[1.05135087984396 0.0152522388599993 -0.0411734295420131 4.25850039898659;0.0279308317588851 0.991694655493429 0.228606715814754 -5.29171158628456;0.0419108935627821 -0.265504088428273 1.09434502333005 -8.09232604177227;0 0 0 1] [1.05135087984396 0.0152522388599993 -0.0411734295420131 4.25850039898659;0.0279308317588851 0.991694655493429 0.228606715814754 -5.29171158628456;0.0419108935627821 -0.265504088428273 1.09434502333005 -8.09232604177227;0 0 0 1] [1 2 3 3 4 4 4 5 5 5 5 6 6] [298.841825608383 433.237780168664 106.560549919661 205.792664663105 184.738268439126 36.7556546850617 83.3087016858802 362.682470140325 488.178755366771 403.354542878336 323.277671596776 371.192804891855 393.185086330147] [2513.39285793035;383.99976400028;1528.45311460549;2465.91914480172;3227.39474662281;194.845430631129;828.599160623112;2939.24912036358;31667.4634421378;37466.0976094995;1329.70791597092;247.448314968159;438.970031369811] -5.74193286895752 [4.25850039898659 -5.29171158628456 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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 16 0.500564516307999 7 0.0662364363670349 0.0647958442568779 [1.09999847412109 1 1] [1.09999847412109 1 1] 1.03440750240073 0 [4.48400020599365 88.7073974609375 258.313201904297 431.8857421875] [0.0103823766112328 0.20539553463459 0.598105430603027 1] T1 [3.21931654010516 43.9456054186152 49.0883827864867 32.7210265386776] [0.00753229623660445 0.102820374071598 0.114853024482727 0.0765580087900162] 152.07177734375 0.352111130952835 0.150777980685234 0.263804346323013 [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 2.80166625976562 2.49552083015442 1.114098072052 1.71428571428571 1.125141129077 1.35 1.3247287273407 1.29591691493988 2.34673922749529 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 20220703-110557 1639 1639 16 0.500564516307999 7 0.0662364363670349 0.0647958442568779 16 0.500564516307999 [240.600604286583 746.889892176101 522.59635546501 0 0] 0.457232699076335 0.00030278569639399 1991.57626920208 1510.08685192769 [0.159328984276266 0.494600619310513 0.346070396413221 0 0] [2.57098728954379 0.610385160470722] [2.56198763847351 0.777732939752273 1] [2.00329849928405 0.242116135320448 0.310437093262145;2.6049217568659 0.171615299743439 0.439129258060945;3.2519435279647 0.27632613250039 0.25043364867691] [0.915883804254754 0.352419521379955 0.517075517075517;4.28415571517678 0.374183341634051 0.482924482924483] 1.28333871363157 [0.711368252088102 6.73276974336411 4.06520108500756 0.5 0.5] 1.0302785696394 8.62109941199976 5.51789079493987 [0.30247860010768 1 1 8573.41670726013 0.366958464882083] [false] [0.00752979423850775 0 0.0645354837179184] [false] [903.955175869332 455.037386827476 481.653967945114 4223.28775180096 6219.4665263019 1268.85007322947] [775.877090789615 430.040779933256 253.750922123359 3968.64885483093 5528.77616008938 1335.31564769745] [106.692199707031 285.015014648438 433.841491699219] [0 0 0.911751270294189 106.692199707031 285.015014648438 433.841491699219 597.416137695312 1200.35607910156] [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 [0.0214067753404379 0.0766744911670685 0.0853779539465904 0 0] [0.0845629572629833 0 0.0845629572629833 0;0.197566605988098 0.0105795316478642 0.208146137635963 2256.06396484375;0.197566605988098 0.0105795316478642 0.208146137635963 2256.06396484375] [0.0478942096233368 0.103823579847813 0.116004668176174] [0.0341823548078537 0.0479279607534409 0.059498768299818] 0.116004668176174

0.0853779539465904

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 [0.0093554500490427 0.0346393957734108 0.0490248575806618 0.0575084686279297 0.0640929415822029 0.072575531899929] [0.0848023219473256 0 0.0848023219473256 0;0.223713797313797 0.0132259100274725 0.23693970734127 6770.0126953125;0.203226060389434 0.0165049906681423 0.219731051057576 11878.83984375;0.182495508438502 0.0188835955526528 0.201379103991154 20361.65234375;0.165251774513206 0.021947554056414 0.18719932856962 38394.01953125;0.165251774513206 0.021947554056414 0.18719932856962 38394.01953125] [0.0109941000118852 0.0405974388122559 0.062202874571085 0.0900966599583626 0.115943990647793 0.122719690203667] [0.00320269633084536 0.0128443101420999 0.0294529721140862 0.0512315183877945 0.0704797804355621 0.0752568915486336] 0.122719690203667

