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[0.11308456422961 0.00981108459659154 -0.0246876124380635] [1.04553174241308 1.11369171291161 1.13997731516667] [0.0102380005828189 0.00570614827815103 0.028080935496145] [3.32140872035315 -25.6653975390483 4.62794593841766] [0.11308456422961 0.00981108459659154 -0.0246876124380635] [1.04553174241308 1.11369171291161 1.13997731516667] [0.0102380005828189 0.00570614827815103 0.028080935496145] /var/lib/condor/execute/dir_16954/ds/sub-22 sub-22_T1w /var/lib/condor/execute/dir_16954/ds/sub-22/sub-22_T1w.nii /var/lib/condor/execute/dir_16954/ds/sub-22/sub-22_T1w.nii /var/lib/condor/execute/dir_16954/ds/sub-22/mri/msub-22_T1w.nii /var/lib/condor/execute/dir_16954/ds/sub-22/mri/p0sub-22_T1w.nii ..16954/ds/sub-22/sub-22_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 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 0.609555807674862 10 0.064988948404789 0.0652772933244705 [1 1 1] [1 1 1] 1 0 [19.5459995269775 265.226470947266 896.242492675781 1468.96496582031] [0.0133059667423368 0.180553302168846 0.610118329524994 1] T1 [13.5408330172582 160.264699349067 165.554039648845 97.8321767961978] [0.0093422494828701 0.110571689903736 0.114220969378948 0.0674975141882896] 520.462280273438 0.354305446147919 0.135038554668427 0.250374555587769 [2 2 2] 2 0.5 [8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 2.76875162124634 2.26957440376282 1.0807900428772 1.51020408163265 1.15238895191872 1.5 1.29977893829346 1.30554580688477 2.16348342586422 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 20220712-165525 1639 1639 12 0.609555807674862 10 0.064988948404789 0.0652772933244705 12 0.609555807674862 [249.602596078431 670.138901960784 498.148231372549 0 0] 0.629356862745098 0.000443868694222221 1961.10246598355 1417.88972941176 [0.176038087377911 0.472631184259161 0.351330728362927 0 0] [2.51957199199807 0.582948093935809] [2.50285172462463 0.709999767306352 1] [1.96925256354051 0.230054582311931 0.297443905646421;2.52914960207214 0.162080389345337 0.432127254680061;3.13977699490728 0.254137287306701 0.270428839673518] [0.945471374349225 0.344355680282768 0.507193572496263;4.09572042316057 0.37635855081031 0.492806427503737] 1.00762119887917 [1.01145990262054 6.33820374028666 4.15967543755257 0.5 0.5] 1.04438686942222 8.61946474620011 5.2051327598061 [0.233093348416415 1 1 8845.759 0.47140830935289] [false] [0.00812125485390425 0 0.0940190628170967] [false] [801.102298039216 448.906250980392 435.36708627451 504.629074509804 2053.637 7827.51664313725] [703.806619607843 425.452466666667 250.49028627451 1147.72405098039 1870.71477647059 7136.26214117647] [329.026000976562 960.5947265625 1479.68298339844] [0 0 21.7435131072998 329.026000976562 960.5947265625 1479.68298339844 2055.01147460938 4950.72802734375] [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 [0.0206198506057262 0.0670655742287636 0.0731557980179787 0 0] [0.082372902774391 0 0.082372902774391 0;0.196686615319956 0.00925571034077694 0.205942325660733 1973.76171875;0.196686615319956 0.00925571034077694 0.205942325660733 1973.76171875] [0.0468659251928329 0.0870349928736687 0.0963498428463936] [0.0336753316223621 0.0412830673158169 0.050862979143858] 0.0963498428463936

0.0731557980179787

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 [0.00934114400297403 0.0324550792574883 0.0442962795495987 0.0519505441188812 0.057880911976099 0.0640526190400124] [0.0831818225037897 0 0.0831818225037897 0;0.219559462759463 0.0124080156822344 0.231967478441697 6351.35302734375;0.200179724667645 0.0157079623298972 0.215887686997542 11305.208984375;0.179711612654321 0.0181986472771944 0.197910259931515 19623.091796875;0.163288763045537 0.0210740235104064 0.184362786555944 36865.90625;0.163288763045537 0.0210740235104064 0.184362786555944 36865.90625] [0.0109646338969469 0.0377531461417675 0.0545823089778423 0.0755434110760689 0.0960149094462395 0.102235428988934] [0.00321323424577713 0.0120643964037299 0.0263945534825325 0.0448550134897232 0.0613324567675591 0.0667763203382492] 0.102235428988934

