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-31.7624072850599] [0.044943333831646 0.000586090757863514 -0.0361172892533446] [1.09494601955787 1.04563086075155 1.16286900612229] [0.00591328616236031 0.00440148994352336 0.041958101242356] [-0.0263697724979497 -5.11212426790631 -31.7624072850599] [0.044943333831646 0.000586090757863514 -0.0361172892533446] [1.09494601955787 1.04563086075155 1.16286900612229] [0.00591328616236031 0.00440148994352336 0.041958101242356] /var/lib/condor/execute/dir_21556/ds/sub-season129 sub-season129_ses-3_acq-MPrageHiRes_T1w /var/lib/condor/execute/dir_21556/ds/sub-season129/sub-season129_ses-3_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_21556/ds/sub-season129/sub-season129_ses-3_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_21556/ds/sub-season129/mri/msub-season129_ses-3_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_21556/ds/sub-season129/mri/p0sub-season129_ses-3_acq-MPrageHiRes_T1w.nii ..s/sub-season129/..son129_ses-3_acq-MPrageHiRes_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 8 0.131102010287254 13.5 0.0651634633541107 0.0642403066158295 [0.880000168754645 0.875000036617963 0.874999971132958] [0.880000168749606 0.875000032555135 0.874999966529498] 0.876669894272699 0 [10.3509998321533 304.757446289062 764.680969238281 1112.677734375] [0.0093027837574482 0.273895531892776 0.6872438788414 1] T1 [19.3256444823708 121.96517131855 101.15580452638 60.3176489689092] [0.0175316836684942 0.11064338684082 0.0917657166719437 0.0547184832394123] 351.264495849609 0.315692931413651 0.0994341447949409 0.264881372451782 [1.76000033750929 1.75000007323593 1.74999994226592] 1.7533397885454 0.5 [8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 3.34793925285339 1.75845742225647 1.11676931381226 1.30612244897959 1.03277550257181 1.675 1.30326926708221 1.28480613231659 1.75591165622767 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 20220712-165916 1639 1639 8 0.131102010287254 13.5 0.0651634633541107 0.0642403066158295 8 0.131102010287254 [224.289330471361 680.650553128724 471.084509832958 0 0] 0.579641767408977 0.000421243816734112 1909.00397479977 1376.02439343304 [0.162998077317351 0.494650063165355 0.342351859517293 0 0] [2.56227924581758 0.592842321926667] [2.55543375015259 0.763316364985756 1] [2.00217039000827 0.242155874418809 0.297497234060661;2.57814900246778 0.165296930968471 0.427925185432501;3.19103320487476 0.261720753849122 0.274577580506838] [0.904149895378969 0.384585296873061 0.537169517884915;4.2147454441021 0.400040231477014 0.462830482115086] 1.01368302446583 [0.777264319636342 6.73365774363066 3.99841701719277 0.5 0.5] 1.04212438167341 8.61455225462411 5.51711996032065 [0.342088971819196 1 1 6507.19738550516 0.332002854087158] [false] [0.00547702796757221 0 0.15945690870285] [false] [806.373032561737 417.438764925453 316.290137742761 446.924884445949 2175.59955669833 6181.71077937476] [725.74253550294 396.323533658271 203.020465679781 344.884106406837 1321.62364413155 6899.13438200685] [361.308685302734 797.2548828125 1100.06481933594] [0 0 14.9114665985107 361.308685302734 797.2548828125 1100.06481933594 1469.44287109375 2560.64379882812] [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 [0.0213332716375589 0.0728474855422974 0.0798874273896217 0 0] [0.0822150454420049 0 0.0822150454420049 0;0.191044160584156 0.0095733605942377 0.200617521178393 2041.5;0.191044160584156 0.0095733605942377 0.200617521178393 2041.5] [0.0462425090372562 0.09447231143713 0.104050785303116] [0.0330986604094505 0.0417820401489735 0.0512457825243473] 0.104050785303116

0.0798874273896217

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 [0.0102289458736777 0.0367313027381897 0.0505435988306999 0.0581050217151642 0.0643587112426758 0.0720409527420998] [0.0833759793587577 0 0.0833759793587577 0;0.214931059218559 0.0136158844627595 0.228546943681319 6969.630859375;0.194761845710506 0.0159281486031913 0.210689994313698 11463.6796875;0.175019049576545 0.0179268238324838 0.192945873409029 19329.9921875;0.157975780902997 0.0207718939516496 0.178747674854646 36337.375;0.157975780902997 0.0207718939516496 0.178747674854646 36337.375] [0.0118997497484088 0.042020034044981 0.0611301623284817 0.083996869623661 0.106241211295128 0.11356807500124] [0.00327152735553682 0.012421602383256 0.0272421110421419 0.0473973639309406 0.0650224760174751 0.0705485939979553] 0.11356807500124

