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[0.113104808324257 -0.0302373243682009 0.0585427003126773] [1.04300541115833 0.971024440745681 1.08940675120755] [-0.00654065507090229 0.00474731201293253 0.0565624155234998] [-2.89229012993834 -10.760035723789 -42.1278630686357] [0.113104808324257 -0.0302373243682009 0.0585427003126773] [1.04300541115833 0.971024440745681 1.08940675120755] [-0.00654065507090229 0.00474731201293253 0.0565624155234998] /var/lib/condor/execute/dir_11856/ds/sub-season102 sub-season102_ses-1_acq-MPrageHiRes_T1w /var/lib/condor/execute/dir_11856/ds/sub-season102/sub-season102_ses-1_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_11856/ds/sub-season102/sub-season102_ses-1_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_11856/ds/sub-season102/mri/msub-season102_ses-1_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_11856/ds/sub-season102/mri/p0sub-season102_ses-1_acq-MPrageHiRes_T1w.nii ..s/sub-season102/..son102_ses-1_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 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 6 0.0897510648877681 7 0.0618025064468384 0.0592489391565323 [0.880001085138604 0.874999985114089 0.875000031544782] [0.880001084567847 0.874999984718353 0.875000034588071] 0.876670203858164 0 [9.64000034332275 326.269470214844 874.493530273438 1241.46374511719] [0.00776502722874284 0.262810289859772 0.704405188560486 0.999999940395355] T1 [59.0360976354571 136.598290325989 113.971602565132 64.1347920670682] [0.0479257665574551 0.110891103744507 0.0925226584076881 0.052064910531044] 369.842071533203 0.297908067703247 0.104034133255482 0.342988163232803 [1.76000217027721 1.74999997022818 1.75000006308956] 1.75334040771633 0.5 [8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 3.61471247673035 1.82449221611023 1.31048655509949 1.20408163265306 1.02243776622194 1.35 1.23605012893677 1.184978723526 1.7913830467905 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 20220712-181228 1639 1639 6 0.0897510648877681 7 0.0618025064468384 0.0592489391565323 6 0.0897510648877681 [253.981359288085 793.407124703125 619.409106197429 0 0] 1.23115945138478 0.00073863764780548 2227.49724892944 1666.79759018864 [0.152376845744864 0.476006882523349 0.371616271731787 0 0] [2.56530736488118 0.590342953239731] [2.5663685798645 0.710094127323198 1] [1.97784313055483 0.238481263332384 0.283440160295794;2.57046571919303 0.168152003110027 0.424839206048731;3.18579730001513 0.249485474608859 0.291720633655475] [0.924061056658816 0.395862012821314 0.545714030862546;4.08931978283007 0.365990521139158 0.454285969137454] 2.52051032975925 [0.586509442256893 6.39883050508889 4.52399913311399 0.5 0.5] 1.07386376478055 8.62394141664225 5.27250213487135 [0.254767486027309 1 1 7370.87532818575 0.307907428196062] [false] [0.00731452461332083 0 0.338345289230347] [false] [948.744968862865 547.195195946309 413.744959137307 513.151162864622 1917.26843543053 6125.72857048625] [838.228957178395 519.561643225367 256.453353781424 530.577728476709 1415.50074754776 6330.42361018354] [410.561401367188 906.107604980469 1230.60595703125] [0 0 23.1649742126465 410.561401367188 906.107604980469 1230.60595703125 1640.62817382812 2694.13354492188] [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 [0.0204503294080496 0.0674047768115997 0.0731644853949547 0 0] [0.0813701457145358 0 0.0813701457145358 0;0.194975707568184 0.00893423394137929 0.203909941509563 1905.20751953125;0.194975707568184 0.00893423394137929 0.203909941509563 1905.20751953125] [0.0431797280907631 0.0852848887443542 0.0939331203699112] [0.0306115243583918 0.0394845344126225 0.0484254583716393] 0.0939331203699112

0.0731644853949547

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 [0.00929920095950365 0.0328448861837387 0.0448141135275364 0.0525176003575325 0.0585501790046692 0.0651033222675323] [0.0816123525528528 0 0.0816123525528528 0;0.215070283882784 0.0117880713904151 0.226858355273199 6034.01904296875;0.196326295275054 0.0149142881979181 0.211240583472973 10733.9921875;0.176263285724752 0.0177948490733321 0.194058134798084 19187.6875;0.158677254533533 0.0209594231052852 0.179636677638818 36665.4296875;0.158677254533533 0.0209594231052852 0.179636677638818 36665.4296875] [0.0106100142002106 0.0368716269731522 0.0535049811005592 0.0764260515570641 0.0994382575154305 0.106667101383209] [0.00309705315157771 0.0116917649284005 0.0260947942733765 0.0464084297418594 0.0647245943546295 0.0704523846507072] 0.106667101383209

