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0.755858744203132] [0.0860284729184691 0.0794030861435994 0.0169443492981532] [1.00485131689849 0.994943861388758 1.10768014929043] [-0.00272250969958708 -0.0167203998900424 0.0176806499853845] [2.37051404299063 -31.9140967226897 0.755858744203132] [0.0860284729184691 0.0794030861435994 0.0169443492981532] [1.00485131689849 0.994943861388758 1.10768014929043] [-0.00272250969958708 -0.0167203998900424 0.0176806499853845] /var/lib/condor/execute/dir_32256/ds/sub-0922 sub-0922_ses-01_T1w /var/lib/condor/execute/dir_32256/ds/sub-0922/sub-0922_ses-01_T1w.nii /var/lib/condor/execute/dir_32256/ds/sub-0922/sub-0922_ses-01_T1w.nii /var/lib/condor/execute/dir_32256/ds/sub-0922/mri/msub-0922_ses-01_T1w.nii /var/lib/condor/execute/dir_32256/ds/sub-0922/mri/p0sub-0922_ses-01_T1w.nii ..256/ds/sub-0922/sub-0922_ses-01_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 64 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 56 1.58073480866475 30.5 0.0804062485694885 0.0967308059334755 [0.937500032668967 0.899993700406777 0.9375] [0.937500033059059 0.89999369969161 0.9375] 0.925166871799569 0 [3.24200010299683 17.9890594482422 38.5587577819824 62.3400192260742] [0.0520051196217537 0.288563579320908 0.618523359298706 1] T1 [1.57360678613224 8.48050399111175 7.61776673419012 5.0801875661438] [0.0266270656138659 0.143498957157135 0.128900542855263 0.0859620645642281] 21.9968376159668 0.352852582931519 0.16027994453907 0.50798511505127 [1.87500006533793 1.79998740081355 1.875] 1.85033374359914 0.5 [8.62343978881836 8.62400054931641 8.62400054931641 8.62400054931641] [8.62399999998759 8.624 8.624 8.624] 0.5 2.7905445098877 2.63192558288574 1.71970510482788 3.75510204081633 1.39518370216619 2.525 1.60812497138977 1.93461608886719 2.43103705077373 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 20220709-171815 1639 1639 56 1.58073480866475 30.5 0.0804062485694885 0.0967308059334755 56 1.58073480866475 [263.120959608138 828.129443943583 595.222458863659 0 0] 1.15285846835448 0.000683591473095719 2325.44216038767 1686.47286241538 [0.156018496041077 0.491042258905684 0.352939245053239 0 0] [2.45723755046599 0.631917615145432] [2.48575854301453 0.765600868151279 1] [1.82539004301509 0.272614532770865 0.273322326685105;2.48419196504726 0.180738911360647 0.431918925949323;3.13149215115336 0.266254855489462 0.294758747365571] [0.771226523639106 0.293627707118136 0.640621430203336;4.02765387649075 0.341106134182137 0.359378569796664] 2.72464675130425 [0.651912644415902 6.66886240850726 4.18856402753661 0.5 0.5] 1.06835914730957 8.62399078823611 5.46990099733403 [0.170955717563629 1 1 11002.2032063909 0.542280657138846] [false] [0.0485022962093353 0.0466859862208366 0.285186976194382] [false] [1043.72734404582 524.185997070046 467.412204547243 3314.03541398596 2999.72023317181 5809.75192886299] [878.659126694545 484.550812886032 265.306902103357 3676.7864489593 2578.66859174671 5389.45882891465] [19.6998996734619 43.8023986816406 61.6016998291016] [0 0 3.32993388175964 19.6998996734619 43.8023986816406 61.6016998291016 82.5525970458984 308.669708251953] [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 [0.0183566492050886 0.065463550388813 0.0717679113149643 0 0] [0.0826370098820778 0 0.0826370098820778 0;0.201796825908098 0.00962460026735303 0.211421426175451 2052.4267578125;0.201796825908098 0.00962460026735303 0.211421426175451 2052.4267578125] [0.0392447076737881 0.0864078626036644 0.0976920053362846] [0.0280593018978834 0.0443730615079403 0.0557468608021736] 0.0976920053362846

