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6.51974317617317] [0.151078039943967 0.00428080697309375 0.00501461564186513] [1.08071551640432 1.06483748103173 1.13585364195619] [0.00703605856025444 -0.0012518890274051 0.000104026991296836] [-2.68597019774728 11.2927663944919 6.51974317617317] [0.151078039943967 0.00428080697309375 0.00501461564186513] [1.08071551640432 1.06483748103173 1.13585364195619] [0.00703605856025444 -0.0012518890274051 0.000104026991296836] /var/lib/condor/execute/dir_10487/ds/sub-season119 sub-season119_ses-3_acq-MPrageHiRes_T1w /var/lib/condor/execute/dir_10487/ds/sub-season119/sub-season119_ses-3_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_10487/ds/sub-season119/sub-season119_ses-3_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_10487/ds/sub-season119/mri/msub-season119_ses-3_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_10487/ds/sub-season119/mri/p0sub-season119_ses-3_acq-MPrageHiRes_T1w.nii ..s/sub-season119/..son119_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 28 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 26 0.471030189268629 17 0.068073995411396 0.0658894404768944 [0.880000312132629 0.874999968686616 0.874999968286882] [0.880000311569909 0.874999974208728 0.874999970741604] 0.876669918699383 0 [12.6929998397827 283.829681396484 741.914794921875 1056.31958007812] [0.0120162507519126 0.268696814775467 0.702358305454254 1] T1 [5.73386992483465 127.64572239822 97.8332421455761 55.3453979419661] [0.00549417827278376 0.122309781610966 0.0937435403466225 0.0530318059027195] 318.228668212891 0.301261752843857 0.106415092945099 0.244899153709412 [1.76000062426526 1.74999993737323 1.74999993657376] 1.75333983739877 0.5 [8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 3.56440687179565 1.85867202281952 1.06721019744873 2.22448979591837 1.11775754731716 1.85 1.3614798784256 1.31778883934021 1.81133735395743 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 20220712-172710 1639 1639 26 0.471030189268629 17 0.068073995411396 0.0658894404768944 26 0.471030189268629 [215.395583549087 705.341906899265 490.802533025928 0 0] 0.770252361508255 0.00054568226808929 1943.46223357111 1411.54002347428 [0.152596157365007 0.499696710804685 0.347707131830308 0 0] [2.63428644680012 0.605930118135362] [2.62789368629456 0.76773790669191 1] [2.07898610326925 0.249406017240555 0.308928334292417;2.66198905867033 0.172189775211573 0.417549340129129;3.30749078593938 0.269686704676129 0.273522325578454] [0.91978964246146 0.418428495533692 0.581732220098582;4.22456260000415 0.321813688886777 0.418267779901418] 1.00317216616329 [0.590448228538204 6.82429437508414 4.09459647683743 0.5 0.5] 1.05456822680893 8.61816048691611 5.59230402962016 [0.0295042991638184 1 11439 9598.87786452427 0.383849892671087] [false] [0.00923822447657585 0.0046076150611043 0.24382272362709] [false] [808.711452112201 444.419128168797 344.310341027756 520.687520908097 1766.81021931057 6414.46152055797] [725.807143087962 420.814097168914 213.380164202509 439.329484436985 1513.44450549107 6578.12986674312] [330.914306640625 772.985778808594 1029.61669921875] [0 0 33.5727157592773 330.914306640625 772.985778808594 1029.61669921875 1378.96789550781 2869.97021484375] [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 [0.0213026516139507 0.0699607580900192 0.0763243362307549 0 0] [0.0807750712589723 0 0.0807750712589723 0;0.190558022525416 0.00894153017957671 0.199499552704993 1906.76342773438;0.190558022525416 0.00894153017957671 0.199499552704993 1906.76342773438] [0.0464037954807281 0.0897884741425514 0.0989421829581261] [0.0331837385892868 0.0402473472058773 0.049701813608408] 0.0989421829581261

0.0763243362307549

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 [0.0098236994817853 0.0346967540681362 0.0472676157951355 0.0547923184931278 0.0596574395895004 0.0659661814570427] [0.0802807679046522 0 0.0802807679046522 0;0.207885973748474 0.0120565342643468 0.219942508012821 6171.4384765625;0.18798776020825 0.0144905482809443 0.202478308489194 10429.021484375;0.169292786861757 0.0164665175072941 0.185759304369051 17755.384765625;0.156004319882837 0.0172892302450535 0.17329355012789 30244.966796875;0.156004319882837 0.0172892302450535 0.17329355012789 30244.966796875] [0.0112536055967212 0.0392004959285259 0.0565431974828243 0.0781412869691849 0.0988138318061829 0.10305006057024] [0.00315396743826568 0.0117053994908929 0.0253027211874723 0.0441553741693497 0.0611403249204159 0.0649576634168625] 0.10305006057024

