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../derivatives/CAT12.8.1_1980 0 32 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 12 0.309911180346902 11 0.0623151548206806 0.0604743659496307 [0.999999975742132 1.00000000345383 1.00000000984566] [0.999999915525688 0.999999997985656 1.00000000664201] 0.999999996347208 0 [0 162203.09375 349571.4375 495552.625] [0 0.327317595481873 0.705417394638062 1] T1 [70381.8199005452 64199.5119333336 46900.5695818301 30097.3834654181] [0.14202693104744 0.129551351070404 0.0946429669857025 0.0607349909842014] 145981.1875 0.294582605361938 0.104286216199398 0.27102991938591 [1.99999995148426 2.00000000690767 2.00000001969131] 1.99999999269442 0.5 [1.89584374427795 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 3.66459441184998 1.82811117172241 1.13201868534088 1.51020408163265 1.07747779508673 1.55 1.24630308151245 1.20948731899261 1.9273049211154 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 20220711-172144 1639 1639 12 0.309911180346902 11 0.0623151548206806 0.0604743659496307 12 0.309911180346902 [317.682033457681 810.359343138653 589.374607842369 0 0] 1.38798812446791 0.000808184002620389 2198.00501935951 1717.4159844387 [0.184976753643939 0.471848026617442 0.343175219738619 0 0] [2.70217960672224 0.640050444202705] [2.71876907348633 0.74896850094403 1] [1.99006382692477 0.265848549319282 0.24654142674254;2.6798600762144 0.190385233861275 0.430769317534529;3.35502511963182 0.266073441897984 0.322689255722931] [0.937982048344551 0.332933081644951 0.54982004167456;4.24999809270153 0.315084714592366 0.45017995832544] 3.05927074905212 [1.17199629389258 6.32413840907762 4.01320437748957 0.5 0.5] 1.08081840026204 8.6239004092456 5.18847064316289 [0.559684085845947 2883 968 4617.04694940466 0.356386512828842] [false] [0 0 0.381329894065857] [false] [981.911113754543 527.679722572421 494.421184051533 665.233135118652 2412.15136426052 6075.6512599776] [859.099025521462 494.099380155659 319.672076436038 798.481391145891 1893.0853194317 6121.35292691671] [190359.796875 373286.1875 485401.40625] [0 0 4364.8662109375 190359.796875 373286.1875 485401.40625 632922.25 1102557.25] [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 [0.0227934289723635 0.0852574110031128 0.0950071662664413 0 0] [0.0888497549898866 0 0.0888497549898866 0;0.196973070233953 0.0125883601579059 0.209561430391859 2684.44262695312;0.196973070233953 0.0125883601579059 0.209561430391859 2684.44262695312] [0.0490117818117142 0.111241571605206 0.123824842274189] [0.0347417667508125 0.0505611188709736 0.0621194876730442] 0.123824842274189

0.0950071662664413

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 [0.0109382513910532 0.0451695770025253 0.060969490557909 0.0695168599486351 0.0755893364548683 0.0853046625852585] [0.0887717415493519 0 0.0887717415493519 0;0.220915369352869 0.0194397206959707 0.24035509004884 9950.70703125;0.199133776774599 0.0200781185955285 0.219211895370127 14450.462890625;0.176953626380913 0.0211280196027765 0.19808164598369 22781.751953125;0.15962221104031 0.0235954423221042 0.183217653362415 41276.7578125;0.15962221104031 0.0235954423221042 0.183217653362415 41276.7578125] [0.0125603880733252 0.0478971861302853 0.0726056918501854 0.0984311550855637 0.121265277266502 0.127836748957634] [0.00354343932121992 0.0143775548785925 0.0309279374778271 0.0510538071393967 0.0678979083895683 0.0728709697723389] 0.127836748957634

