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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_105506/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 26 1.02557964681393 14.5 0.0698769390583038 0.069916769862175 [1 1 1] [1 1 1] 1 183.627883911133 [9.27099990844727 57.4869995117188 219.768005371094 357.1669921875] [0.0259570460766554 0.160952717065811 0.615308821201324 1] T1 [9.46982323762744 37.6309684910175 40.3257887412007 26.8136901887559] [0.0272202715277672 0.108167290687561 0.115913346409798 0.0770738646388054] 126.560264587402 0.35434478521347 0.395949959754944 0.168349087238312 0.336252301931381 [2 2 2] 2 2.91811203956604 10.5 [8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 2.76816153526306 2.74776172637939 1.29378056526184 2.22448979591837 1.25639491170348 1.725 1.39753878116608 1.39833545684814 2.7114082822873 2.54370564066376 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 20231030-235811 1639 1639 26 1.02557964681393 14.5 0.0698769390583038 0.069916769862175 26 1.02557964681393 [229.888168627451 749.764890196078 494.648992156863 0 0] 0.474376470588235 0.000321763420374258 2004.31359259516 1474.30205098039 [0.155930169448369 0.508555821174836 0.335514009376795 0 0] [2.70163868320587 0.642562566164893] [2.70098114013672 0.781199979531655 1] [2.10496405653174 0.262799748702672 0.314953072320262;2.74543845670742 0.186619329386097 0.417823406129454;3.43270486812188 0.279386887676561 0.267223521550284] [0.975063895391189 0.375822118781735 0.599717381064531;4.33147968329046 0.283381676680565 0.400282618935469] 1.13040479776123 [0.650326319115828 6.98340196075496 3.87561080058898 0.5 0.5] 1.03217634203743 8.6216029909635 5.71718337215034 [0 1 0 11534.336 0.379842947061393] [false] [0.00146664632484317 0.00117862736806273 0.0420577377080917] [false] [876.367635294118 444.981929411765 350.91888627451 681.258003921569 919.153356862745 8673.05199215686] [793.863196078431 419.101235294118 217.390149019608 545.569588235294 766.373054901961 8792.06899215686] [82.9139022827148 241.454406738281 353.055999755859] [-4.52798986434937 -4.527991771698 4.15588998794556 82.9139022827148 241.454406738281 353.055999755859 488.127044677734 638.558227539062] [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 [0.0204634722322226 0.071354903280735 0.0781007036566734 0 0] [0.0805583158556391 0 0.0805583158556391 0;0.189239868310605 0.00947422998435214 0.198714098294958 2020.36059570312;0.189239868310605 0.00947422998435214 0.198714098294958 2020.36059570312] [0.0442573837935925 0.0920775905251503 0.101654000580311] [0.0315279513597488 0.0425151772797108 0.0522022545337677] 0.101654000580311

0.0781007036566734

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 [0.00974631775170565 0.0353482253849506 0.0487861521542072 0.0559348203241825 0.0620305463671684 0.0689041167497635] [0.0812509720577129 0 0.0812509720577129 0;0.212006105006105 0.0126342338217338 0.224640338827839 6467.1484375;0.191176014676704 0.015433783105256 0.20660979778196 11107.87890625;0.171930803985451 0.0173235238447488 0.1892543278302 18679.470703125;0.15581164150403 0.0200338465314033 0.175845488035434 35046.26953125;0.15581164150403 0.0200338465314033 0.175845488035434 35046.26953125] [0.0112649518996477 0.0399469994008541 0.0581058077514172 0.0793090090155602 0.100204683840275 0.106905519962311] [0.00321069615893066 0.01220743637532 0.0261695720255375 0.044737558811903 0.0616705827414989 0.0671265423297882] 0.106905519962311

