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../derivatives/CAT12.8.1_1980 0 24 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 0.12784042908601 10.5 0.0585213303565979 0.0559164434671402 [0.999999991239892 0.999999983832577 1.00000000947011] [0.999999992593906 0.999999966366077 1.00000000995041] 0.999999994847525 0 [1.22099995613098 59.6070213317871 142.307266235352 195.951141357422] [0.00623114453628659 0.304193288087845 0.726238489151001 1] T1 [21.9119318158252 21.3253409009903 17.885273279779 9.54292122371175] [0.112524598836899 0.109512269496918 0.0918464511632919 0.0490058735013008] 53.9802322387695 0.275478005409241 0.112666442990303 0.177780523896217 [1.99999998247978 1.99999996766515 2.00000001894021] 1.99999998969505 0.5 [5.48201417922974 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 3.95116329193115 1.94841289520264 0.900745332241058 1.20408163265306 1.0319601072715 1.525 1.17042660713196 1.11832880973816 1.97538398377245 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 20220712-145100 1639 1639 6 0.12784042908601 10.5 0.0585213303565979 0.0559164434671402 6 0.12784042908601 [312.402484405177 653.723414970114 481.703039926003 0 0] 1.23167447151165 0.000850704415471927 1893.86536178187 1447.82893930129 [0.215773062635382 0.451519787472679 0.332707149891939 0 0] [2.59606331817722 0.63753207630255] [2.59388399124146 0.773647711738426 1] [1.98185386572639 0.256809105718803 0.301289426701051;2.62337839662798 0.183764178446021 0.425986907359651;3.29854983122498 0.278062254687803 0.272723665939298] [0.923061091544665 0.319675685949459 0.555730757859466;4.26353834171473 0.352283776173493 0.444269242140534] 1.05430789842273 [1.72509092376764 5.9590479071961 3.82520024949604 0.5 0.5] 1.08507044154719 8.6123899387531 4.89047552527049 [0.506336847941081 2506 206 6211.71990398281 0.340062493314474] [false] [0.00546531612053514 0 0.0969317406415939] [false] [772.368838732456 434.740464915463 444.393095987915 556.514657207983 1660.27311308865 9230.72335615771] [685.815947305704 407.581889289224 304.271665050118 428.529461186992 1092.6802287741 9664.05100935239] [66.4077987670898 145.567199707031 191.107894897461] [0 0 1.49924921989441 66.4077987670898 145.567199707031 191.107894897461 253.457946777344 469.865875244141] [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 [0.0227065328508615 0.0777254477143288 0.0862221196293831 0 0] [0.0884461023178803 0 0.0884461023178803 0;0.206791633889884 0.011726277501357 0.218517911391241 2500.60522460938;0.206791633889884 0.011726277501357 0.218517911391241 2500.60522460938] [0.0472088418900967 0.102866001427174 0.114516526460648] [0.0330692529678345 0.0486887320876122 0.0599715150892735] 0.114516526460648

0.0862221196293831

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 [0.0105905700474977 0.0407038405537605 0.0528545454144478 0.0623652376234531 0.0691297352313995 0.0776060819625854] [0.0878853791426921 0 0.0878853791426921 0;0.224408318070818 0.0164878624847375 0.240896180555556 8439.724609375;0.207228724823263 0.0184312901592929 0.225660014982556 13265.220703125;0.185196212667119 0.0207591767777518 0.205955389444871 22384.0390625;0.166602023719627 0.0236847811555186 0.190286804875145 41433.04296875;0.166602023719627 0.0236847811555186 0.190286804875145 41433.04296875] [0.0122900530695915 0.0428654290735722 0.0648193955421448 0.0900253728032112 0.114705838263035 0.121315412223339] [0.0033164257183671 0.0130538512021303 0.0293078422546387 0.0505858920514584 0.0690455585718155 0.0747214257717133] 0.121315412223339