0.0853046625852585

------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./execute/dir_7213/ds/sub-sc036/sub-sc036_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 30s APP: Rough bias correction: Initialize 6s Estimate background 6s Initial correction 6s Refine background 3s Final correction 6s Final scaling 6s 38s Correct center-of-mass 2s Affine registration 9s SPM preprocessing 1 (estimate 1 - TPM registration): 77s SPM preprocessing 1 (estimate 2): 59s SPM preprocessing 2 (write): Write Segmentation 15s Update Segmentation 19s Update Skull-Stripping 39s Update probability maps 8s 81s Global intensity correction: 14s SANLM denoising after intensity normalization (medium): 13s Fast Optimized Shooting registration 29s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 2s Prepare segments (LASmod = 1.05) 16s Estimate local tissue thresholds (WM) 18s Estimate local tissue thresholds (GM) 24s Intensity transformation 0s SANLM denoising after LAS (medium) 18s 85s ROI segmentation (partitioning): Atlas -> subject space 7s Major structures 4s Ventricle detection 20s Blood vessel detection 11s WMH detection (WMHCstr=0.50 > WMHCstr'=0.09) 30s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 4s Final corrections 4s 82s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 37s AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.08,0.98 0.04] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 5s Level 1 cleanup (brain masking) 3s Level 2 cleanup (CSF correction) 2s Level 3 cleanup (CSF/WM PVE) 3s 12s 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 | 0.0888 0.0000 0.0888 | 32.0000 2 | 2.50 | 0.0844 0.0016 0.0860 | 29.4886 3 | 2.50 | 0.0831 0.0024 0.0855 | 26.9772 4 | 2.50 | 0.0825 0.0027 0.0852 | 24.6107 5 | 2.50 | 0.0820 0.0029 0.0850 | 22.6548 6 | 2.50 | 0.0816 0.0030 0.0847 | 20.6989 7 | 2.50 | 0.0812 0.0032 0.0844 | 18.9688 8 | 2.50 | 0.0808 0.0033 0.0841 | 17.4455 9 | 2.50 | 0.0804 0.0034 0.0838 | 15.9223 10 | 2.50 | 0.0800 0.0035 0.0835 | 14.6627 11 | 2.50 | 0.0795 0.0036 0.0831 | 13.4764 12 | 2.50 | 0.0791 0.0037 0.0828 | 12.3015 13 | 2.50 | 0.0786 0.0038 0.0824 | 11.3776 14 | 2.50 | 0.0782 0.0039 0.0821 | 10.4537 15 | 2.25 | 0.0787 0.0040 0.0827 | 9.5920 16 | 2.25 | 0.0751 0.0058 0.0810 | 8.8725 17 | 2.25 | 0.0736 0.0065 0.0801 | 8.1530 29 | 2.00 | 0.0752 0.0030 0.0781 | 3.3283 30 | 2.00 | 0.0687 0.0056 0.0744 | 3.1221 31 | 2.00 | 0.0664 0.0067 0.0731 | 2.9160 43 | 1.75 | 0.0650 0.0039 0.0690 | 1.5785 44 | 1.75 | 0.0606 0.0062 0.0668 | 1.5194 45 | 1.75 | 0.0590 0.0070 0.0660 | 1.4626 57 | 1.50 | 0.0574 0.0052 0.0626 | 1.0900 58 | 1.50 | 0.0542 0.0072 0.0615 | 1.0730 59 | 1.50 | 0.0532 0.0079 0.0611 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 161s Prepare output 10s 171s Jacobian determinant (RMS): 0.013 0.048 0.073 0.098 0.121 | 0.127837 Template Matching: 0.089 0.221 0.199 0.177 0.160 | 0.159622 Write result maps: 21s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 44s CSF distance: 17s PBT2x thickness: 51s 119s Create initial surface 100s Topology correction: 104s Surface refinement: 97s Reduction of surface collisions with optimization: 83s Spherical mapping with areal smoothing 93s Spherical registration 291s rh: Thickness estimation (0.50 mm ): WM distance: 39s CSF distance: 18s PBT2x thickness: 52s 116s Create initial surface 97s Topology correction: 104s Surface refinement: 97s Reduction of surface collisions with optimization: 83s Spherical mapping with areal smoothing 100s Spherical registration 301s Final surface processing results: Average thickness (FS): 2.7022 0.6400 mm Surface intensity / position RMSE: 0.0623 / 0.0605 Euler number / defect number / defect size: 12.0 / 11.0 / 0.31% Display thickness: /var/lib/condor/execute/dir_7213/ds/sub-sc036/surf/lh.thickness.sub-sc036_T1w Display thickness: /var/lib/condor/execute/dir_7213/ds/sub-sc036/surf/rh.thickness.sub-sc036_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_7213/ds/sub-sc036/sub-sc036_T1w.nii Surface ROI estimation: 12s Surface and thickness estimation takes: 1886s ROI estimation in native space: ROI estimation of 'cobra' atlas 8s ROI estimation of 'neuromorphometrics' atlas 27s ROI estimation of 'lpba40' atlas 8s ROI estimation of 'hammers' atlas 19s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 7s ROI estimation of 'aal3' atlas 11s ROI estimation of 'mori' atlas 16s ROI estimation of 'anatomy3' atlas 23s ROI estimation of 'julichbrain' atlas 30s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 48s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 72s Write results 73s 306s Quality check: 6s Print 'Graphics' figure to: /var/lib/condor/execute/dir_7213/ds/sub-sc036/report/catreport_sub-sc036_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 50 minute(s) and 58 second(s). Image Quality Rating (IQR): 85.73% (B) GM volume (GMV): 47.18% (810.36 / 1717.42 ml) GM thickness (GMT): 2.70 0.64 mm Segmentations are saved in /var/lib/condor/execute/dir_7213/ds/sub-sc036/mri Reports are saved in /var/lib/condor/execute/dir_7213/ds/sub-sc036/report Labels are saved in /var/lib/condor/execute/dir_7213/ds/sub-sc036/label ------------------------------------------------------------------------