0.0717679113149643

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 [0.00768427597358823 0.0316823720932007 0.0386839509010315 0.047633521258831 0.0553646646440029 0.0615089312195778] [0.0848177800703436 0 0.0848177800703436 0;0.224610057997558 0.0138924345619658 0.238502492559524 7111.18994140625;0.214504812341603 0.0162681921184272 0.230773004460031 11708.4130859375;0.194969764122596 0.0192058939992646 0.214175658121861 20709.177734375;0.178243702814698 0.0231201706252254 0.201363873439923 40445.33984375;0.178243702814698 0.0231201706252254 0.201363873439923 40445.33984375] [0.0088942376896739 0.0310432408004999 0.0501526519656181 0.0734162032604218 0.0996799990534782 0.107059843838215] [0.00282077142037451 0.011384385637939 0.0273685716092587 0.0486897304654121 0.0693302303552628 0.0756810307502747] 0.107059843838215

0.0615089312195778

------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./dir_32256/ds/sub-0922/sub-0922_ses-01_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 143s APP: Rough bias correction: Initialize 11s Estimate background 14s Initial correction 31s Refine background 6s Final correction 15s Final scaling 10s 98s Correct center-of-mass 6s Affine registration 32s SPM preprocessing 1 (estimate 1 - TPM registration): 127s SPM preprocessing 1 (estimate 2): 91s SPM preprocessing 2 (write): Write Segmentation 31s Update Segmentation 33s Update Skull-Stripping 73s Update probability maps 15s 151s Global intensity correction: 27s SANLM denoising after intensity normalization (medium): 18s Fast Optimized Shooting registration 52s Local adaptive segmentation (LASstr=0.50): Prepare maps 7s Prepare partitions 6s Prepare segments (LASmod = 1.16) 27s Estimate local tissue thresholds (WM) 34s Estimate local tissue thresholds (GM) 52s Intensity transformation 0s SANLM denoising after LAS (medium) 60s 191s ROI segmentation (partitioning): Atlas -> subject space 12s Major structures 6s Ventricle detection 32s Blood vessel detection 19s WMH detection (WMHCstr=0.50 > WMHCstr'=0.02) 48s Manual stroke lesion detection 0s Closing of deep structures 3s Side alignment 6s Final corrections 7s 134s Blood vessel correction (BVCstr=0.50): 3s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 51s AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.08,0.98 0.05] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 7s Level 1 cleanup (brain masking) 5s Level 2 cleanup (CSF correction) 3s Level 3 cleanup (CSF/WM PVE) 5s 19s 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 | 0.0848 0.0000 0.0848 | 32.0000 2 | 2.50 | 0.0827 0.0010 0.0837 | 29.4886 3 | 2.50 | 0.0821 0.0015 0.0836 | 26.9772 4 | 2.50 | 0.0818 0.0017 0.0835 | 24.6107 5 | 2.50 | 0.0816 0.0018 0.0834 | 22.6548 6 | 2.50 | 0.0813 0.0019 0.0832 | 20.6989 7 | 2.50 | 0.0811 0.0019 0.0831 | 18.9688 8 | 2.50 | 0.0809 0.0020 0.0829 | 17.4455 9 | 2.50 | 0.0807 0.0021 0.0827 | 15.9223 10 | 2.50 | 0.0804 0.0022 0.0826 | 14.6627 11 | 2.50 | 0.0802 0.0022 0.0824 | 13.4764 12 | 2.50 | 0.0799 0.0023 0.0822 | 12.3015 13 | 2.50 | 0.0796 0.0023 0.0820 | 11.3776 14 | 2.50 | 0.0794 0.0024 