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-28.5866945851532] [0.369566409485471 0.00900288400635214 0.0128928250723339] [1.00886083079274 1.1389625843347 1.16010355115432] [-0.0102548404187387 0.00212501268206062 0.00674517743773676] [-5.68562079886267 -22.1107190242389 -28.5866945851532] [0.369566409485471 0.00900288400635214 0.0128928250723339] [1.00886083079274 1.1389625843347 1.16010355115432] [-0.0102548404187387 0.00212501268206062 0.00674517743773676] /var/lib/condor/execute/dir_14141/ds/sub-027 sub-027_ses-t2_T1w /var/lib/condor/execute/dir_14141/ds/sub-027/sub-027_ses-t2_T1w.nii /var/lib/condor/execute/dir_14141/ds/sub-027/sub-027_ses-t2_T1w.nii /var/lib/condor/execute/dir_14141/ds/sub-027/mri/msub-027_ses-t2_T1w.nii /var/lib/condor/execute/dir_14141/ds/sub-027/mri/p0sub-027_ses-t2_T1w.nii ..4141/ds/sub-027/sub-027_ses-t2_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 20 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 28 1.15617098003809 15.5 0.0639687329530716 0.0701561570167542 [1.00000016887177 1.00000001506058 1.00000001596067] [1.00000016884646 1.00000001501718 1.00000001608479] 1.00000006663101 0 [0 19404.572265625 43415.01953125 62123.85546875] [0 0.312352985143661 0.698846161365509 1] T1 [5915.32743754859 7167.81719135871 6284.06505703576 3565.27146654461] [0.0952182933688164 0.115379467606544 0.101153813302517 0.0573897324502468] 18708.8359375 0.301153808832169 0.132630482316017 0.241589024662971 [2.00000033774353 2.00000003012116 2.00000003192135] 2.00000013326202 0.5 [1.89584374427795 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 3.56602621078491 2.23500537872314 1.05900061130524 2.3265306122449 1.28904274500952 1.775 1.27937459945679 1.40312314033508 2.13967042106675 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 20220713-061602 1639 1639 28 1.15617098003809 15.5 0.0639687329530716 0.0701561570167542 28 1.15617098003809 [337.492291010453 597.592539095512 494.659902828022 0 0] 0.791513883752126 0.000553605035584119 1766.31723693298 1429.74473293399 [0.236050732159638 0.417971491924428 0.345977775915934 0 0] [2.35565053284965 0.621712086506224] [2.32498574256897 0.79033853964816 1] [1.72961339114275 0.27992566972284 0.293918680854062;2.36439981997428 0.183278814872731 0.479656120076105;3.08304325831203 0.304474051415753 0.226425199069833] [0.763166251755804 0.233322404813029 0.470588235294118;4.12225899874553 0.340793819520765 0.529411764705882] 1.02105003478685 [2.08927320689005 5.35652823140137 4.06353764216836 0.5 0.5] 1.05536050355841 8.56600609223459 4.43801286723599 [0.459361111111111 10134 2694 5605.34512046917 0.378132478097852] [false] [0 0 0.353821575641632] [false] [736.611978656931 441.293598039868 505.751316810438 1299.2508754694 4490.4783135502 3730.09126739439] [639.120782693135 414.213302429128 344.314559041222 77.4011919468323 17.1793524545918 8875.79545313242] [21425.412109375 46037.765625 60390.6484375] [0 0 10278.8779296875 21425.412109375 46037.765625 60390.6484375 79873.265625 113497.4375] [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 [0.0221753474324942 0.0887059420347214 0.100336916744709 0 0] [0.0903013793407988 0 0.0903013793407988 0;0.19810687336458 0.0147670743559875 0.212873947720568 3149.04907226562;0.19810687336458 0.0147670743559875 0.212873947720568 3149.04907226562] [0.0494596585631371 0.118070118129253 0.13642892241478] [0.0355005636811256 0.0542913414537907 0.0706039667129517] 0.13642892241478

0.100336916744709

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 [0.0105981724336743 0.0485299117863178 0.0625359565019608 0.0719616413116455 0.0784678682684898 0.0911786556243896] [0.0913389077659573 0 0.0913389077659573 0;0.224391025641026 0.0236570379273504 0.248048063568376 12109.4462890625;0.204859330885132 0.0241521983142215 0.229011529199353 17382.626953125;0.180502852596562 0.0248257056487139 0.205328558245276 26768.86328125;0.161912843634189 0.0275459877166015 0.189458831350791 48187.65625;0.161912843634189 0.0275459877166015 0.189458831350791 48187.65625] [0.0125844990834594 0.049278449267149 0.0812855064868927 0.111943475902081 0.140458837151527 0.149200066924095] [0.00380253233015537 0.0158249102532864 0.0357839614152908 0.0601197518408298 0.0806257948279381 0.0862311199307442] 0.149200066924095