0.0776060819625854

------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./dir_399/ds/sub-35/sub-35_acq-highres_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 57s APP: Rough bias correction: Initialize 10s Estimate background 9s Initial correction 8s Refine background 5s Final correction 7s Final scaling 7s 56s Correct center-of-mass 9s Affine registration 15s SPM preprocessing 1 (estimate 1 - TPM registration): 7s Use initial fine affine registration. 6s Use previous fine affine registration. 86s SPM preprocessing 1 (estimate 2): 93s SPM preprocessing 2 (write): Write Segmentation 26s Update Segmentation 27s Update Skull-Stripping 60s Update probability maps 13s 125s Global intensity correction: 25s SANLM denoising after intensity normalization (medium): 13s Fast Optimized Shooting registration 51s Local adaptive segmentation (LASstr=0.50): Prepare maps 6s Prepare partitions 4s Prepare segments (LASmod = 1.04) 20s Estimate local tissue thresholds (WM) 23s Estimate local tissue thresholds (GM) 31s Intensity transformation 0s SANLM denoising after LAS (medium) 40s 128s ROI segmentation (partitioning): Atlas -> subject space 12s Major structures 5s Ventricle detection 17s Blood vessel detection 12s WMH detection (WMHCstr=0.50 > WMHCstr'=0.16) 31s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 5s Final corrections 7s 91s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 53s AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.07,0.98 0.05] 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) 4s 15s 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 | 0.0879 0.0000 0.0879 | 32.0000 2 | 2.50 | 0.0851 0.0012 0.0863 | 29.4886 3 | 2.50 | 0.0842 0.0019 0.0861 | 26.9772 4 | 2.50 | 0.0838 0.0021 0.0860 | 24.6107 5 | 2.50 | 0.0835 0.0023 0.0858 | 22.6548 6 | 2.50 | 0.0832 0.0024 0.0856 | 20.6989 7 | 2.50 | 0.0830 0.0025 0.0854 | 18.9688 8 | 2.50 | 0.0826 0.0026 0.0852 | 17.4455 9 | 2.50 | 0.0823 0.0027 0.0850 | 15.9223 10 | 2.50 | 0.0820 0.0028 0.0848 | 14.6627 11 | 2.50 | 0.0817 0.0029 0.0845 | 13.4764 12 | 2.50 | 0.0814 0.0029 0.0843 | 12.3015 13 | 2.50 | 0.0810 0.0030 0.0840 | 11.3776 14 | 2.50 | 0.0807 0.0031 0.0838 | 10.4537 15 | 2.25 | 0.0800 0.0032 0.0832 | 9.5920 16 | 2.25 | 0.0768 0.0047 0.0815 | 8.8725 17 | 2.25 | 0.0756 0.0053 0.0808 | 8.1530 18 | 2.25 | 0.0748 0.0055 0.0803 | 7.5234 29 | 2.00 | 0.0769 0.0026 0.0795 | 3.3283 30 | 2.00 | 0.0711 0.0052 0.0762 | 3.1221 31 | 2.00 | 0.0691 0.0061 0.0752 | 2.9160 43 | 1.75 | 0.0681 0.0035 0.0716 | 1.5785 44 | 1.75 | 0.0633 0.0060 0.0694 | 1.5194 45 | 1.75 | 0.0617 0.0069 0.0687 | 1.4626 57 | 1.50 | 0.0600 0.0050 0.0650 | 1.0900 58 | 1.50 | 0.0566 0.0072 0.0639 | 1.0730 59 | 1.50 | 0.0555 0.0079 0.0634 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 274s Prepare output 14s 287s Jacobian determinant (RMS): 0.012 0.043 0.065 0.090 0.115 | 0.121315 Template Matching: 0.088 0.224 0.207 0.185 0.167 | 0.166602 Write result maps: 38s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 59s CSF distance: 21s PBT2x thickness: 62s 150s Create initial surface 109s Topology correction: 121s Surface refinement: 112s Reduction of surface collisions with optimization: 100s Spherical mapping with areal smoothing 109s Spherical registration 321s rh: Thickness estimation (0.50 mm ): WM distance: 60s CSF distance: 24s PBT2x thickness: 62s 154s Create initial surface 108s Topology correction: 121s Surface refinement: 109s Reduction of surface collisions with optimization: 92s Spherical mapping with areal smoothing 107s Spherical registration 302s Final surface processing results: Average thickness (FS): 2.5961 0.6375 mm Surface intensity / position RMSE: 0.0585 / 0.0559 Euler number / defect number / defect size: 6.0 / 10.5 / 0.13% Display thickness: /var/lib/condor/execute/dir_399/ds/sub-35/surf/lh.thickness.sub-35_acq-highres_T1w Display thickness: /var/lib/condor/execute/dir_399/ds/sub-35/surf/rh.thickness.sub-35_acq-highres_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_399/ds/sub-35/sub-35_acq-highres_T1w.nii Surface ROI estimation: 10s Surface and thickness estimation takes: 2136s ROI estimation in native space: ROI estimation of 'cobra' atlas 18s ROI estimation of 'neuromorphometrics' atlas 64s ROI estimation of 'lpba40' atlas 18s ROI estimation of 'hammers' atlas 45s ROI estimation of 'thalamus' atlas 3s ROI estimation of 'ibsr' atlas 16s ROI estimation of 'aal3' atlas 26s ROI estimation of 'mori' atlas 39s ROI estimation of 'anatomy3' atlas 58s ROI estimation of 'julichbrain' atlas 76s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 27s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 35s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 120s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 183s Write results 184s 732s Quality check: 7s Print 'Graphics' figure to: /var/lib/condor/execute/dir_399/ds/sub-35/report/catreport_sub-35_acq-highres_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 69 minute(s) and 29 second(s). Image Quality Rating (IQR): 85.25% (B) GM volume (GMV): 45.15% (653.72 / 1447.83 ml) GM thickness (GMT): 2.60 0.64 mm Segmentations are saved in /var/lib/condor/execute/dir_399/ds/sub-35/mri Reports are saved in /var/lib/condor/execute/dir_399/ds/sub-35/report Labels are saved in /var/lib/condor/execute/dir_399/ds/sub-35/label ------------------------------------------------------------------------