0.0818 | 10.4537 15 | 2.25 | 0.0804 0.0025 0.0829 | 9.5920 16 | 2.25 | 0.0776 0.0038 0.0815 | 8.8725 17 | 2.25 | 0.0766 0.0043 0.0809 | 8.1530 18 | 2.25 | 0.0759 0.0045 0.0804 | 7.5234 19 | 2.25 | 0.0753 0.0046 0.0799 | 6.9630 20 | 2.25 | 0.0749 0.0046 0.0795 | 6.4027 29 | 2.00 | 0.0776 0.0026 0.0802 | 3.3283 30 | 2.00 | 0.0731 0.0046 0.0777 | 3.1221 31 | 2.00 | 0.0715 0.0054 0.0769 | 2.9160 43 | 1.75 | 0.0712 0.0031 0.0742 | 1.5785 44 | 1.75 | 0.0665 0.0055 0.0721 | 1.5194 45 | 1.75 | 0.0650 0.0064 0.0714 | 1.4626 57 | 1.50 | 0.0641 0.0046 0.0687 | 1.0900 58 | 1.50 | 0.0606 0.0069 0.0675 | 1.0730 59 | 1.50 | 0.0594 0.0077 0.0671 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 209s Prepare output 18s 228s Jacobian determinant (RMS): 0.009 0.031 0.050 0.073 0.100 | 0.107060 Template Matching: 0.085 0.225 0.215 0.195 0.178 | 0.178244 Write result maps: 39s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 51s CSF distance: 24s PBT2x thickness: 71s 155s Create initial surface 129s Topology correction: 138s Surface refinement: 154s Reduction of surface collisions with optimization: 112s Spherical mapping with areal smoothing 124s Spherical registration 357s rh: Thickness estimation (0.50 mm ): WM distance: 63s CSF distance: 24s PBT2x thickness: 69s 164s Create initial surface 122s Topology correction: 134s Surface refinement: 144s Reduction of surface collisions with optimization: 106s Spherical mapping with areal smoothing 125s Spherical registration 360s Final surface processing results: Average thickness (FS): 2.4575 0.6309 mm Surface intensity / position RMSE: 0.0804 / 0.0967 Euler number / defect number / defect size: 56.0 / 30.5 / 1.58% Display thickness: /var/lib/condor/execute/dir_32256/ds/sub-0922/surf/lh.thickness.sub-0922_ses-01_T1w Display thickness: /var/lib/condor/execute/dir_32256/ds/sub-0922/surf/rh.thickness.sub-0922_ses-01_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_32256/ds/sub-0922/sub-0922_ses-01_T1w.nii Surface ROI estimation: 11s Surface and thickness estimation takes: 2466s ROI estimation in native space: ROI estimation of 'cobra' atlas 16s ROI estimation of 'neuromorphometrics' atlas 54s ROI estimation of 'lpba40' atlas 15s ROI estimation of 'hammers' atlas 36s ROI estimation of 'thalamus' atlas 3s ROI estimation of 'ibsr' atlas 13s ROI estimation of 'aal3' atlas 22s ROI estimation of 'mori' atlas 33s ROI estimation of 'anatomy3' atlas 45s ROI estimation of 'julichbrain' atlas 60s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 23s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 42s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 95s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 147s Write results 149s 607s Quality check: 10s Print 'Graphics' figure to: /var/lib/condor/execute/dir_32256/ds/sub-0922/report/catreport_sub-0922_ses-01_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 78 minute(s) and 14 second(s). Image Quality Rating (IQR): 80.69% (B-) GM volume (GMV): 49.10% (828.13 / 1686.47 ml) GM thickness (GMT): 2.46 0.63 mm Segmentations are saved in /var/lib/condor/execute/dir_32256/ds/sub-0922/mri Reports are saved in /var/lib/condor/execute/dir_32256/ds/sub-0922/report Labels are saved in /var/lib/condor/execute/dir_32256/ds/sub-0922/label ------------------------------------------------------------------------