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../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 30 1.19368866728445 15.5 0.0751504153013229 0.0830121040344238 [1 1 1] [1 1 1] 1 0 [16.1604995727539 292.056518554688 1098.71618652344 1763.52697753906] [0.00916373822838068 0.165609329938889 0.623022019863129 1] T1 [10.9914221725235 209.718518919164 193.063837294831 116.114968297052] [0.0062902788631618 0.120019771158695 0.110488466918468 0.0664514154195786] 630.003173828125 0.357240438461304 0.122603185474873 0.305739313364029 [2 2 2] 2 0.5 [8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 2.72472667694092 2.09105920791626 1.21810340881348 2.42857142857143 1.29842216682111 1.775 1.5030083656311 1.66024208068848 2.04905951282441 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 20220711-083857 1639 1639 30 1.19368866728445 15.5 0.0751504153013229 0.0830121040344238 30 1.19368866728445 [171.380568627451 803.899501960784 573.819905882353 0 0] 0.868188235294118 0.000560446871397006 2172.83677479039 1549.09997647059 [0.110632348609234 0.518946171435855 0.370421479954911 0 0] [2.6065554462901 0.646304560092284] [2.62546014785767 0.807753715713661 1] [1.9649896272137 0.276443666795556 0.281088818704415;2.63480151742745 0.186587971451405 0.429034786757856;3.30584829996956 0.282950739525623 0.289876394537729] [0.845688387380353 0.328156053113081 0.616485600965684;4.2483269491856 0.320561669679638 0.383514399034316] 1.5116699328362 [0.5 7.17001026285659 4.50254094746607 0.5 0.5] 1.0560446871397 8.62384487694112 5.88092582105052 [0.219186522743919 1 1 9006.165 0.34379145512521] [false] [0.00601838622242212 0.00337470835074782 0.32374519109726] [false] [946.939490196078 511.895188235294 300.985831372549 766.765580392157 2374.81912941177 7195.73965882353] [852.090074509804 486.704050980392 164.484894117647 919.983764705882 2128.1578627451 6983.008] [402.485198974609 1193.08361816406 1775.759765625] [0 0 18.3555889129639 402.485198974609 1193.08361816406 1775.759765625 2462.39697265625 4723.47265625] [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 [0.0195881109684706 0.0625562444329262 0.067560575902462 0 0] [0.0773504409087854 0 0.0773504409087854 0;0.184633179443652 0.00792357500861673 0.192556754452269 1689.6865234375;0.184633179443652 0.00792357500861673 0.192556754452269 1689.6865234375] [0.0432153679430485 0.079458937048912 0.0872549489140511] [0.0310068298131227 0.0373095646500587 0.0458771996200085] 0.0872549489140511

0.067560575902462

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 [0.00897309929132462 0.0317607447504997 0.0427804328501225 0.0496967285871506 0.054763600230217 0.0610250048339367] [0.078642610120131 0 0.078642610120131 0;0.204733745421245 0.0115655563186813 0.216299301739927 5920.119140625;0.18657447788143 0.0140555706874764 0.200630048568907 10115.962890625;0.169033648281695 0.0160987578679127 0.185132406149608 17358.83984375;0.156463668281931 0.0170891640902379 0.173552832372168 29894.98046875;0.156463668281931 0.0170891640902379 0.173552832372168 29894.98046875] [0.0104040270671248 0.0364638678729534 0.0531528741121292 0.0758167281746864 0.0997028350830078 0.104739457368851] [0.00306457909755409 0.0117224706336856 0.0261849481612444 0.0466329157352448 0.0654779151082039 0.0699285119771957] 0.104739457368851

