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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 36 1.35944030956912 22.5 0.0687689036130905 0.0738988369703293 [0.999992027435451 0.999999968848981 1.00000001355366] [0.99999202751789 0.999999968787983 1.00000001338354] 0.999997336619746 0 [0 19792.82421875 44363.73046875 63864.33984375] [0 0.309919804334641 0.69465571641922 1] T1 [3358.70894933842 7263.73488011672 6355.87491059223 3657.87668027158] [0.0525913052260876 0.113736942410469 0.0995215028524399 0.0572757311165333] 19500.609375 0.305344253778458 0.15272082388401 0.306378334760666 [1.9999840548709 1.99999993769796 2.00000002710733] 1.99999467323949 0.5 [1.89584374427795 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 3.50316953659058 2.5234112739563 1.21968829631805 2.73469387755102 1.33986007739228 2.125 1.37537813186646 1.47797679901123 2.3562185193089 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 20220713-035654 1639 1639 36 1.35944030956912 22.5 0.0687689036130905 0.0738988369703293 36 1.35944030956912 [296.512818986889 663.989412123133 587.192425759798 0 0] 1.4465962842915 0.000934678089034184 1972.27718242783 1547.69465686982 [0.191583538568635 0.429018352667856 0.379398108763509 0 0] [2.48640263241731 0.650135218182522] [2.50685143470764 0.812803183929439 1] [1.74830396325346 0.294040338078051 0.243803765674332;2.47956176455697 0.190625653064898 0.463781268774047;3.15289857733511 0.29010157013158 0.292414965551621] [0.775066160263043 0.217810222657137 0.531377106333527;4.22935818896655 0.383127084222215 0.468622893666473] 1.50239360401496 [1.29065263233899 5.55492731084511 4.66375913727567 0.5 0.5] 1.09346780890342 8.6201445227127 4.66965706012704 [0.435662712191358 8330 2077 5851.002249172 0.381323312072047] [false] [0 0 0.395853370428085] [false] [799.274331145994 553.502643973372 459.32229454883 1037.91244002446 4026.93685071831 4212.71202512866] [696.612845567336 520.261289976389 286.876990098416 1130.31472522503 3472.65453846498 4261.21895126566] [22588.9609375 46859.5625 61814.46484375] [0 0 800.806030273438 22588.9609375 46859.5625 61814.46484375 81427.21875 113935.8203125] [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 [0.0228330921381712 0.0920687094330788 0.102267771959305 0 0] [0.0855863585668643 0 0.0855863585668643 0;0.186279919682717 0.0127762752134545 0.199056194896171 2724.51513671875;0.186279919682717 0.0127762752134545 0.199056194896171 2724.51513671875] [0.0513514690101147 0.116124354302883 0.128286987543106] [0.0371028482913971 0.0508250519633293 0.0616475865244865] 0.128286987543106

0.102267771959305

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 [0.0115716811269522 0.0465080142021179 0.0681397542357445 0.0769911482930183 0.082510307431221 0.093913696706295] [0.0862565669785401 0 0.0862565669785401 0;0.217553006715507 0.0185258356227106 0.236078842338217 9482.912109375;0.189164815231648 0.0208701983940278 0.210035013625676 15020.5322265625;0.16735055892669 0.0212830636802449 0.188633622606935 22948.931640625;0.151029998662363 0.023404588278495 0.174434586940858 40942.88671875;0.151029998662363 0.023404588278495 0.174434586940858 40942.88671875] [0.0132515076547861 0.0514725409448147 0.0780489519238472 0.107229299843311 0.130280777812004 0.138228848576546] [0.00378249329514802 0.0155470762401819 0.0321524478495121 0.0521497391164303 0.0688046962022781 0.0741406232118607] 0.138228848576546

