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[0.220576659646018 0.0447700800612438 0.0333532822266892] [1.09230257849454 1.09654129683503 1.15899041569396] [0.00439397919985101 -0.000197743342773651 0.00507026836182279] [1.79203959933246 7.89427697539324 -16.063726894061] [0.220576659646018 0.0447700800612438 0.0333532822266892] [1.09230257849454 1.09654129683503 1.15899041569396] [0.00439397919985101 -0.000197743342773651 0.00507026836182279] /var/lib/condor/execute/dir_10175/ds/sub-season108 sub-season108_ses-3_acq-MPrageHiRes_T1w /var/lib/condor/execute/dir_10175/ds/sub-season108/sub-season108_ses-3_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_10175/ds/sub-season108/sub-season108_ses-3_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_10175/ds/sub-season108/mri/msub-season108_ses-3_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_10175/ds/sub-season108/mri/p0sub-season108_ses-3_acq-MPrageHiRes_T1w.nii ..s/sub-season108/..son108_ses-3_acq-MPrageHiRes_T1w /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii [1 1 2 3 4 2] mni [0 0.001 0.5 0.05 0.2] 0.0001 0.5 0.5 0.001 60 3 0 1 0 1.4 2 0.5 0 -Inf 0.5 0.5 0.5 2 0.5 0 1 optimal [1 0.3] ../derivatives/CAT12.8.1_1980 0 28 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 22 0.623732055935441 15 0.0725946426391602 0.0763023570179939 [0.880005874076767 0.874999976681145 0.875000023169822] [0.880005873347893 0.87499997616593 0.875000020771293] 0.876671800646971 0 [12.289999961853 279.501525878906 710.55078125 1022.97747802734] [0.0120139494538307 0.273223549127579 0.69459080696106 1] T1 [8.96110123750875 117.914285272535 94.2401579508173 57.5405551776181] [0.00886634178459644 0.116667404770851 0.0932436138391495 0.0569320917129517] 316.225830078125 0.309122949838638 0.125995606184006 0.272923529148102 [1.76001174815353 1.74999995336229 1.75000004633964] 1.75334360129394 0.5 [8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 3.44648909568787 2.1397590637207 1.13671517372131 2.02040816326531 1.15593301398386 1.75 1.4518928527832 1.52604711055756 2.00807684521269 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 20220712-172044 1639 1639 22 0.623732055935441 15 0.0725946426391602 0.0763023570179939 22 0.623732055935441 [186.25706259507 653.772072254052 462.299251532816 0 0] 0.913597883565998 0.00070151114966027 1863.14398464974 1302.32838638194 [0.143018507883807 0.502002474253308 0.354979017862885 0 0] [2.46615720845059 0.609204818699067] [2.48467540740967 0.710943029986135 1] [1.8398649191256 0.2473800161166 0.271577968858936;2.47851785909249 0.174361710320359 0.431805052953089;3.10172835834261 0.25139360910369 0.296616978187975] [0.863582041319119 0.316273266479178 0.584857921370183;4.00002311464212 0.36868297945165 0.415142078629817] 1.22392995268805 [0.5 6.86570535656085 4.22519787828458 0.5 0.5] 1.07015111496603 8.60653490366739 5.62884661337497 [0.370433058057513 1 1 6226.8949849792 0.338455460988144] [false] [0 0 0.155891999602318] [false] [783.574175680699 410.499050792407 281.579290967308 535.842252259308 2257.21643165241 6118.9802777084] [694.654615131573 384.009444303501 173.272479189411 403.960308340992 1225.33543765654 7009.69965957512] [335.841094970703 742.560729980469 997.755981445312] [0 0 15.2718849182129 335.841094970703 742.560729980469 997.755981445312 1328.71337890625 2329.87109375] [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 [0.0228404831141233 0.0729715079069138 0.0798535421490669 0 0] [0.0820867592642526 0 0.0820867592642526 0;0.190219837935174 0.00924437386648995 0.199464211801664 1971.34423828125;0.190219837935174 0.00924437386648995 0.199464211801664 1971.34423828125] [0.0472592674195766 0.0941307097673416 0.102878607809544] [0.0333933383226395 0.0404528602957726 0.0496108308434486] 0.102878607809544

0.0798535421490669

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 [0.0105941230431199 0.0371844060719013 0.0505404435098171 0.0580258890986443 0.0640276670455933 0.0714578181505203] [0.0828860452922863 0 0.0828860452922863 0;0.213731013431013 0.0133104223901099 0.227041435821123 6813.2724609375;0.193516490797708 0.0156387234798433 0.209155214277551 11255.376953125;0.174118954911191 0.017563241159814 0.191682196071005 18937.951171875;0.157713165953355 0.0202575587052756 0.177970724658631 35437.62109375;0.157713165953355 0.0202575587052756 0.177970724658631 35437.62109375] [0.0122181950137019 0.0422147698700428 0.0609540492296219 0.0843231827020645 0.106685124337673 0.112606056034565] [0.00333046703599393 0.0122659346088767 0.0267976950854063 0.0475092865526676 0.0657835975289345 0.0708396807312965] 0.112606056034565