0.0651033222675323

------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./sub-season102_ses-1_acq-MPrageHiRes_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 28s APP: Rough bias correction: Initialize 10s Estimate background 12s Initial correction 24s Refine background 5s Final correction 18s Final scaling 11s 90s Correct center-of-mass 3s Affine registration 15s SPM preprocessing 1 (estimate 1 - TPM registration): 139s SPM preprocessing 1 (estimate 2): 122s SPM preprocessing 2 (write): Write Segmentation 27s Update Segmentation 34s Update Skull-Stripping 69s Update probability maps 13s 144s Global intensity correction: 26s SANLM denoising after intensity normalization (medium): 14s Fast Optimized Shooting registration 47s Local adaptive segmentation (LASstr=0.50): Prepare maps 9s Prepare partitions 4s Prepare segments (LASmod = 1.00) 29s Estimate local tissue thresholds (WM) 29s Estimate local tissue thresholds (GM) 40s Intensity transformation 0s SANLM denoising after LAS (medium) 34s 151s ROI segmentation (partitioning): Atlas -> subject space 15s Major structures 7s Ventricle detection 28s Blood vessel detection 18s WMH detection (WMHCstr=0.50 > WMHCstr'=0.03) 54s Manual stroke lesion detection 0s Closing of deep structures 3s Side alignment 8s Final corrections 8s 142s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 68s 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) 8s Level 1 cleanup (brain masking) 5s Level 2 cleanup (CSF correction) 3s Level 3 cleanup (CSF/WM PVE) 5s 21s 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 | 0.0816 0.0000 0.0816 | 32.0000 2 | 2.50 | 0.0793 0.0011 0.0803 | 29.4886 3 | 2.50 | 0.0786 0.0016 0.0802 | 26.9772 4 | 2.50 | 0.0783 0.0018 0.0801 | 24.6107 5 | 2.50 | 0.0780 0.0019 0.0799 | 22.6548 6 | 2.50 | 0.0778 0.0020 0.0798 | 20.6989 7 | 2.50 | 0.0775 0.0021 0.0796 | 18.9688 8 | 2.50 | 0.0773 0.0022 0.0795 | 17.4455 9 | 2.50 | 0.0770 0.0022 0.0793 | 15.9223 10 | 2.50 | 0.0767 0.0023 0.0791 | 14.6627 11 | 2.50 | 0.0765 0.0024 0.0789 | 13.4764 12 | 2.50 | 0.0762 0.0025 0.0787 | 12.3015 13 | 2.50 | 0.0759 0.0025 0.0785 | 11.3776 14 | 2.50 | 0.0757 0.0026 0.0783 | 10.4537 15 | 2.25 | 0.0743 0.0027 0.0769 | 9.5920 16 | 2.25 | 0.0717 0.0039 0.0756 | 8.8725 29 | 2.00 | 0.0730 0.0018 0.0748 | 3.3283 30 | 2.00 | 0.0674 0.0040 0.0714 | 3.1221 31 | 2.00 | 0.0654 0.0050 0.0704 | 2.9160 43 | 1.75 | 0.0646 0.0029 0.0674 | 1.5785 44 | 1.75 | 0.0602 0.0051 0.0653 | 1.5194 45 | 1.75 | 0.0588 0.0059 0.0647 | 1.4626 57 | 1.50 | 0.0571 0.0043 0.0613 | 1.0900 58 | 1.50 | 0.0539 0.0063 0.0603 | 1.0730 59 | 1.50 | 0.0529 0.0070 0.0599 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 225s Prepare output 14s 239s Jacobian determinant (RMS): 0.011 0.037 0.054 0.076 0.099 | 0.106667 Template Matching: 0.082 0.215 0.196 0.176 0.159 | 0.158677 Write result maps: 43s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 51s CSF distance: 25s PBT2x thickness: 65s 150s Create initial surface 111s Topology correction: 126s Surface refinement: 113s Reduction of surface collisions with optimization: 112s Spherical mapping with areal smoothing 112s Spherical registration 264s rh: Thickness estimation (0.50 mm ): WM distance: 43s CSF distance: 21s PBT2x thickness: 63s 137s Create initial surface 111s Topology correction: 126s Surface refinement: 122s Reduction of surface collisions with optimization: 110s Spherical mapping with areal smoothing 109s Spherical registration 258s Final surface processing results: Average thickness (FS): 2.5653 0.5902 mm Surface intensity / position RMSE: 0.0618 / 0.0592 Euler number / defect number / defect size: 6.0 / 7.0 / 0.09% Display thickness: /var/lib/condor/execute/dir_11856/ds/sub-season102/surf/lh.thickness.sub-season102_ses-1_acq-MPrageHiRes_T1w Display thickness: /var/lib/condor/execute/dir_11856/ds/sub-season102/surf/rh.thickness.sub-season102_ses-1_acq-MPrageHiRes_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_11856/ds/sub-season102/sub-season102_ses-1_acq-MPrageHiRes_T1w.nii Surface ROI estimation: 8s Surface and thickness estimation takes: 2086s ROI estimation in native space: ROI estimation of 'cobra' atlas 17s ROI estimation of 'neuromorphometrics' atlas 65s ROI estimation of 'lpba40' atlas 19s ROI estimation of 'hammers' atlas 46s ROI estimation of 'thalamus' atlas 3s ROI estimation of 'ibsr' atlas 16s ROI estimation of 'aal3' atlas 26s ROI estimation of 'mori' atlas 39s ROI estimation of 'anatomy3' atlas 56s ROI estimation of 'julichbrain' atlas 76s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 34s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 43s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 148s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 220s Write results 222s 812s Quality check: 8s Print 'Graphics' figure to: /var/lib/condor/execute/dir_11856/ds/sub-season102/report/catreport_sub-season102_ses-1_acq-MPrageHiRes_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 72 minute(s) and 38 second(s). Image Quality Rating (IQR): 87.09% (B+) GM volume (GMV): 47.60% (793.41 / 1666.80 ml) GM thickness (GMT): 2.57 0.59 mm Segmentations are saved in /var/lib/condor/execute/dir_11856/ds/sub-season102/mri Reports are saved in /var/lib/condor/execute/dir_11856/ds/sub-season102/report Labels are saved in /var/lib/condor/execute/dir_11856/ds/sub-season102/label ------------------------------------------------------------------------