025 0.0743 | 9.5920 16 | 2.25 | 0.0691 0.0039 0.0730 | 8.8725 29 | 2.00 | 0.0698 0.0018 0.0716 | 3.3283 30 | 2.00 | 0.0641 0.0040 0.0681 | 3.1221 31 | 2.00 | 0.0622 0.0049 0.0671 | 2.9160 43 | 1.75 | 0.0609 0.0028 0.0638 | 1.5785 44 | 1.75 | 0.0570 0.0049 0.0619 | 1.5194 45 | 1.75 | 0.0557 0.0056 0.0613 | 1.4626 57 | 1.50 | 0.0540 0.0041 0.0581 | 1.0900 58 | 1.50 | 0.0513 0.0058 0.0571 | 1.0730 Shooting registration with 2.50:-0.25:1.50 mm takes: 138s Prepare output 9s 148s Jacobian determinant (RMS): 0.010 0.037 0.055 0.079 0.101 | 0.105668 Template Matching: 0.079 0.207 0.187 0.167 0.154 | 0.153891 Write result maps: 23s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 28s CSF distance: 15s PBT2x thickness: 41s 90s Create initial surface 81s Topology correction: 90s Surface refinement: 78s Reduction of surface collisions with optimization: 65s Spherical mapping with areal smoothing 81s Spherical registration 297s rh: Thickness estimation (0.50 mm ): WM distance: 24s CSF distance: 13s PBT2x thickness: 42s 85s Create initial surface 81s Topology correction: 88s Surface refinement: 72s Reduction of surface collisions with optimization: 69s Spherical mapping with areal smoothing 95s Spherical registration 306s Final surface processing results: Average thickness (FS): 2.5590 0.6009 mm Surface intensity / position RMSE: 0.0639 / 0.0619 Euler number / defect number / defect size: 8.0 / 10.0 / 0.11% Display thickness: /var/lib/condor/execute/dir_32266/ds/sub-sc026/surf/lh.thickness.sub-sc026_T1w Display thickness: /var/lib/condor/execute/dir_32266/ds/sub-sc026/surf/rh.thickness.sub-sc026_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_32266/ds/sub-sc026/sub-sc026_T1w.nii Surface ROI estimation: 8s Surface and thickness estimation takes: 1668s ROI estimation in native space: ROI estimation of 'cobra' atlas 7s ROI estimation of 'neuromorphometrics' atlas 28s 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 17s ROI estimation of 'anatomy3' atlas 24s ROI estimation of 'julichbrain' atlas 33s 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 76s Write results 76s 317s Quality check: 5s Print 'Graphics' figure to: /var/lib/condor/execute/dir_32266/ds/sub-sc026/report/catreport_sub-sc026_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 46 minute(s) and 41 second(s). Image Quality Rating (IQR): 85.75% (B) GM volume (GMV): 48.51% (669.72 / 1380.65 ml) GM thickness (GMT): 2.56 0.60 mm Segmentations are saved in /var/lib/condor/execute/dir_32266/ds/sub-sc026/mri Reports are saved in /var/lib/condor/execute/dir_32266/ds/sub-sc026/report Labels are saved in /var/lib/condor/execute/dir_32266/ds/sub-sc026/label ------------------------------------------------------------------------