0.0720409527420998

------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./sub-season129_ses-3_acq-MPrageHiRes_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 39s APP: Rough bias correction: Initialize 8s Estimate background 9s Initial correction 18s Refine background 4s Final correction 13s Final scaling 9s 68s Correct center-of-mass 6s Affine registration 14s SPM preprocessing 1 (estimate 1 - TPM registration): 101s SPM preprocessing 1 (estimate 2): 84s SPM preprocessing 2 (write): Write Segmentation 21s Update Segmentation 25s Update Skull-Stripping 53s Update probability maps 11s 110s Global intensity correction: 20s SANLM denoising after intensity normalization (medium): 12s Fast Optimized Shooting registration 35s Local adaptive segmentation (LASstr=0.50): Prepare maps 5s Prepare partitions 6s Prepare segments (LASmod = 1.00) 19s Estimate local tissue thresholds (WM) 23s Estimate local tissue thresholds (GM) 32s Intensity transformation 0s SANLM denoising after LAS (medium) 32s 121s ROI segmentation (partitioning): Atlas -> subject space 9s Major structures 5s Ventricle detection 25s Blood vessel detection 13s WMH detection (WMHCstr=0.50 > WMHCstr'=0.01) 38s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 4s Final corrections 5s 102s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 42s 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) 4s Level 2 cleanup (CSF correction) 2s Level 3 cleanup (CSF/WM PVE) 4s 15s 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 | 0.0834 0.0000 0.0834 | 32.0000 2 | 2.50 | 0.0805 0.0013 0.0818 | 29.4886 3 | 2.50 | 0.0797 0.0019 0.0816 | 26.9772 4 | 2.50 | 0.0793 0.0021 0.0814 | 24.6107 5 | 2.50 | 0.0789 0.0023 0.0812 | 22.6548 6 | 2.50 | 0.0787 0.0024 0.0810 | 20.6989 7 | 2.50 | 0.0784 0.0025 0.0808 | 18.9688 8 | 2.50 | 0.0781 0.0026 0.0806 | 17.4455 9 | 2.50 | 0.0778 0.0026 0.0804 | 15.9223 10 | 2.50 | 0.0774 0.0028 0.0802 | 14.6627 11 | 2.50 | 0.0771 0.0028 0.0799 | 13.4764 12 | 2.50 | 0.0768 0.0029 0.0797 | 12.3015 13 | 2.50 | 0.0764 0.0030 0.0794 | 11.3776 14 | 2.50 | 0.0761 0.0030 0.0792 | 10.4537 15 | 2.25 | 0.0746 0.0031 0.0777 | 9.5920 16 | 2.25 | 0.0716 0.0045 0.0762 | 8.8725 29 | 2.00 | 0.0726 0.0020 0.0746 | 3.3283 30 | 2.00 | 0.0669 0.0044 0.0712 | 3.1221 31 | 2.00 | 0.0649 0.0053 0.0702 | 2.9160 43 | 1.75 | 0.0639 0.0031 0.0669 | 1.5785 44 | 1.75 | 0.0598 0.0052 0.0650 | 1.5194 45 | 1.75 | 0.0583 0.0060 0.0643 | 1.4626 57 | 1.50 | 0.0566 0.0044 0.0610 | 1.0900 58 | 1.50 | 0.0537 0.0063 0.0599 | 1.0730 59 | 1.50 | 0.0527 0.0069 0.0596 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 157s Prepare output 11s 168s Jacobian determinant (RMS): 0.012 0.042 0.061 0.084 0.106 | 0.113568 Template Matching: 0.083 0.215 0.195 0.175 0.158 | 0.157976 Write result maps: 27s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 30s CSF distance: 15s PBT2x thickness: 42s 93s Create initial surface 80s Topology correction: 91s Surface refinement: 65s Reduction of surface collisions with optimization: 63s Spherical mapping with areal smoothing 82s Spherical registration 301s rh: Thickness estimation (0.50 mm ): WM distance: 38s CSF distance: 15s PBT2x thickness: 43s 102s Create initial surface 79s Topology correction: 86s Surface refinement: 67s Reduction of surface collisions with optimization: 62s Spherical mapping with areal smoothing 76s Spherical registration 276s Final surface processing results: Average thickness (FS): 2.5623 0.5926 mm Surface intensity / position RMSE: 0.0652 / 0.0642 Euler number / defect number / defect size: 8.0 / 13.5 / 0.13% Display thickness: /var/lib/condor/execute/dir_21556/ds/sub-season129/surf/lh.thickness.sub-season129_ses-3_acq-MPrageHiRes_T1w Display thickness: /var/lib/condor/execute/dir_21556/ds/sub-season129/surf/rh.thickness.sub-season129_ses-3_acq-MPrageHiRes_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_21556/ds/sub-season129/sub-season129_ses-3_acq-MPrageHiRes_T1w.nii Surface ROI estimation: 7s Surface and thickness estimation takes: 1613s ROI estimation in native space: ROI estimation of 'cobra' atlas 9s ROI estimation of 'neuromorphometrics' atlas 34s ROI estimation of 'lpba40' atlas 10s ROI estimation of 'hammers' atlas 24s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 9s ROI estimation of 'aal3' atlas 14s ROI estimation of 'mori' atlas 20s ROI estimation of 'anatomy3' atlas 29s ROI estimation of 'julichbrain' atlas 40s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 16s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 28s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 64s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 95s Write results 95s 395s Quality check: 6s Print 'Graphics' figure to: /var/lib/condor/execute/dir_21556/ds/sub-season129/report/catreport_sub-season129_ses-3_acq-MPrageHiRes_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 51 minute(s) and 41 second(s). Image Quality Rating (IQR): 87.44% (B+) GM volume (GMV): 49.47% (680.65 / 1376.02 ml) GM thickness (GMT): 2.56 0.59 mm Segmentations are saved in /var/lib/condor/execute/dir_21556/ds/sub-season129/mri Reports are saved in /var/lib/condor/execute/dir_21556/ds/sub-season129/report Labels are saved in /var/lib/condor/execute/dir_21556/ds/sub-season129/label ------------------------------------------------------------------------