0.072575531899929

------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./condor/execute/dir_29596/ds/sub-97/sub-97_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 27s APP: Rough bias correction: Initialize 6s Estimate background 9s Initial correction 9s Refine background 4s Final correction 7s Final scaling 9s 49s Correct center-of-mass 4s Affine registration 10s SPM preprocessing 1 (estimate 1 - TPM registration): 78s SPM preprocessing 1 (estimate 2): 52s SPM preprocessing 2 (write): Write Segmentation 15s Update Segmentation 17s Update Skull-Stripping 37s Update probability maps 8s 77s Global intensity correction: 14s SANLM denoising after intensity normalization (medium): 10s Fast Optimized Shooting registration 32s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 2s Prepare segments (LASmod = 1.00) 14s Estimate local tissue thresholds (WM) 19s Estimate local tissue thresholds (GM) 23s Intensity transformation 0s SANLM denoising after LAS (medium) 23s 88s ROI segmentation (partitioning): Atlas -> subject space 7s Major structures 3s Ventricle detection 12s Blood vessel detection 9s WMH detection (WMHCstr=0.48 > WMHCstr'=0.02) 23s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 3s Final corrections 4s 62s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 35s AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.07,0.99 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 | 0.0848 0.0000 0.0848 | 32.0000 2 | 2.50 | 0.0822 0.0012 0.0833 | 29.4886 3 | 2.50 | 0.0814 0.0018 0.0832 | 26.9772 4 | 2.50 | 0.0810 0.0020 0.0830 | 24.6107 5 | 2.50 | 0.0807 0.0022 0.0828 | 22.6548 6 | 2.50 | 0.0804 0.0023 0.0826 | 20.6989 7 | 2.50 | 0.0801 0.0024 0.0825 | 18.9688 8 | 2.50 | 0.0798 0.0025 0.0823 | 17.4455 9 | 2.50 | 0.0795 0.0025 0.0820 | 15.9223 10 | 2.50 | 0.0792 0.0026 0.0818 | 14.6627 11 | 2.50 | 0.0789 0.0027 0.0816 | 13.4764 12 | 2.50 | 0.0786 0.0028 0.0813 | 12.3015 13 | 2.50 | 0.0782 0.0029 0.0811 | 11.3776 14 | 2.50 | 0.0779 0.0029 0.0808 | 10.4537 15 | 2.25 | 0.0775 0.0030 0.0805 | 9.5920 16 | 2.25 | 0.0746 0.0044 0.0790 | 8.8725 29 | 2.00 | 0.0761 0.0020 0.0782 | 3.3283 30 | 2.00 | 0.0699 0.0045 0.0744 | 3.1221 31 | 2.00 | 0.0677 0.0055 0.0732 | 2.9160 43 | 1.75 | 0.0668 0.0032 0.0699 | 1.5785 44 | 1.75 | 0.0623 0.0055 0.0678 | 1.5194 45 | 1.75 | 0.0608 0.0063 0.0671 | 1.4626 57 | 1.50 | 0.0594 0.0046 0.0640 | 1.0900 58 | 1.50 | 0.0562 0.0067 0.0628 | 1.0730 59 | 1.50 | 0.0551 0.0073 0.0624 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 156s Prepare output 10s 166s Jacobian determinant (RMS): 0.011 0.041 0.062 0.090 0.116 | 0.122720 Template Matching: 0.085 0.224 0.203 0.182 0.165 | 0.165252 Write result maps: 22s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 33s CSF distance: 14s PBT2x thickness: 44s 97s Create initial surface 83s Topology correction: 92s Surface refinement: 81s Reduction of surface collisions with optimization: 70s Spherical mapping with areal smoothing 81s Spherical registration 272s rh: Thickness estimation (0.50 mm ): WM distance: 30s CSF distance: 14s PBT2x thickness: 41s 90s Create initial surface 75s Topology correction: 84s Surface refinement: 96s Reduction of surface collisions with optimization: 65s Spherical mapping with areal smoothing 73s Spherical registration 261s Final surface processing results: Average thickness (FS): 2.5710 0.6104 mm Surface intensity / position RMSE: 0.0662 / 0.0648 Euler number / defect number / defect size: 16.0 / 7.0 / 0.50% Display thickness: /var/lib/condor/execute/dir_29596/ds/sub-97/surf/lh.thickness.sub-97_T1w Display thickness: /var/lib/condor/execute/dir_29596/ds/sub-97/surf/rh.thickness.sub-97_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_29596/ds/sub-97/sub-97_T1w.nii Surface ROI estimation: 7s Surface and thickness estimation takes: 1604s ROI estimation in native space: ROI estimation of 'cobra' atlas 7s ROI estimation of 'neuromorphometrics' atlas 25s ROI estimation of 'lpba40' atlas 7s ROI estimation of 'hammers' atlas 18s ROI estimation of 'thalamus' atlas 1s ROI estimation of 'ibsr' atlas 6s ROI estimation of 'aal3' atlas 10s ROI estimation of 'mori' atlas 15s ROI estimation of 'anatomy3' atlas 21s ROI estimation of 'julichbrain' atlas 28s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 20s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 46s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 69s Write results 70s 286s Quality check: 4s Print 'Graphics' figure to: /var/lib/condor/execute/dir_29596/ds/sub-97/report/catreport_sub-97_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 45 minute(s) and 2 second(s). Image Quality Rating (IQR): 81.53% (B-) GM volume (GMV): 49.46% (746.89 / 1510.09 ml) GM thickness (GMT): 2.57 0.61 mm Segmentations are saved in /var/lib/condor/execute/dir_29596/ds/sub-97/mri Reports are saved in /var/lib/condor/execute/dir_29596/ds/sub-97/report Labels are saved in /var/lib/condor/execute/dir_29596/ds/sub-97/label ------------------------------------------------------------------------