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-21.3886993818962] [0.0808784426364179 0.00734493614538172 0.0246496594081341] [1.13101106696568 1.02862519789179 1.09489267156681] [-0.00119058482288755 0.00922503079760452 -0.00522003714088933] [5.29020147872361 3.9637887128325 -21.3886993818962] [0.0808784426364179 0.00734493614538172 0.0246496594081341] [1.13101106696568 1.02862519789179 1.09489267156681] [-0.00119058482288755 0.00922503079760452 -0.00522003714088933] /var/lib/condor/execute/dir_57358/ds/sub-season214 sub-season214_ses-3_acq-MPrageHiRes_T1w /var/lib/condor/execute/dir_57358/ds/sub-season214/sub-season214_ses-3_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_57358/ds/sub-season214/sub-season214_ses-3_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_57358/ds/sub-season214/mri/msub-season214_ses-3_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_57358/ds/sub-season214/mri/p0sub-season214_ses-3_acq-MPrageHiRes_T1w.nii ..s/sub-season214/..son214_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 52 2.98340257802564 27 0.0785906985402107 0.0973872989416122 [0.880001910765747 0.875000025500278 0.875000001053985] [0.88000191071534 0.875000018663359 0.875000002630789] 0.876670483405125 0 [10.3070001602173 316.273040771484 812.005065917969 1176.57397460938] [0.00876018032431602 0.268808454275131 0.690143644809723 1] T1 [35.1193310166956 155.968592802103 110.060892366007 62.0135810756232] [0.0301125999540091 0.133733183145523 0.0943702384829521 0.0531727150082588] 367.790832519531 0.31259474158287 0.0935315936803818 0.269517242908478 [1.76000382153149 1.75000005100056 1.75000000210797] 1.75334096681025 0.5 [8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 3.39441204071045 1.67372369766235 1.12826693058014 3.55102040816327 1.74585064450641 2.35 1.57181394100189 1.94774603843689 1.71675235022411 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 20220712-174814 1639 1639 52 2.98340257802564 27 0.0785906985402107 0.0973872989416122 52 2.98340257802564 [172.74757532359 737.752791583678 512.886911647826 0 0] 0.677601110289226 0.000476048311305038 1997.77816935686 1423.38727855509 [0.121363720138731 0.518307844041281 0.360328435819988 0 0] [2.60032176457789 0.667676461586899] [2.64896941184998 0.890609451682132 1] [1.91761459050238 0.317773675051187 0.265777455772052;2.62808714047197 0.193142543618913 0.419682995920161;3.30521021126867 0.282574140802445 0.314539548307787] [0.716238222637938 0.308471229431119 0.710702188043578;4.17466589559483 0.284033403843584 0.289297811956422] 1.01302030557118 [0.5 7.15854604959198 4.32127219504288 0.5 0.5] 1.0476048311305 8.62135585120999 5.86681510460534 [0.30295991897583 1 1 6894.22471254159 0.333460500401008] [false] [0.00630701053887606 0 0.181353613734245] [false] [870.430643743956 450.397719613296 248.202509521768 635.494905904619 2248.64960991677 5998.32281529293] [787.840773855813 427.185076152545 156.7848571141 567.060493826574 1338.57860236887 6613.55999847952] [369.219909667969 850.114074707031 1162.5009765625] [0 0 14.8978309631348 369.219909667969 850.114074707031 1162.5009765625 1559.14147949219 2972.72290039062] [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 [0.0190048944205046 0.0658977404236794 0.0717149674892426 0 0] [0.0806229046794499 0 0.0806229046794499 0;0.18581955487273 0.00919555501491368 0.195015109887644 1960.93371582031;0.18581955487273 0.00919555501491368 0.195015109887644 1960.93371582031] [0.0467615313827991 0.0858950465917587 0.0944933742284775] [0.0342672988772392 0.0387771315872669 0.0474207997322083] 0.0944933742284775

0.0717149674892426

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 [0.00871637091040611 0.0322940312325954 0.0445018708705902 0.05174919962883 0.0577210448682308 0.0641828924417496] [0.0822043243805545 0 0.0822043243805545 0;0.208262820512821 0.0142725818452381 0.222535402358059 7305.77783203125;0.188546295254213 0.0158831883990575 0.20442948365327 11431.3212890625;0.169936901936617 0.0175591656285473 0.187496067565164 18933.556640625;0.153628334304168 0.0203935420159625 0.174021876320131 35675.50390625;0.153628334304168 0.0203935420159625 0.174021876320131 35675.50390625] [0.0104958200827241 0.0382802374660969 0.0555646792054176 0.0764089971780777 0.0978711619973183 0.104534387588501] [0.00322354538366199 0.0121928630396724 0.0259412564337254 0.0452000945806503 0.0635979995131493 0.0690911263227463] 0.104534387588501