0.0689041167497635

------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0025954/ses-2/sub-0025954_ses-2_run-1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 41s APP: Rough bias correction: Initialize 5s Estimate background 4s Initial correction 4s Refine background 3s Final correction 4s Final scaling 4s 30s Correct center-of-mass 3s Affine registration 7s SPM preprocessing 1 (estimate 1 - TPM registration): 62s SPM preprocessing 1 (estimate 2): 51s SPM preprocessing 2 (write): Write Segmentation 14s Update Segmentation 15s Update Skull-Stripping 34s Update probability maps 8s 71s Global intensity correction: 12s SANLM denoising after intensity normalization (medium): 21s Fast Optimized Shooting registration 26s Local adaptive segmentation (LASstr=0.50): Prepare maps 3s Prepare partitions 2s Prepare segments (LASmod = 1.10) 11s Estimate local tissue thresholds (WM) 14s Estimate local tissue thresholds (GM) 21s Intensity transformation 0s SANLM denoising after LAS (medium) 29s 84s ROI segmentation (partitioning): Atlas -> subject space 6s Major structures 3s Ventricle detection 9s Blood vessel detection 7s WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 20s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 3s Final corrections 4s 53s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 27s AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.07,0.98 0.05] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 3s Level 1 cleanup (brain masking) 2s Level 2 cleanup (CSF correction) 1s Level 3 cleanup (CSF/WM PVE) 2s 9s 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 | 0.0813 0.0000 0.0813 | 32.0000 2 | 2.50 | 0.0788 0.0011 0.0799 | 29.4886 3 | 2.50 | 0.0781 0.0017 0.0798 | 26.9772 4 | 2.50 | 0.0778 0.0019 0.0796 | 24.6107 5 | 2.50 | 0.0775 0.0020 0.0795 | 22.6548 6 | 2.50 | 0.0772 0.0021 0.0793 | 20.6989 7 | 2.50 | 0.0770 0.0022 0.0792 | 18.9688 8 | 2.50 | 0.0767 0.0023 0.0790 | 17.4455 9 | 2.50 | 0.0764 0.0024 0.0788 | 15.9223 10 | 2.50 | 0.0761 0.0025 0.0786 | 14.6627 11 | 2.50 | 0.0758 0.0025 0.0784 | 13.4764 12 | 2.50 | 0.0756 0.0026 0.0782 | 12.3015 13 | 2.50 | 0.0752 0.0027 0.0779 | 11.3776 14 | 2.50 | 0.0750 0.0028 0.0777 | 10.4537 15 | 2.25 | 0.0735 0.0028 0.0763 | 9.5920 16 | 2.25 | 0.0707 0.0042 0.0749 | 8.8725 29 | 2.00 | 0.0715 0.0019 0.0734 | 3.3283 30 | 2.00 | 0.0657 0.0042 0.0699 | 3.1221 31 | 2.00 | 0.0637 0.0051 0.0689 | 2.9160 43 | 1.75 | 0.0626 0.0030 0.0656 | 1.5785 44 | 1.75 | 0.0586 0.0050 0.0637 | 1.5194 45 | 1.75 | 0.0573 0.0058 0.0631 | 1.4626 57 | 1.50 | 0.0558 0.0042 0.0600 | 1.0900 58 | 1.50 | 0.0529 0.0061 0.0589 | 1.0730 59 | 1.50 | 0.0519 0.0067 0.0586 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 153s Prepare output 8s 161s Jacobian determinant (RMS): 0.011 0.040 0.058 0.079 0.100 | 0.106906 Template Matching: 0.081 0.212 0.191 0.172 0.156 | 0.155812 Write result maps: 43s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 22s CSF distance: 12s PBT2x thickness: 35s 74s Create initial surface 66s Topology correction: 73s Surface refinement: 58s Reduction of surface collisions with optimization: 56s Spherical mapping with areal smoothing 64s Spherical registration 209s rh: Thickness estimation (0.50 mm ): WM distance: 20s CSF distance: 12s PBT2x thickness: 35s 72s Create initial surface 65s Topology correction: 73s Surface refinement: 54s Reduction of surface collisions with optimization: 55s Spherical mapping with areal smoothing 90s Spherical registration 248s Final surface processing results: Average thickness (FS): 2.7016 0.6425 mm Surface intensity / position RMSE: 0.0699 / 0.0699 Euler number / defect number / defect size: 26.0 / 14.5 / 1.03% Display thickness: /var/lib/condor/execute/dir_105506/ds/BNU_2/sub-0025954/ses-2/surf/lh.thickness.sub-0025954_ses-2_run-1_T1w Display thickness: /var/lib/condor/execute/dir_105506/ds/BNU_2/sub-0025954/ses-2/surf/rh.thickness.sub-0025954_ses-2_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_105506/ds/BNU_2/sub-0025954/ses-2/sub-0025954_ses-2_run-1_T1w.nii Surface ROI estimation: 9s Surface and thickness estimation takes: 1344s ROI estimation in native space: ROI estimation of 'cobra' atlas 21s ROI estimation of 'neuromorphometrics' atlas 79s ROI estimation of 'lpba40' atlas 23s ROI estimation of 'hammers' atlas 52s ROI estimation of 'thalamus' atlas 4s ROI estimation of 'ibsr' atlas 19s ROI estimation of 'aal3' atlas 32s ROI estimation of 'mori' atlas 43s ROI estimation of 'anatomy3' atlas 59s ROI estimation of 'julichbrain' atlas 62s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 28s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 41s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 66s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 92s ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s Write results 9s 632s Quality check: 9s Print 'Graphics' figure to: /var/lib/condor/execute/dir_105506/ds/BNU_2/sub-0025954/ses-2/report/catreport_sub-0025954_ses-2_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 45 minute(s) and 45 second(s). Image Quality Rating (IQR): 79.56% (C+) GM volume (GMV): 50.86% (749.76 / 1474.30 ml) GM thickness (GMT): 2.70 0.64 mm Segmentations are saved in /var/lib/condor/execute/dir_105506/ds/BNU_2/sub-0025954/ses-2/mri Reports are saved in /var/lib/condor/execute/dir_105506/ds/BNU_2/sub-0025954/ses-2/report Labels are saved in /var/lib/condor/execute/dir_105506/ds/BNU_2/sub-0025954/ses-2/label ------------------------------------------------------------------------