0.093913696706295

------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./dir_11847/ds/sub-041/sub-041_ses-t0_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 11s APP: Rough bias correction: Initialize 5s Estimate background 6s Initial correction 6s Refine background 3s Final correction 4s Final scaling 5s 34s Correct center-of-mass 2s Affine registration 9s SPM preprocessing 1 (estimate 1 - TPM registration): 72s SPM preprocessing 1 (estimate 2): 52s SPM preprocessing 2 (write): Write Segmentation 13s Update Segmentation 16s Update Skull-Stripping 33s Update probability maps 7s 68s Global intensity correction: 12s SANLM denoising after intensity normalization (medium): 6s Fast Optimized Shooting registration 26s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 2s Prepare segments (LASmod = 1.17) 12s Estimate local tissue thresholds (WM) 15s Estimate local tissue thresholds (GM) 18s Intensity transformation 0s SANLM denoising after LAS (medium) 16s 68s ROI segmentation (partitioning): Atlas -> subject space 6s Major structures 3s Ventricle detection 12s Blood vessel detection 8s WMH detection (WMHCstr=0.50 > WMHCstr'=0.07) 25s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 3s Final corrections 3s 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 0.06,0.68 0.07,0.98 0.05] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 4s Level 1 cleanup (brain masking) 3s 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 | 0.0863 0.0000 0.0863 | 32.0000 2 | 2.50 | 0.0825 0.0015 0.0840 | 29.4886 3 | 2.50 | 0.0814 0.0023 0.0837 | 26.9772 4 | 2.50 | 0.0808 0.0027 0.0835 | 24.6107 5 | 2.50 | 0.0803 0.0029 0.0832 | 22.6548 6 | 2.50 | 0.0799 0.0030 0.0830 | 20.6989 7 | 2.50 | 0.0795 0.0032 0.0827 | 18.9688 8 | 2.50 | 0.0791 0.0033 0.0824 | 17.4455 9 | 2.50 | 0.0786 0.0034 0.0821 | 15.9223 10 | 2.50 | 0.0781 0.0036 0.0817 | 14.6627 11 | 2.50 | 0.0777 0.0037 0.0814 | 13.4764 12 | 2.50 | 0.0772 0.0038 0.0810 | 12.3015 13 | 2.50 | 0.0767 0.0040 0.0807 | 11.3776 14 | 2.50 | 0.0762 0.0041 0.0803 | 10.4537 15 | 2.25 | 0.0764 0.0043 0.0806 | 9.5920 16 | 2.25 | 0.0725 0.0062 0.0787 | 8.8725 29 | 2.00 | 0.0731 0.0028 0.0759 | 3.3283 30 | 2.00 | 0.0657 0.0058 0.0715 | 3.1221 31 | 2.00 | 0.0631 0.0070 0.0700 | 2.9160 43 | 1.75 | 0.0615 0.0041 0.0656 | 1.5785 44 | 1.75 | 0.0572 0.0063 0.0635 | 1.5194 45 | 1.75 | 0.0558 0.0071 0.0629 | 1.4626 57 | 1.50 | 0.0543 0.0053 0.0596 | 1.0900 58 | 1.50 | 0.0513 0.0072 0.0585 | 1.0730 59 | 1.50 | 0.0503 0.0078 0.0581 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 133s Prepare output 9s 141s Jacobian determinant (RMS): 0.013 0.051 0.078 0.107 0.130 | 0.138229 Template Matching: 0.086 0.218 0.189 0.167 0.151 | 0.151030 Write result maps: 18s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 46s CSF distance: 13s PBT2x thickness: 38s 103s Create initial surface 75s Topology correction: 82s Surface refinement: 54s Reduction of surface collisions with optimization: 58s Spherical mapping with areal smoothing 65s Spherical registration 249s rh: Thickness estimation (0.50 mm ): WM distance: 47s CSF distance: 12s PBT2x thickness: 38s 103s Create initial surface 74s Topology correction: 80s Surface refinement: 63s Reduction of surface collisions with optimization: 58s Spherical mapping with areal smoothing 65s Spherical registration 250s Final surface processing results: Average thickness (FS): 2.4864 0.6500 mm Surface intensity / position RMSE: 0.0688 / 0.0739 Euler number / defect number / defect size: 36.0 / 22.5 / 1.36% Display thickness: /var/lib/condor/execute/dir_11847/ds/sub-041/surf/lh.thickness.sub-041_ses-t0_T1w Display thickness: /var/lib/condor/execute/dir_11847/ds/sub-041/surf/rh.thickness.sub-041_ses-t0_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_11847/ds/sub-041/sub-041_ses-t0_T1w.nii Surface ROI estimation: 6s Surface and thickness estimation takes: 1452s ROI estimation in native space: ROI estimation of 'cobra' atlas 6s ROI estimation of 'neuromorphometrics' atlas 22s ROI estimation of 'lpba40' atlas 6s ROI estimation of 'hammers' atlas 16s ROI estimation of 'thalamus' atlas 1s ROI estimation of 'ibsr' atlas 6s ROI estimation of 'aal3' atlas 9s ROI estimation of 'mori' atlas 13s ROI estimation of 'anatomy3' atlas 19s ROI estimation of 'julichbrain' atlas 25s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 10s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 18s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 41s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 60s Write results 61s 254s Quality check: 4s Print 'Graphics' figure to: /var/lib/condor/execute/dir_11847/ds/sub-041/report/catreport_sub-041_ses-t0_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 40 minute(s) and 3 second(s). Image Quality Rating (IQR): 81.44% (B-) GM volume (GMV): 42.90% (663.99 / 1547.69 ml) GM thickness (GMT): 2.49 0.65 mm Segmentations are saved in /var/lib/condor/execute/dir_11847/ds/sub-041/mri Reports are saved in /var/lib/condor/execute/dir_11847/ds/sub-041/report Labels are saved in /var/lib/condor/execute/dir_11847/ds/sub-041/label ------------------------------------------------------------------------