0.0911786556243896

------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./dir_14141/ds/sub-027/sub-027_ses-t2_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 11s APP: Rough bias correction: Initialize 6s Estimate background 8s Initial correction 7s Refine background 4s Final correction 5s Final scaling 7s 44s Correct center-of-mass 10s Affine registration 15s SPM preprocessing 1 (estimate 1 - TPM registration): 115s SPM preprocessing 1 (estimate 2): 86s SPM preprocessing 2 (write): Write Segmentation 17s Update Segmentation 20s Update Skull-Stripping 42s Update probability maps 8s 87s Global intensity correction: 17s SANLM denoising after intensity normalization (medium): 6s Fast Optimized Shooting registration 40s Local adaptive segmentation (LASstr=0.50): Prepare maps 5s Prepare partitions 2s Prepare segments (LASmod = 1.01) 15s Estimate local tissue thresholds (WM) 17s Estimate local tissue thresholds (GM) 22s Intensity transformation 0s SANLM denoising after LAS (medium) 15s 80s ROI segmentation (partitioning): Atlas -> subject space 9s Major structures 4s Ventricle detection 13s Blood vessel detection 9s WMH detection (WMHCstr=0.50 > WMHCstr'=0.16) 24s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 4s Final corrections 4s 69s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 41s AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.07,0.98 0.05] 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 | 0.0913 0.0000 0.0913 | 32.0000 2 | 2.50 | 0.0873 0.0016 0.0888 | 29.4886 3 | 2.50 | 0.0860 0.0024 0.0884 | 26.9772 4 | 2.50 | 0.0854 0.0028 0.0882 | 24.6107 5 | 2.50 | 0.0849 0.0030 0.0879 | 22.6548 6 | 2.50 | 0.0845 0.0031 0.0876 | 20.6989 7 | 2.50 | 0.0840 0.0033 0.0873 | 18.9688 8 | 2.50 | 0.0836 0.0035 0.0870 | 17.4455 9 | 2.50 | 0.0831 0.0036 0.0867 | 15.9223 10 | 2.50 | 0.0826 0.0037 0.0863 | 14.6627 11 | 2.50 | 0.0821 0.0039 0.0860 | 13.4764 12 | 2.50 | 0.0816 0.0040 0.0856 | 12.3015 13 | 2.50 | 0.0811 0.0041 0.0852 | 11.3776 14 | 2.50 | 0.0806 0.0043 0.0848 | 10.4537 15 | 2.25 | 0.0829 0.0044 0.0873 | 9.5920 16 | 2.25 | 0.0788 0.0064 0.0852 | 8.8725 17 | 2.25 | 0.0770 0.0073 0.0842 | 8.1530 18 | 2.25 | 0.0757 0.0077 0.0834 | 7.5234 19 | 2.25 | 0.0748 0.0079 0.0827 | 6.9630 29 | 2.00 | 0.0770 0.0041 0.0811 | 3.3283 30 | 2.00 | 0.0707 0.0069 0.0776 | 3.1221 31 | 2.00 | 0.0683 0.0081 0.0763 | 2.9160 43 | 1.75 | 0.0670 0.0047 0.0716 | 1.5785 44 | 1.75 | 0.0619 0.0073 0.0693 | 1.5194 45 | 1.75 | 0.0602 0.0083 0.0684 | 1.4626 57 | 1.50 | 0.0587 0.0061 0.0649 | 1.0900 58 | 1.50 | 0.0552 0.0084 0.0636 | 1.0730 59 | 1.50 | 0.0540 0.0092 0.0632 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 211s Prepare output 10s 220s Jacobian determinant (RMS): 0.013 0.049 0.081 0.112 0.140 | 0.149200 Template Matching: 0.091 0.224 0.205 0.181 0.162 | 0.161913 Write result maps: 26s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 67s CSF distance: 15s PBT2x thickness: 46s 136s Create initial surface 82s Topology correction: 81s Surface refinement: 68s Reduction of surface collisions with optimization: 64s Spherical mapping with areal smoothing 78s Spherical registration 230s rh: Thickness estimation (0.50 mm ): WM distance: 98s CSF distance: 16s PBT2x thickness: 46s 166s Create initial surface 80s Topology correction: 85s Surface refinement: 98s Reduction of surface collisions with optimization: 67s Spherical mapping with areal smoothing 79s Spherical registration 236s Final surface processing results: Average thickness (FS): 2.3556 0.6217 mm Surface intensity / position RMSE: 0.0640 / 0.0702 Euler number / defect number / defect size: 28.0 / 15.5 / 1.16% Display thickness: /var/lib/condor/execute/dir_14141/ds/sub-027/surf/lh.thickness.sub-027_ses-t2_T1w Display thickness: /var/lib/condor/execute/dir_14141/ds/sub-027/surf/rh.thickness.sub-027_ses-t2_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_14141/ds/sub-027/sub-027_ses-t2_T1w.nii Surface ROI estimation: 7s Surface and thickness estimation takes: 1634s ROI estimation in native space: ROI estimation of 'cobra' atlas 12s ROI estimation of 'neuromorphometrics' atlas 43s ROI estimation of 'lpba40' atlas 12s ROI estimation of 'hammers' atlas 30s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 11s ROI estimation of 'aal3' atlas 18s ROI estimation of 'mori' atlas 26s ROI estimation of 'anatomy3' atlas 37s ROI estimation of 'julichbrain' atlas 49s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 18s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 23s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 79s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 119s Write results 120s 480s Quality check: 5s Print 'Graphics' figure to: /var/lib/condor/execute/dir_14141/ds/sub-027/report/catreport_sub-027_ses-t2_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 51 minute(s) and 24 second(s). Image Quality Rating (IQR): 83.60% (B) GM volume (GMV): 41.80% (597.59 / 1429.74 ml) GM thickness (GMT): 2.36 0.62 mm Segmentations are saved in /var/lib/condor/execute/dir_14141/ds/sub-027/mri Reports are saved in /var/lib/condor/execute/dir_14141/ds/sub-027/report Labels are saved in /var/lib/condor/execute/dir_14141/ds/sub-027/label ------------------------------------------------------------------------