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-15.5465538879023] [0.187710025415466 0.0350114648635582 0.032474473225996] [1.00870576145466 1.02944921468193 1.06482986266295] [0.0111044780233938 -0.00164612003961391 -0.00327703926523263] [3.68543555372403 -2.80634554552017 -15.5465538879023] [0.187710025415466 0.0350114648635582 0.032474473225996] [1.00870576145466 1.02944921468193 1.06482986266295] [0.0111044780233938 -0.00164612003961391 -0.00327703926523263] /var/lib/condor/execute/dir_57709/ds/sub-season117 sub-season117_ses-3_acq-MPrageHiRes_T1w /var/lib/condor/execute/dir_57709/ds/sub-season117/sub-season117_ses-3_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_57709/ds/sub-season117/sub-season117_ses-3_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_57709/ds/sub-season117/mri/msub-season117_ses-3_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_57709/ds/sub-season117/mri/p0sub-season117_ses-3_acq-MPrageHiRes_T1w.nii ..s/sub-season117/..son117_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 64 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 20 0.415792273939194 13.5 0.0659656971693039 0.0708039551973343 [0.87999747821453 0.87499999269616 0.875000003092694] [0.879997478411085 0.874999993040985 0.875000003554054] 0.876668990040222 0 [9.7790002822876 349.07568359375 924.050842285156 1322.38684082031] [0.0073949615471065 0.263973951339722 0.698774933815002 0.999999940395355] T1 [32.3848077392162 163.632803614319 126.017253462663 70.8900605671987] [0.0246721114963293 0.124662362039089 0.0960052534937859 0.0540070347487926] 401.303680419922 0.303469181060791 0.102763414382935 0.295623272657394 [1.75999495642906 1.74999998539232 1.75000000618539] 1.75333798008044 0.5 [8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 3.53129577636719 1.80625057220459 1.19301402568817 1.91836734693878 1.1039480684848 1.675 1.31931400299072 1.41607904434204 1.78116775803497 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 20220712-175728 1639 1639 20 0.415792273939194 13.5 0.0659656971693039 0.0708039551973343 20 0.415792273939194 [228.630712632356 773.156513294986 635.696181597981 0 0] 1.01909811507512 0.000622356300156499 2172.62477033171 1637.48340752532 [0.139623224016589 0.472161433662056 0.388215342321354 0 0] [2.52953319162661 0.625522681398271] [2.51588988304138 0.814094144826674 1] [1.93315772975661 0.258381650712872 0.302509877360861;2.55043574121434 0.178656490936907 0.434158540205997;3.22481696939364 0.29781899472532 0.263331582433142] [0.814583467608341 0.36198456938876 0.50954954954955;4.2691575202059 0.361058746788359 0.49045045045045] 2.23194211869383 [0.5 6.3297671275513 4.82211462502432 0.5 0.5] 1.06223563001565 8.62384430269628 5.24626524505344 [0.207451616014753 1 1 7838.83034749512 0.34638025712689] [false] [0.00652296468615532 0 0.252866685390472] [false] [950.315491994778 559.240122888292 338.046606033728 1107.9319297884 2509.21525802792 5134.3788038557] [851.226946352875 531.532043406942 209.438380687006 1390.19077970018 2263.12997352771 4645.34086744512] [436.767211914062 956.711975097656 1308.95520019531] [0 0 19.2380771636963 436.767211914062 956.711975097656 1308.95520019531 1745.04919433594 3778.30859375] [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 [0.0194970611482859 0.0684942081570625 0.0748492032289505 0 0] [0.0795331132941458 0 0.0795331132941458 0;0.187436803334615 0.00933177073319562 0.196768574067811 1989.9814453125;0.187436803334615 0.00933177073319562 0.196768574067811 1989.9814453125] [0.0414024665951729 0.0889216363430023 0.0989398211240768] [0.029555169865489 0.0413021817803383 0.0510010942816734] 0.0989398211240768

0.0748492032289505

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 [0.00939894467592239 0.0342903286218643 0.0484150461852551 0.0571182295680046 0.0636992901563644 0.0716866627335548] [0.0823604408110521 0 0.0823604408110521 0;0.217413018925519 0.0127114392551893 0.230124458180708 6506.66796875;0.196851483649015 0.0160753374700575 0.212926821119073 11569.61328125;0.17636848877185 0.0186180158218427 0.194986504593692 20075.28515625;0.159185388826612 0.0218853435563034 0.181070732382915 38285.19140625;0.159185388826612 0.0218853435563034 0.181070732382915 38285.19140625] [0.0108541585505009 0.0392010100185871 0.0590683631598949 0.0844663307070732 0.109380297362804 0.117669641971588] [0.00329788541421294 0.0126481130719185 0.0281205475330353 0.0491769313812256 0.0695087015628815 0.075212374329567] 0.117669641971588