0.0641828924417496

------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./sub-season214_ses-3_acq-MPrageHiRes_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 34s APP: Rough bias correction: Initialize 9s Estimate background 11s Initial correction 11s Refine background 5s Final correction 10s Final scaling 9s 64s Correct center-of-mass 5s Affine registration 15s SPM preprocessing 1 (estimate 1 - TPM registration): 123s SPM preprocessing 1 (estimate 2): 93s SPM preprocessing 2 (write): Write Segmentation 25s Update Segmentation 30s Update Skull-Stripping 66s Update probability maps 13s 135s Global intensity correction: 24s SANLM denoising after intensity normalization (medium): 14s Fast Optimized Shooting registration 43s Local adaptive segmentation (LASstr=0.50): Prepare maps 7s Prepare partitions 4s Prepare segments (LASmod = 1.00) 24s Estimate local tissue thresholds (WM) 31s Estimate local tissue thresholds (GM) 46s Intensity transformation 0s SANLM denoising after LAS (medium) 39s 156s ROI segmentation (partitioning): Atlas -> subject space 11s Major structures 6s Ventricle detection 22s Blood vessel detection 17s WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 46s Manual stroke lesion detection 0s Closing of deep structures 3s Side alignment 6s Final corrections 7s 117s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 53s 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) 7s Level 1 cleanup (brain masking) 5s Level 2 cleanup (CSF correction) 3s Level 3 cleanup (CSF/WM PVE) 5s 20s 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 | 0.0822 0.0000 0.0822 | 32.0000 2 | 2.50 | 0.0789 0.0013 0.0803 | 29.4886 3 | 2.50 | 0.0780 0.0020 0.0800 | 26.9772 4 | 2.50 | 0.0775 0.0023 0.0798 | 24.6107 5 | 2.50 | 0.0771 0.0025 0.0796 | 22.6548 6 | 2.50 | 0.0768 0.0026 0.0794 | 20.6989 7 | 2.50 | 0.0765 0.0027 0.0792 | 18.9688 8 | 2.50 | 0.0762 0.0028 0.0789 | 17.4455 9 | 2.50 | 0.0758 0.0028 0.0787 | 15.9223 10 | 2.50 | 0.0755 0.0029 0.0784 | 14.6627 11 | 2.50 | 0.0751 0.0030 0.0781 | 13.4764 12 | 2.50 | 0.0748 0.0031 0.0778 | 12.3015 13 | 2.50 | 0.0744 0.0032 0.0775 | 11.3776 14 | 2.50 | 0.0740 0.0032 0.0772 | 10.4537 15 | 2.25 | 0.0723 0.0033 0.0756 | 9.5920 16 | 2.25 | 0.0694 0.0048 0.0742 | 8.8725 29 | 2.00 | 0.0705 0.0021 0.0726 | 3.3283 30 | 2.00 | 0.0648 0.0044 0.0692 | 3.1221 31 | 2.00 | 0.0628 0.0053 0.0681 | 2.9160 43 | 1.75 | 0.0620 0.0031 0.0650 | 1.5785 44 | 1.75 | 0.0580 0.0051 0.0631 | 1.5194 45 | 1.75 | 0.0566 0.0059 0.0625 | 1.4626 57 | 1.50 | 0.0551 0.0043 0.0594 | 1.0900 58 | 1.50 | 0.0522 0.0062 0.0584 | 1.0730 59 | 1.50 | 0.0512 0.0068 0.0580 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 183s Prepare output 15s 199s Jacobian determinant (RMS): 0.010 0.038 0.056 0.076 0.098 | 0.104534 Template Matching: 0.082 0.208 0.189 0.170 0.154 | 0.153628 Write result maps: 35s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 35s CSF distance: 20s PBT2x thickness: 55s 117s Create initial surface 95s Topology correction: 121s Surface refinement: 98s Reduction of surface collisions with optimization: 84s Spherical mapping with areal smoothing 103s Spherical registration 323s rh: Thickness estimation (0.50 mm ): WM distance: 35s CSF distance: 18s PBT2x thickness: 56s 117s Create initial surface 99s Topology correction: 126s Surface refinement: 94s Reduction of surface collisions with optimization: 79s Spherical mapping with areal smoothing 97s Spherical registration 284s Final surface processing results: Average thickness (FS): 2.6003 0.6677 mm Surface intensity / position RMSE: 0.0786 / 0.0974 Euler number / defect number / defect size: 52.0 / 27.0 / 2.98% Display thickness: /var/lib/condor/execute/dir_57358/ds/sub-season214/surf/lh.thickness.sub-season214_ses-3_acq-MPrageHiRes_T1w Display thickness: /var/lib/condor/execute/dir_57358/ds/sub-season214/surf/rh.thickness.sub-season214_ses-3_acq-MPrageHiRes_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_57358/ds/sub-season214/sub-season214_ses-3_acq-MPrageHiRes_T1w.nii Surface ROI estimation: 8s Surface and thickness estimation takes: 1951s ROI estimation in native space: ROI estimation of 'cobra' atlas 10s ROI estimation of 'neuromorphometrics' atlas 36s ROI estimation of 'lpba40' atlas 10s ROI estimation of 'hammers' atlas 25s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 9s ROI estimation of 'aal3' atlas 15s ROI estimation of 'mori' atlas 21s ROI estimation of 'anatomy3' atlas 32s ROI estimation of 'julichbrain' atlas 43s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 30s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 76s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 101s Write results 102s 428s Quality check: 7s Print 'Graphics' figure to: /var/lib/condor/execute/dir_57358/ds/sub-season214/report/catreport_sub-season214_ses-3_acq-MPrageHiRes_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 60 minute(s) and 58 second(s). Image Quality Rating (IQR): 87.83% (B+) GM volume (GMV): 51.83% (737.75 / 1423.39 ml) GM thickness (GMT): 2.60 0.67 mm Segmentations are saved in /var/lib/condor/execute/dir_57358/ds/sub-season214/mri Reports are saved in /var/lib/condor/execute/dir_57358/ds/sub-season214/report Labels are saved in /var/lib/condor/execute/dir_57358/ds/sub-season214/label ------------------------------------------------------------------------