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/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_2040 0 1 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] /var/lib/condor/execute/dir_92055/ds/code/Tian_Subcortex_S2_7T.nii 1 gm wm csf [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 12 0.46080700776894 7 0.0615805462002754 0.0621420443058014 [1 1 1] [1 1 1] 1 189.552017211914 [7.03000020980835 70.7419967651367 208.667999267578 340.230010986328] [0.0206624921411276 0.207924038171768 0.613314509391785 1] T1 [4.79958836139412 36.6568504850816 38.1526417227139 24.9578509427771] [0.0144045259803534 0.110014550387859 0.114503718912601 0.0749035105109215] 120.565452575684 0.354364544153214 0.376297175884247 0.144304305315018 0.31567907333374 [2 2 2] 2 2.81784272193909 10.5 [8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 2.76786518096924 2.40258836746216 1.242755651474 1.51020408163265 1.11520175194224 1.35 1.23161089420319 1.24284088611603 2.5486798347298 2.26106976492313 voxel dimensions RMS error of voxel size normalized gradient slope of the white matter boundary 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 2040 /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 20231031-004020 1639 1639 12 0.46080700776894 7 0.0615805462002754 0.0621420443058014 12 0.46080700776894 [283.347137254902 716.854482352941 527.754866666667 0 0] 0.408725490196078 0.000267498121751255 2091.24260648347 1527.95648627451 [0.185441889085313 0.469158964140915 0.345399146773772 0 0] [2.50657260248076 0.596659286268077] [2.50624084472656 0.725328901059574 1] [1.92893864220907 0.23802500359064 0.292780598854662;2.5281432821683 0.167959393441888 0.440441857310521;3.14897607280478 0.263125090064276 0.266777543834817] [0.912351778884249 0.330929822614937 0.521245964575517;4.11034447325151 0.373146018487534 0.478754035424483] 1.38027214186902 [1.18035001949197 6.27584346517448 4.05314559579332 0.5 0.5] 1.02674981217513 8.62338622035984 5.15133302326396 [0 1 0 11141.12 0.356248493418536] [false] [0.00146424630656838 0.00121899414807558 0.0359685458242893] [false] [876.527094117647 463.083180392157 496.449192156863 502.516960784314 959.761831372549 8395.33199215686] [763.551650980392 435.700384313726 284.169325490196 442.498901960784 836.595466666667 8379.45983137255] [82.9602966308594 227.918197631836 337.839904785156] [-4.65846014022827 -4.65846109390259 3.50691437721252 82.9602966308594 227.918197631836 337.839904785156 465.279724121094 825.258178710938] [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 [0.0195431839674711 0.0733532607555389 0.0807426050305367 0 0] [0.0843363956910889 0 0.0843363956910889 0;0.196437968497946 0.0107261524910257 0.207164120988972 2287.33056640625;0.196437968497946 0.0107261524910257 0.207164120988972 2287.33056640625] [0.047125767916441 0.0963740646839142 0.107093974947929] [0.0345513634383678 0.0458367429673672 0.0559484921395779] 0.107093974947929

0.0807426050305367

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 [0.00900911912322044 0.0333918556571007 0.0478941015899181 0.0565233044326305 0.0631170123815536 0.0699590519070625] [0.0844688438948323 0 0.0844688438948323 0;0.219775671550672 0.0138870917277167 0.233662763278388 7108.455078125;0.197787448312658 0.0170591864132806 0.214846634725939 12277.701171875;0.177499551945149 0.0189181053400719 0.196417657285221 20398.86328125;0.160252676275171 0.0216290970325886 0.18188177330776 37836.92578125;0.160252676275171 0.0216290970325886 0.18188177330776 37836.92578125] [0.0105997174978256 0.0388803742825985 0.0584290139377117 0.0813563317060471 0.102048590779305 0.108638189733028] [0.00328695704229176 0.0128677058964968 0.0269839391112328 0.0448479913175106 0.0604448243975639 0.0657031163573265] 0.108638189733028

