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[0.180152862049689 0.0171424967938184 0.0504569249495714] [1.05813670305264 0.974684525302208 1.06701292772116] [0.0150535116108253 0.00158854650390358 -0.00329410464904019] [2.49753782872491 -6.47550318949932 -32.8886152691833] [0.180152862049689 0.0171424967938184 0.0504569249495714] [1.05813670305264 0.974684525302208 1.06701292772116] [0.0150535116108253 0.00158854650390358 -0.00329410464904019] /var/lib/condor/execute/dir_21555/ds/sub-season111 sub-season111_ses-1_acq-MPrageHiRes_T1w /var/lib/condor/execute/dir_21555/ds/sub-season111/sub-season111_ses-1_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_21555/ds/sub-season111/sub-season111_ses-1_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_21555/ds/sub-season111/mri/msub-season111_ses-1_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_21555/ds/sub-season111/mri/p0sub-season111_ses-1_acq-MPrageHiRes_T1w.nii ..s/sub-season111/..son111_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 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 14 0.215989325999584 14 0.0616380721330643 0.0603869967162609 [0.88000334242474 0.874999971248244 0.87499999653085] [0.880003342659999 0.874999969778278 0.874999996705991] 0.876670942884145 0 [11.5649995803833 340.918365478516 870.381713867188 1234.83911132812] [0.00936559215188026 0.27608323097229 0.704854309558868 1] T1 [6.07939667125965 133.413165248958 114.840802820537 66.1707066840129] [0.00496977427974343 0.109062358736992 0.0938798561692238 0.0540931113064289] 367.903015136719 0.297935992479324 0.106684632599354 0.333870500326157 [1.76000668484948 1.74999994249649 1.7499999930617] 1.75334188576829 0.5 [8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 3.61429333686829 1.86254143714905 1.28787326812744 1.61224489795918 1.0539973314999 1.7 1.23276138305664 1.20773994922638 1.81366225940123 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 20220712-171434 1639 1639 14 0.215989325999584 14 0.0616380721330643 0.0603869967162609 14 0.215989325999584 [327.854572324633 745.764699654852 598.209428313723 0 0] 0.776030810156327 0.000464180815905497 2154.34286777318 1671.82870029321 [0.196105361911261 0.446077220425788 0.357817417662951 0 0] [2.55225130011473 0.60626944525869] [2.56242346763611 0.716435883167847 1] [1.97964252839574 0.237102633779991 0.309645416779448;2.58871173680527 0.171210510611201 0.409871370906053;3.2003832226778 0.254265923810059 0.2804832123145] [0.920319492608026 0.379923663134423 0.55584872471416;4.09482879492316 0.311794915432797 0.44415127528584] 2.57197888920357 [1.37186354007294 5.86130065419878 4.27617488618805 0.5 0.5] 1.04641808159055 8.6237863856614 4.83965238321911 [0.0296556609017508 1 10892 9597.41417819258 0.33106802614096] [false] [0.00716424500569701 0.00372157525271177 0.275203615427017] [false] [897.8769874105 531.426218497235 503.149606751102 1073.18994629652 2005.62774630334 5412.88333296044] [804.524119212374 504.195001181952 315.81593827804 801.29078608884 1824.23101605607 5640.69492807813] [398.505004882812 897.412780761719 1208.98815917969] [0 0 34.2084884643555 398.505004882812 897.412780761719 1208.98815917969 1614.22973632812 3140.55126953125] [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 [0.021722624078393 0.0814946368336678 0.089623898267746 0 0] [0.0826883243531788 0 0.0826883243531788 0;0.188117367308251 0.0108510082652446 0.198968375573496 2313.95581054688;0.188117367308251 0.0108510082652446 0.198968375573496 2313.95581054688] [0.0490392260253429 0.102868095040321 0.1129195317626] [0.035261943936348 0.0447059720754623 0.0542695783078671] 0.1129195317626
0.089623898267746
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 [0.0106361601501703 0.0402546040713787 0.0573398806154728 0.0648076236248016 0.0699439272284508 0.0777257531881332] [0.0831197706973867 0 0.0831197706973867 0;0.213945833333333 0.0144046331272894 0.228350466460623 7373.37158203125;0.190440868187553 0.0170934014881994 0.207534269675752 12302.326171875;0.169867491110777 0.0185830495749217 0.188450540685699 20037.58203125;0.152776019191095 0.0208870771615277 0.173663096352623 36538.87109375;0.152776019191095 0.0208870771615277 0.173663096352623 36538.87109375] [0.0122112203389406 0.0450149774551392 0.0657950714230537 0.0880898460745811 0.106095239520073 0.112344138324261] [0.0033873813226819 0.0132008092477918 0.0271659418940544 0.0451498553156853 0.0599251687526703 0.0647284537553787] 0.112344138324261
0.0777257531881332