0.0716866627335548

------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./sub-season117_ses-3_acq-MPrageHiRes_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 31s APP: Rough bias correction: Initialize 9s Estimate background 11s Initial correction 32s Refine background 5s Final correction 21s Final scaling 12s 99s Correct center-of-mass 2s Affine registration 18s SPM preprocessing 1 (estimate 1 - TPM registration): 125s SPM preprocessing 1 (estimate 2): 111s SPM preprocessing 2 (write): Write Segmentation 26s Update Segmentation 33s Update Skull-Stripping 67s Update probability maps 13s 139s Global intensity correction: 24s SANLM denoising after intensity normalization (medium): 15s Fast Optimized Shooting registration 43s Local adaptive segmentation (LASstr=0.50): Prepare maps 7s Prepare partitions 4s Prepare segments (LASmod = 1.06) 27s Estimate local tissue thresholds (WM) 35s Estimate local tissue thresholds (GM) 49s Intensity transformation 0s SANLM denoising after LAS (medium) 39s 167s ROI segmentation (partitioning): Atlas -> subject space 13s Major structures 7s Ventricle detection 24s Blood vessel detection 20s WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 56s Manual stroke lesion detection 0s Closing of deep structures 3s Side alignment 6s Final corrections 7s 136s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 52s 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 22s 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 | 0.0824 0.0000 0.0824 | 32.0000 2 | 2.50 | 0.0798 0.0012 0.0810 | 29.4886 3 | 2.50 | 0.0791 0.0017 0.0808 | 26.9772 4 | 2.50 | 0.0787 0.0020 0.0806 | 24.6107 5 | 2.50 | 0.0784 0.0021 0.0805 | 22.6548 6 | 2.50 | 0.0781 0.0022 0.0803 | 20.6989 7 | 2.50 | 0.0779 0.0023 0.0801 | 18.9688 8 | 2.50 | 0.0776 0.0024 0.0799 | 17.4455 9 | 2.50 | 0.0773 0.0024 0.0797 | 15.9223 10 | 2.50 | 0.0770 0.0025 0.0795 | 14.6627 11 | 2.50 | 0.0767 0.0026 0.0793 | 13.4764 12 | 2.50 | 0.0764 0.0027 0.0790 | 12.3015 13 | 2.50 | 0.0761 0.0028 0.0788 | 11.3776 14 | 2.50 | 0.0757 0.0028 0.0786 | 10.4537 15 | 2.25 | 0.0753 0.0029 0.0782 | 9.5920 16 | 2.25 | 0.0725 0.0042 0.0767 | 8.8725 29 | 2.00 | 0.0737 0.0019 0.0757 | 3.3283 30 | 2.00 | 0.0677 0.0043 0.0721 | 3.1221 31 | 2.00 | 0.0656 0.0054 0.0710 | 2.9160 43 | 1.75 | 0.0646 0.0031 0.0677 | 1.5785 44 | 1.75 | 0.0603 0.0054 0.0656 | 1.5194 45 | 1.75 | 0.0588 0.0062 0.0650 | 1.4626 57 | 1.50 | 0.0574 0.0045 0.0619 | 1.0900 58 | 1.50 | 0.0541 0.0066 0.0607 | 1.0730 59 | 1.50 | 0.0531 0.0073 0.0604 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 185s Prepare output 16s 201s Jacobian determinant (RMS): 0.011 0.039 0.059 0.084 0.109 | 0.117670 Template Matching: 0.082 0.217 0.197 0.176 0.159 | 0.159185 Write result maps: 40s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 47s CSF distance: 21s PBT2x thickness: 60s 136s Create initial surface 109s Topology correction: 121s Surface refinement: 89s Reduction of surface collisions with optimization: 86s Spherical mapping with areal smoothing 98s Spherical registration 294s rh: Thickness estimation (0.50 mm ): WM distance: 47s CSF distance: 17s PBT2x thickness: 51s 121s Create initial surface 90s Topology correction: 105s Surface refinement: 81s Reduction of surface collisions with optimization: 75s Spherical mapping with areal smoothing 93s Spherical registration 282s Final surface processing results: Average thickness (FS): 2.5296 0.6254 mm Surface intensity / position RMSE: 0.0660 / 0.0708 Euler number / defect number / defect size: 20.0 / 13.5 / 0.42% Display thickness: /var/lib/condor/execute/dir_57709/ds/sub-season117/surf/lh.thickness.sub-season117_ses-3_acq-MPrageHiRes_T1w Display thickness: /var/lib/condor/execute/dir_57709/ds/sub-season117/surf/rh.thickness.sub-season117_ses-3_acq-MPrageHiRes_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_57709/ds/sub-season117/sub-season117_ses-3_acq-MPrageHiRes_T1w.nii Surface ROI estimation: 8s Surface and thickness estimation takes: 1896s ROI estimation in native space: ROI estimation of 'cobra' atlas 10s ROI estimation of 'neuromorphometrics' atlas 35s 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 21s ROI estimation of 'anatomy3' atlas 30s ROI estimation of 'julichbrain' atlas 39s 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 63s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 94s Write results 95s 395s Quality check: 8s Print 'Graphics' figure to: /var/lib/condor/execute/dir_57709/ds/sub-season117/report/catreport_sub-season117_ses-3_acq-MPrageHiRes_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 60 minute(s) and 51 second(s). Image Quality Rating (IQR): 87.19% (B+) GM volume (GMV): 47.22% (773.16 / 1637.48 ml) GM thickness (GMT): 2.53 0.63 mm Segmentations are saved in /var/lib/condor/execute/dir_57709/ds/sub-season117/mri Reports are saved in /var/lib/condor/execute/dir_57709/ds/sub-season117/report Labels are saved in /var/lib/condor/execute/dir_57709/ds/sub-season117/label ------------------------------------------------------------------------