0.0640526190400124

------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./condor/execute/dir_16954/ds/sub-22/sub-22_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 29s APP: Rough bias correction: Initialize 6s Estimate background 6s Initial correction 5s Refine background 3s Final correction 4s Final scaling 5s 36s Correct center-of-mass 5s Affine registration 9s SPM preprocessing 1 (estimate 1 - TPM registration): 66s SPM preprocessing 1 (estimate 2): 56s SPM preprocessing 2 (write): Write Segmentation 15s Update Segmentation 17s Update Skull-Stripping 40s Update probability maps 8s 80s Global intensity correction: 15s SANLM denoising after intensity normalization (medium): 8s Fast Optimized Shooting registration 30s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 2s Prepare segments (LASmod = 1.09) 13s Estimate local tissue thresholds (WM) 16s Estimate local tissue thresholds (GM) 22s Intensity transformation 0s SANLM denoising after LAS (medium) 26s 86s ROI segmentation (partitioning): Atlas -> subject space 7s Major structures 3s Ventricle detection 12s Blood vessel detection 8s WMH detection (WMHCstr=0.50 > WMHCstr'=0.03) 23s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 3s Final corrections 4s 62s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 30s 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) 4s Level 1 cleanup (brain masking) 2s Level 2 cleanup (CSF correction) 1s Level 3 cleanup (CSF/WM PVE) 2s 10s 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 | 0.0832 0.0000 0.0832 | 32.0000 2 | 2.50 | 0.0807 0.0011 0.0818 | 29.4886 3 | 2.50 | 0.0800 0.0017 0.0817 | 26.9772 4 | 2.50 | 0.0796 0.0019 0.0815 | 24.6107 5 | 2.50 | 0.0793 0.0020 0.0814 | 22.6548 6 | 2.50 | 0.0791 0.0021 0.0812 | 20.6989 7 | 2.50 | 0.0788 0.0022 0.0810 | 18.9688 8 | 2.50 | 0.0785 0.0023 0.0808 | 17.4455 9 | 2.50 | 0.0783 0.0024 0.0806 | 15.9223 10 | 2.50 | 0.0780 0.0025 0.0804 | 14.6627 11 | 2.50 | 0.0777 0.0025 0.0802 | 13.4764 12 | 2.50 | 0.0774 0.0026 0.0800 | 12.3015 13 | 2.50 | 0.0771 0.0027 0.0797 | 11.3776 14 | 2.50 | 0.0768 0.0027 0.0795 | 10.4537 15 | 2.25 | 0.0760 0.0028 0.0788 | 9.5920 16 | 2.25 | 0.0732 0.0041 0.0773 | 8.8725 29 | 2.00 | 0.0748 0.0019 0.0766 | 3.3283 30 | 2.00 | 0.0688 0.0043 0.0731 | 3.1221 31 | 2.00 | 0.0667 0.0052 0.0720 | 2.9160 43 | 1.75 | 0.0657 0.0030 0.0687 | 1.5785 44 | 1.75 | 0.0613 0.0053 0.0666 | 1.5194 45 | 1.75 | 0.0599 0.0061 0.0660 | 1.4626 57 | 1.50 | 0.0585 0.0044 0.0629 | 1.0900 58 | 1.50 | 0.0554 0.0064 0.0618 | 1.0730 59 | 1.50 | 0.0544 0.0070 0.0615 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 144s Prepare output 9s 153s Jacobian determinant (RMS): 0.011 0.038 0.055 0.076 0.096 | 0.102235 Template Matching: 0.083 0.220 0.200 0.180 0.163 | 0.163289 Write result maps: 22s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 32s CSF distance: 15s PBT2x thickness: 42s 95s Create initial surface 82s Topology correction: 95s Surface refinement: 81s Reduction of surface collisions with optimization: 70s Spherical mapping with areal smoothing 80s Spherical registration 301s rh: Thickness estimation (0.50 mm ): WM distance: 43s CSF distance: 15s PBT2x thickness: 42s 106s Create initial surface 81s Topology correction: 91s Surface refinement: 68s Reduction of surface collisions with optimization: 64s Spherical mapping with areal smoothing 76s Spherical registration 263s Final surface processing results: Average thickness (FS): 2.5196 0.5829 mm Surface intensity / position RMSE: 0.0650 / 0.0653 Euler number / defect number / defect size: 12.0 / 10.0 / 0.61% Display thickness: /var/lib/condor/execute/dir_16954/ds/sub-22/surf/lh.thickness.sub-22_T1w Display thickness: /var/lib/condor/execute/dir_16954/ds/sub-22/surf/rh.thickness.sub-22_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_16954/ds/sub-22/sub-22_T1w.nii Surface ROI estimation: 7s Surface and thickness estimation takes: 1639s ROI estimation in native space: ROI estimation of 'cobra' atlas 7s ROI estimation of 'neuromorphometrics' atlas 25s ROI estimation of 'lpba40' atlas 7s ROI estimation of 'hammers' atlas 18s ROI estimation of 'thalamus' atlas 1s ROI estimation of 'ibsr' atlas 6s ROI estimation of 'aal3' atlas 10s ROI estimation of 'mori' atlas 15s ROI estimation of 'anatomy3' atlas 22s ROI estimation of 'julichbrain' atlas 29s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 20s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 46s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 70s Write results 70s 290s Quality check: 4s Print 'Graphics' figure to: /var/lib/condor/execute/dir_16954/ds/sub-22/report/catreport_sub-22_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 45 minute(s) and 1 second(s). Image Quality Rating (IQR): 83.37% (B) GM volume (GMV): 47.26% (670.14 / 1417.89 ml) GM thickness (GMT): 2.52 0.58 mm Segmentations are saved in /var/lib/condor/execute/dir_16954/ds/sub-22/mri Reports are saved in /var/lib/condor/execute/dir_16954/ds/sub-22/report Labels are saved in /var/lib/condor/execute/dir_16954/ds/sub-22/label ------------------------------------------------------------------------