0.0699590519070625

------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0025627/ses-1/sub-0025627_ses-1_run-1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 65s APP: Rough bias correction: Initialize 7s Estimate background 7s Initial correction 8s Refine background 3s Final correction 6s Final scaling 6s 44s Correct center-of-mass 5s Affine registration 10s SPM preprocessing 1 (estimate 1 - TPM registration): 95s SPM preprocessing 1 (estimate 2): 106s SPM preprocessing 2 (write): Write Segmentation 21s Update Segmentation 23s Update Skull-Stripping 49s Update probability maps 10s 105s Global intensity correction: 19s SANLM denoising after intensity normalization (medium): 34s Fast Optimized Shooting registration 41s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 3s Prepare segments (LASmod = 1.05) 17s Estimate local tissue thresholds (WM) 24s Estimate local tissue thresholds (GM) 37s Intensity transformation 0s SANLM denoising after LAS (medium) 51s 141s ROI segmentation (partitioning): Atlas -> subject space 9s Major structures 4s Ventricle detection 16s Blood vessel detection 13s WMH detection (WMHCstr=0.50 > WMHCstr'=0.07) 30s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 4s Final corrections 5s 83s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 39s AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.04] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 5s 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 | 0.0845 0.0000 0.0845 | 32.0000 2 | 2.50 | 0.0818 0.0012 0.0830 | 29.4886 3 | 2.50 | 0.0810 0.0018 0.0828 | 26.9772 4 | 2.50 | 0.0806 0.0021 0.0826 | 24.6107 5 | 2.50 | 0.0802 0.0022 0.0824 | 22.6548 6 | 2.50 | 0.0799 0.0023 0.0822 | 20.6989 7 | 2.50 | 0.0796 0.0024 0.0821 | 18.9688 8 | 2.50 | 0.0793 0.0025 0.0819 | 17.4455 9 | 2.50 | 0.0790 0.0026 0.0816 | 15.9223 10 | 2.50 | 0.0787 0.0027 0.0814 | 14.6627 11 | 2.50 | 0.0784 0.0028 0.0812 | 13.4764 12 | 2.50 | 0.0780 0.0029 0.0809 | 12.3015 13 | 2.50 | 0.0777 0.0030 0.0807 | 11.3776 14 | 2.50 | 0.0774 0.0030 0.0804 | 10.4537 15 | 2.25 | 0.0762 0.0031 0.0794 | 9.5920 16 | 2.25 | 0.0733 0.0046 0.0779 | 8.8725 29 | 2.00 | 0.0744 0.0021 0.0765 | 3.3283 30 | 2.00 | 0.0680 0.0047 0.0727 | 3.1221 31 | 2.00 | 0.0659 0.0057 0.0716 | 2.9160 43 | 1.75 | 0.0649 0.0033 0.0682 | 1.5785 44 | 1.75 | 0.0606 0.0055 0.0661 | 1.5194 45 | 1.75 | 0.0592 0.0063 0.0655 | 1.4626 57 | 1.50 | 0.0575 0.0046 0.0621 | 1.0900 58 | 1.50 | 0.0544 0.0066 0.0610 | 1.0730 59 | 1.50 | 0.0534 0.0072 0.0606 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 215s Prepare output 14s 229s Jacobian determinant (RMS): 0.011 0.039 0.058 0.081 0.102 | 0.108638 Template Matching: 0.084 0.220 0.198 0.177 0.160 | 0.160253 Write result maps: 43s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 53s CSF distance: 20s PBT2x thickness: 61s 142s Create initial surface 107s Topology correction: 122s Surface refinement: 108s Reduction of surface collisions with optimization: 94s Spherical mapping with areal smoothing 123s Spherical registration 343s rh: Thickness estimation (0.50 mm ): WM distance: 57s CSF distance: 21s PBT2x thickness: 61s 146s Create initial surface 105s Topology correction: 124s Surface refinement: 127s Reduction of surface collisions with optimization: 88s Spherical mapping with areal smoothing 121s Spherical registration 364s Final surface processing results: Average thickness (FS): 2.5065 0.5966 mm Surface intensity / position RMSE: 0.0616 / 0.0621 Euler number / defect number / defect size: 12.0 / 7.0 / 0.46% Display thickness: /var/lib/condor/execute/dir_92055/ds/JHNU/sub-0025627/ses-1/surf/lh.thickness.sub-0025627_ses-1_run-1_T1w Display thickness: /var/lib/condor/execute/dir_92055/ds/JHNU/sub-0025627/ses-1/surf/rh.thickness.sub-0025627_ses-1_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_92055/ds/JHNU/sub-0025627/ses-1/sub-0025627_ses-1_run-1_T1w.nii Surface ROI estimation: 11s Surface and thickness estimation takes: 2238s ROI estimation in native space: ROI estimation of 'cobra' atlas 11s ROI estimation of 'neuromorphometrics' atlas 36s ROI estimation of 'lpba40' atlas 11s ROI estimation of 'hammers' atlas 25s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 9s ROI estimation of 'aal3' atlas 15s ROI estimation of 'mori' atlas 22s ROI estimation of 'anatomy3' atlas 31s ROI estimation of 'julichbrain' atlas 44s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 18s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 31s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 70s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 110s ROI estimation of 'Tian_Subcortex_S2_7T' atlas 10s Write results 12s 445s Quality check: 16s Print 'Graphics' figure to: /var/lib/condor/execute/dir_92055/ds/JHNU/sub-0025627/ses-1/report/catreport_sub-0025627_ses-1_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 64 minute(s) and 46 second(s). Image Quality Rating (IQR): 82.39% (B-) GM volume (GMV): 46.92% (716.85 / 1527.96 ml) GM thickness (GMT): 2.51 0.60 mm Segmentations are saved in /var/lib/condor/execute/dir_92055/ds/JHNU/sub-0025627/ses-1/mri Reports are saved in /var/lib/condor/execute/dir_92055/ds/JHNU/sub-0025627/ses-1/report Labels are saved in /var/lib/condor/execute/dir_92055/ds/JHNU/sub-0025627/ses-1/label ------------------------------------------------------------------------