0.0659661814570427

------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./sub-season119_ses-3_acq-MPrageHiRes_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 60s APP: Rough bias correction: Initialize 9s Estimate background 9s Initial correction 14s Refine background 5s Final correction 12s Final scaling 12s 70s Correct center-of-mass 7s Affine registration 20s SPM preprocessing 1 (estimate 1 - TPM registration): 104s SPM preprocessing 1 (estimate 2): 106s SPM preprocessing 2 (write): Write Segmentation 24s Update Segmentation 27s Update Skull-Stripping 57s Update probability maps 12s 119s Global intensity correction: 22s SANLM denoising after intensity normalization (medium): 18s Fast Optimized Shooting registration 46s Local adaptive segmentation (LASstr=0.50): Prepare maps 6s Prepare partitions 4s Prepare segments (LASmod = 1.03) 20s Estimate local tissue thresholds (WM) 26s Estimate local tissue thresholds (GM) 37s Intensity transformation 0s SANLM denoising after LAS (medium) 36s 134s ROI segmentation (partitioning): Atlas -> subject space 12s Major structures 5s Ventricle detection 19s Blood vessel detection 14s WMH detection (WMHCstr=0.50 > WMHCstr'=0.02) 41s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 5s Final corrections 6s 105s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 40s 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) 6s Level 1 cleanup (brain masking) 4s Level 2 cleanup (CSF correction) 2s Level 3 cleanup (CSF/WM PVE) 4s 16s 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 | 0.0803 0.0000 0.0803 | 32.0000 2 | 2.50 | 0.0779 0.0011 0.0790 | 29.4886 3 | 2.50 | 0.0772 0.0017 0.0789 | 26.9772 4 | 2.50 | 0.0768 0.0019 0.0787 | 24.6107 5 | 2.50 | 0.0766 0.0020 0.0786 | 22.6548 6 | 2.50 | 0.0763 0.0021 0.0784 | 20.6989 7 | 2.50 | 0.0761 0.0022 0.0783 | 18.9688 8 | 2.50 | 0.0758 0.0023 0.0781 | 17.4455 9 | 2.50 | 0.0756 0.0023 0.0779 | 15.9223 10 | 2.50 | 0.0753 0.0024 0.0777 | 14.6627 11 | 2.50 | 0.0750 0.0025 0.0775 | 13.4764 12 | 2.50 | 0.0747 0.0025 0.0773 | 12.3015 13 | 2.50 | 0.0744 0.0026 0.0771 | 11.3776 14 | 2.50 | 0.0742 0.0027 0.0768 | 10.4537 15 | 2.25 | 0.0720 0.0027 0.0747 | 9.5920 16 | 2.25 | 0.0693 0.0040 0.0733 | 8.8725 29 | 2.00 | 0.0700 0.0018 0.0718 | 3.3283 30 | 2.00 | 0.0645 0.0039 0.0685 | 3.1221 31 | 2.00 | 0.0627 0.0048 0.0675 | 2.9160 43 | 1.75 | 0.0615 0.0028 0.0643 | 1.5785 44 | 1.75 | 0.0577 0.0048 0.0625 | 1.5194 45 | 1.75 | 0.0564 0.0055 0.0619 | 1.4626 57 | 1.50 | 0.0548 0.0040 0.0587 | 1.0900 58 | 1.50 | 0.0520 0.0058 0.0578 | 1.0730 Shooting registration with 2.50:-0.25:1.50 mm takes: 189s Prepare output 13s 202s Jacobian determinant (RMS): 0.011 0.039 0.057 0.078 0.099 | 0.103050 Template Matching: 0.080 0.208 0.188 0.169 0.156 | 0.156004 Write result maps: 38s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 44s CSF distance: 17s PBT2x thickness: 51s 119s Create initial surface 85s Topology correction: 94s Surface refinement: 79s Reduction of surface collisions with optimization: 62s Spherical mapping with areal smoothing 90s Spherical registration 263s rh: Thickness estimation (0.50 mm ): WM distance: 53s CSF distance: 16s PBT2x thickness: 49s 124s Create initial surface 80s Topology correction: 92s Surface refinement: 77s Reduction of surface collisions with optimization: 62s Spherical mapping with areal smoothing 90s Spherical registration 259s Final surface processing results: Average thickness (FS): 2.6344 0.6058 mm Surface intensity / position RMSE: 0.0681 / 0.0659 Euler number / defect number / defect size: 26.0 / 17.0 / 0.47% Display thickness: /var/lib/condor/execute/dir_10487/ds/sub-season119/surf/lh.thickness.sub-season119_ses-3_acq-MPrageHiRes_T1w Display thickness: /var/lib/condor/execute/dir_10487/ds/sub-season119/surf/rh.thickness.sub-season119_ses-3_acq-MPrageHiRes_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_10487/ds/sub-season119/sub-season119_ses-3_acq-MPrageHiRes_T1w.nii Surface ROI estimation: 8s Surface and thickness estimation takes: 1682s ROI estimation in native space: ROI estimation of 'cobra' atlas 18s 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 27s ROI estimation of 'mori' atlas 40s ROI estimation of 'anatomy3' atlas 58s ROI estimation of 'julichbrain' atlas 77s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 28s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 38s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 125s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 183s Write results 184s 744s Quality check: 6s Print 'Graphics' figure to: /var/lib/condor/execute/dir_10487/ds/sub-season119/report/catreport_sub-season119_ses-3_acq-MPrageHiRes_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 61 minute(s) and 47 second(s). Image Quality Rating (IQR): 86.89% (B+) GM volume (GMV): 49.97% (705.34 / 1411.54 ml) GM thickness (GMT): 2.63 0.61 mm Segmentations are saved in /var/lib/condor/execute/dir_10487/ds/sub-season119/mri Reports are saved in /var/lib/condor/execute/dir_10487/ds/sub-season119/report Labels are saved in /var/lib/condor/execute/dir_10487/ds/sub-season119/label ------------------------------------------------------------------------