------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./sub-season111_ses-1_acq-MPrageHiRes_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 50s APP: Rough bias correction: Initialize 8s Estimate background 10s Initial correction 13s Refine background 4s Final correction 11s Final scaling 10s 63s Correct center-of-mass 6s Affine registration 19s SPM preprocessing 1 (estimate 1 - TPM registration): 104s SPM preprocessing 1 (estimate 2): 103s SPM preprocessing 2 (write): Write Segmentation 20s Update Segmentation 26s Update Skull-Stripping 56s Update probability maps 11s 113s Global intensity correction: 21s SANLM denoising after intensity normalization (medium): 36s Fast Optimized Shooting registration 36s Local adaptive segmentation (LASstr=0.50): Prepare maps 7s Prepare partitions 6s Prepare segments (LASmod = 1.00) 24s Estimate local tissue thresholds (WM) 25s Estimate local tissue thresholds (GM) 35s Intensity transformation 0s SANLM denoising after LAS (medium) 40s 141s ROI segmentation (partitioning): Atlas -> subject space 11s Major structures 6s Ventricle detection 27s Blood vessel detection 16s WMH detection (WMHCstr=0.50 > WMHCstr'=0.10) 46s Manual stroke lesion detection 0s Closing of deep structures 3s Side alignment 6s Final corrections 5s 119s 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) 7s Level 1 cleanup (brain masking) 4s Level 2 cleanup (CSF correction) 2s Level 3 cleanup (CSF/WM PVE) 4s 18s 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 | 0.0831 0.0000 0.0831 | 32.0000 2 | 2.50 | 0.0803 0.0012 0.0815 | 29.4886 3 | 2.50 | 0.0795 0.0019 0.0813 | 26.9772 4 | 2.50 | 0.0790 0.0021 0.0812 | 24.6107 5 | 2.50 | 0.0787 0.0023 0.0810 | 22.6548 6 | 2.50 | 0.0784 0.0024 0.0808 | 20.6989 7 | 2.50 | 0.0781 0.0025 0.0806 | 18.9688 8 | 2.50 | 0.0777 0.0026 0.0804 | 17.4455 9 | 2.50 | 0.0774 0.0027 0.0802 | 15.9223 10 | 2.50 | 0.0771 0.0029 0.0799 | 14.6627 11 | 2.50 | 0.0767 0.0030 0.0797 | 13.4764 12 | 2.50 | 0.0764 0.0030 0.0794 | 12.3015 13 | 2.50 | 0.0760 0.0032 0.0791 | 11.3776 14 | 2.50 | 0.0756 0.0032 0.0789 | 10.4537 15 | 2.25 | 0.0741 0.0033 0.0775 | 9.5920 16 | 2.25 | 0.0713 0.0048 0.0761 | 8.8725 29 | 2.00 | 0.0719 0.0022 0.0740 | 3.3283 30 | 2.00 | 0.0656 0.0047 0.0703 | 3.1221 31 | 2.00 | 0.0635 0.0057 0.0692 | 2.9160 43 | 1.75 | 0.0621 0.0033 0.0654 | 1.5785 44 | 1.75 | 0.0580 0.0054 0.0634 | 1.5194 45 | 1.75 | 0.0566 0.0062 0.0628 | 1.4626 57 | 1.50 | 0.0548 0.0045 0.0593 | 1.0900 58 | 1.50 | 0.0519 0.0064 0.0583 | 1.0730 59 | 1.50 | 0.0509 0.0070 0.0579 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 158s Prepare output 13s 170s Jacobian determinant (RMS): 0.012 0.045 0.066 0.088 0.106 | 0.112344 Template Matching: 0.083 0.214 0.190 0.170 0.153 | 0.152776 Write result maps: 30s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 43s CSF distance: 18s PBT2x thickness: 49s 116s Create initial surface 96s Topology correction: 97s Surface refinement: 112s Reduction of surface collisions with optimization: 74s Spherical mapping with areal smoothing 83s Spherical registration 273s rh: Thickness estimation (0.50 mm ): WM distance: 52s CSF distance: 16s PBT2x thickness: 46s 121s Create initial surface 90s Topology correction: 97s Surface refinement: 81s Reduction of surface collisions with optimization: 72s Spherical mapping with areal smoothing 75s Spherical registration 267s Final surface processing results: Average thickness (FS): 2.5522 0.6063 mm Surface intensity / position RMSE: 0.0616 / 0.0604 Euler number / defect number / defect size: 14.0 / 14.0 / 0.22% Display thickness: /var/lib/condor/execute/dir_21555/ds/sub-season111/surf/lh.thickness.sub-season111_ses-1_acq-MPrageHiRes_T1w Display thickness: /var/lib/condor/execute/dir_21555/ds/sub-season111/surf/rh.thickness.sub-season111_ses-1_acq-MPrageHiRes_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_21555/ds/sub-season111/sub-season111_ses-1_acq-MPrageHiRes_T1w.nii Surface ROI estimation: 7s Surface and thickness estimation takes: 1754s 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 14s ROI estimation of 'mori' atlas 20s ROI estimation of 'anatomy3' atlas 29s ROI estimation of 'julichbrain' atlas 38s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 27s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 66s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 92s Write results 92s 392s Quality check: 7s Print 'Graphics' figure to: /var/lib/condor/execute/dir_21555/ds/sub-season111/report/catreport_sub-season111_ses-1_acq-MPrageHiRes_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 55 minute(s) and 59 second(s). Image Quality Rating (IQR): 86.86% (B+) GM volume (GMV): 44.61% (745.76 / 1671.83 ml) GM thickness (GMT): 2.55 0.61 mm Segmentations are saved in /var/lib/condor/execute/dir_21555/ds/sub-season111/mri Reports are saved in /var/lib/condor/execute/dir_21555/ds/sub-season111/report Labels are saved in /var/lib/condor/execute/dir_21555/ds/sub-season111/label ------------------------------------------------------------------------