0.0714578181505203

------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./sub-season108_ses-3_acq-MPrageHiRes_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 47s APP: Rough bias correction: Initialize 9s Estimate background 8s Initial correction 19s Refine background 5s Final correction 14s Final scaling 10s 74s Correct center-of-mass 5s Affine registration 13s SPM preprocessing 1 (estimate 1 - TPM registration): 116s SPM preprocessing 1 (estimate 2): 109s SPM preprocessing 2 (write): Write Segmentation 24s Update Segmentation 26s Update Skull-Stripping 57s Update probability maps 12s 118s Global intensity correction: 22s SANLM denoising after intensity normalization (medium): 14s Fast Optimized Shooting registration 46s Local adaptive segmentation (LASstr=0.50): Prepare maps 6s Prepare partitions 3s Prepare segments (LASmod = 1.00) 19s Estimate local tissue thresholds (WM) 25s Estimate local tissue thresholds (GM) 34s Intensity transformation 0s SANLM denoising after LAS (medium) 32s 124s ROI segmentation (partitioning): Atlas -> subject space 12s Major structures 5s Ventricle detection 23s Blood vessel detection 13s WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 39s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 5s Final corrections 7s 105s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 42s AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.08,0.98 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 | 0.0829 0.0000 0.0829 | 32.0000 2 | 2.50 | 0.0799 0.0013 0.0812 | 29.4886 3 | 2.50 | 0.0791 0.0019 0.0811 | 26.9772 4 | 2.50 | 0.0787 0.0022 0.0809 | 24.6107 5 | 2.50 | 0.0784 0.0023 0.0807 | 22.6548 6 | 2.50 | 0.0781 0.0024 0.0805 | 20.6989 7 | 2.50 | 0.0779 0.0025 0.0803 | 18.9688 8 | 2.50 | 0.0776 0.0026 0.0801 | 17.4455 9 | 2.50 | 0.0773 0.0026 0.0799 | 15.9223 10 | 2.50 | 0.0770 0.0027 0.0797 | 14.6627 11 | 2.50 | 0.0767 0.0028 0.0794 | 13.4764 12 | 2.50 | 0.0763 0.0028 0.0792 | 12.3015 13 | 2.50 | 0.0760 0.0029 0.0790 | 11.3776 14 | 2.50 | 0.0757 0.0030 0.0787 | 10.4537 15 | 2.25 | 0.0742 0.0031 0.0773 | 9.5920 16 | 2.25 | 0.0712 0.0044 0.0757 | 8.8725 29 | 2.00 | 0.0722 0.0020 0.0742 | 3.3283 30 | 2.00 | 0.0664 0.0043 0.0707 | 3.1221 31 | 2.00 | 0.0645 0.0052 0.0697 | 2.9160 43 | 1.75 | 0.0635 0.0030 0.0665 | 1.5785 44 | 1.75 | 0.0594 0.0051 0.0645 | 1.5194 45 | 1.75 | 0.0580 0.0059 0.0639 | 1.4626 57 | 1.50 | 0.0565 0.0043 0.0607 | 1.0900 58 | 1.50 | 0.0535 0.0061 0.0597 | 1.0730 59 | 1.50 | 0.0526 0.0068 0.0593 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 223s Prepare output 13s 235s Jacobian determinant (RMS): 0.012 0.042 0.061 0.084 0.107 | 0.112606 Template Matching: 0.083 0.214 0.194 0.174 0.158 | 0.157713 Write result maps: 37s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 32s CSF distance: 16s PBT2x thickness: 47s 102s Create initial surface 80s Topology correction: 91s Surface refinement: 78s Reduction of surface collisions with optimization: 58s Spherical mapping with areal smoothing 85s Spherical registration 256s rh: Thickness estimation (0.50 mm ): WM distance: 42s CSF distance: 16s PBT2x thickness: 46s 110s Create initial surface 78s Topology correction: 91s Surface refinement: 72s Reduction of surface collisions with optimization: 59s Spherical mapping with areal smoothing 87s Spherical registration 269s Final surface processing results: Average thickness (FS): 2.4662 0.6091 mm Surface intensity / position RMSE: 0.0726 / 0.0763 Euler number / defect number / defect size: 22.0 / 15.0 / 0.62% Display thickness: /var/lib/condor/execute/dir_10175/ds/sub-season108/surf/lh.thickness.sub-season108_ses-3_acq-MPrageHiRes_T1w Display thickness: /var/lib/condor/execute/dir_10175/ds/sub-season108/surf/rh.thickness.sub-season108_ses-3_acq-MPrageHiRes_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_10175/ds/sub-season108/sub-season108_ses-3_acq-MPrageHiRes_T1w.nii Surface ROI estimation: 8s Surface and thickness estimation takes: 1618s ROI estimation in native space: ROI estimation of 'cobra' atlas 18s ROI estimation of 'neuromorphometrics' atlas 65s ROI estimation of 'lpba40' atlas 19s ROI estimation of 'hammers' atlas 46s ROI estimation of 'thalamus' atlas 3s ROI estimation of 'ibsr' atlas 16s ROI estimation of 'aal3' atlas 27s ROI estimation of 'mori' atlas 40s ROI estimation of 'anatomy3' atlas 58s ROI estimation of 'julichbrain' atlas 77s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 29s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 37s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 124s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 185s Write results 186s 747s Quality check: 7s Print 'Graphics' figure to: /var/lib/condor/execute/dir_10175/ds/sub-season108/report/catreport_sub-season108_ses-3_acq-MPrageHiRes_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 60 minute(s) and 51 second(s). Image Quality Rating (IQR): 84.92% (B) GM volume (GMV): 50.20% (653.77 / 1302.33 ml) GM thickness (GMT): 2.47 0.61 mm Segmentations are saved in /var/lib/condor/execute/dir_10175/ds/sub-season108/mri Reports are saved in /var/lib/condor/execute/dir_10175/ds/sub-season108/report Labels are saved in /var/lib/condor/execute/dir_10175/ds/sub-season108/label ------------------------------------------------------------------------