0.0610250048339367

------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./execute/dir_1457/ds/sub-11/sub-11_ses-01_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 72s APP: Rough bias correction: Initialize 6s Estimate background 6s Initial correction 6s Refine background 3s Final correction 5s Final scaling 6s 38s Correct center-of-mass 3s Affine registration 10s SPM preprocessing 1 (estimate 1 - TPM registration): 71s SPM preprocessing 1 (estimate 2): 58s SPM preprocessing 2 (write): Write Segmentation 17s Update Segmentation 19s Update Skull-Stripping 41s Update probability maps 8s 85s Global intensity correction: 16s SANLM denoising after intensity normalization (medium): 20s Fast Optimized Shooting registration 32s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 2s Prepare segments (LASmod = 1.00) 15s Estimate local tissue thresholds (WM) 19s Estimate local tissue thresholds (GM) 26s Intensity transformation 0s SANLM denoising after LAS (medium) 34s 103s ROI segmentation (partitioning): Atlas -> subject space 7s Major structures 4s Ventricle detection 17s Blood vessel detection 9s WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 26s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 3s Final corrections 4s 72s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 32s AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.99 0.04] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 4s Level 1 cleanup (brain masking) 3s Level 2 cleanup (CSF correction) 2s Level 3 cleanup (CSF/WM PVE) 3s 11s 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 | 0.0786 0.0000 0.0786 | 32.0000 2 | 2.50 | 0.0763 0.0011 0.0773 | 29.4886 3 | 2.50 | 0.0756 0.0016 0.0772 | 26.9772 4 | 2.50 | 0.0753 0.0018 0.0771 | 24.6107 5 | 2.50 | 0.0750 0.0019 0.0769 | 22.6548 6 | 2.50 | 0.0748 0.0020 0.0768 | 20.6989 7 | 2.50 | 0.0746 0.0021 0.0766 | 18.9688 8 | 2.50 | 0.0743 0.0021 0.0764 | 17.4455 9 | 2.50 | 0.0741 0.0022 0.0763 | 15.9223 10 | 2.50 | 0.0738 0.0023 0.0761 | 14.6627 11 | 2.50 | 0.0735 0.0023 0.0759 | 13.4764 12 | 2.50 | 0.0733 0.0024 0.0757 | 12.3015 13 | 2.50 | 0.0730 0.0025 0.0755 | 11.3776 14 | 2.50 | 0.0727 0.0025 0.0752 | 10.4537 15 | 2.25 | 0.0709 0.0026 0.0734 | 9.5920 16 | 2.25 | 0.0682 0.0039 0.0721 | 8.8725 29 | 2.00 | 0.0693 0.0017 0.0711 | 3.3283 30 | 2.00 | 0.0640 0.0038 0.0678 | 3.1221 31 | 2.00 | 0.0622 0.0047 0.0669 | 2.9160 43 | 1.75 | 0.0614 0.0027 0.0641 | 1.5785 44 | 1.75 | 0.0576 0.0047 0.0623 | 1.5194 45 | 1.75 | 0.0563 0.0054 0.0617 | 1.4626 57 | 1.50 | 0.0549 0.0039 0.0588 | 1.0900 58 | 1.50 | 0.0522 0.0057 0.0579 | 1.0730 Shooting registration with 2.50:-0.25:1.50 mm takes: 133s Prepare output 10s 143s Jacobian determinant (RMS): 0.010 0.036 0.053 0.076 0.100 | 0.104739 Template Matching: 0.079 0.205 0.187 0.169 0.156 | 0.156464 Write result maps: 23s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 31s CSF distance: 16s PBT2x thickness: 48s 101s Create initial surface 94s Topology correction: 115s Surface refinement: 106s Reduction of surface collisions with optimization: 90s Spherical mapping with areal smoothing 104s Spherical registration 271s rh: Thickness estimation (0.50 mm ): WM distance: 30s CSF distance: 16s PBT2x thickness: 47s 100s Create initial surface 90s Topology correction: 105s Surface refinement: 95s Reduction of surface collisions with optimization: 86s Spherical mapping with areal smoothing 92s Spherical registration 287s Final surface processing results: Average thickness (FS): 2.6066 0.6450 mm Surface intensity / position RMSE: 0.0752 / 0.0830 Euler number / defect number / defect size: 30.0 / 15.5 / 1.19% Display thickness: /var/lib/condor/execute/dir_1457/ds/sub-11/surf/lh.thickness.sub-11_ses-01_T1w Display thickness: /var/lib/condor/execute/dir_1457/ds/sub-11/surf/rh.thickness.sub-11_ses-01_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_1457/ds/sub-11/sub-11_ses-01_T1w.nii Surface ROI estimation: 8s Surface and thickness estimation takes: 1833s ROI estimation in native space: ROI estimation of 'cobra' atlas 8s ROI estimation of 'neuromorphometrics' atlas 28s ROI estimation of 'lpba40' atlas 8s ROI estimation of 'hammers' atlas 20s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 7s ROI estimation of 'aal3' atlas 11s ROI estimation of 'mori' atlas 17s ROI estimation of 'anatomy3' atlas 24s ROI estimation of 'julichbrain' atlas 32s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 13s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 23s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 51s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 76s Write results 77s 322s Quality check: 5s Print 'Graphics' figure to: /var/lib/condor/execute/dir_1457/ds/sub-11/report/catreport_sub-11_ses-01_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 50 minute(s) and 25 second(s). Image Quality Rating (IQR): 84.51% (B) GM volume (GMV): 51.89% (803.90 / 1549.10 ml) GM thickness (GMT): 2.61 0.65 mm Segmentations are saved in /var/lib/condor/execute/dir_1457/ds/sub-11/mri Reports are saved in /var/lib/condor/execute/dir_1457/ds/sub-11/report Labels are saved in /var/lib/condor/execute/dir_1457/ds/sub-11/label ------------------------------------------------------------------------