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-33.8057356952694] [0.0831006565905451 -0.0324528111595928 -0.0287210284758544] [1.0467992758491 0.972899804080256 1.12529649520902] [-0.0273473739616696 0.023999260210685 0.0203983400654224] [0.166535796279161 -9.04531601326368 -33.8057356952694] [0.0831006565905451 -0.0324528111595928 -0.0287210284758544] [1.0467992758491 0.972899804080256 1.12529649520902] [-0.0273473739616696 0.023999260210685 0.0203983400654224] /var/lib/condor/execute/dir_377798/ds/sub-season127 sub-season127_ses-3_acq-MPrageHiRes_T1w /var/lib/condor/execute/dir_377798/ds/sub-season127/sub-season127_ses-3_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_377798/ds/sub-season127/sub-season127_ses-3_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_377798/ds/sub-season127/mri/msub-season127_ses-3_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_377798/ds/sub-season127/mri/p0sub-season127_ses-3_acq-MPrageHiRes_T1w.nii ..s/sub-season127/..son127_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 12 0.288366650590358 18 0.0677556991577148 0.0662119090557098 [0.879998141040695 0.875000041249352 0.874999985053819] [0.879998140112651 0.875000047356633 0.874999982709038] 0.876669221973265 0 [9.90299987792969 334.443237304688 846.250549316406 1202.8134765625] [0.00823319610208273 0.278050780296326 0.703559219837189 1] T1 [20.554321989378 129.528410506596 111.502874520018 64.810649368142] [0.0172303970903158 0.108581833541393 0.0934712812304497 0.0543298497796059] 359.52294921875 0.29890164732933 0.10830894857645 0.329137563705444 [1.75999628208139 1.7500000824987 1.74999997010764] 1.75333844394653 0.5 [8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 3.59980869293213 1.88585913181305 1.27613484859467 1.51020408163265 1.07209166264759 1.9 1.3551139831543 1.3242381811142 1.82793684069946 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 20220712-180214 1639 1639 12 0.288366650590358 18 0.0677556991577148 0.0662119090557098 12 0.288366650590358 [229.61574200574 770.398107867405 568.443804202272 0 0] 0.85219950265752 0.00054333599663542 2138.10957533069 1568.45765407542 [0.14639588222807 0.491181962015763 0.362422155756166 0 0] [2.57224515425267 0.591064580345943] [2.56513428688049 0.705000922065248 1] [2.00513816721681 0.232176384938348 0.301098431472199;2.58497597343203 0.167838665968443 0.412691445863845;3.20387826461637 0.249441260988166 0.286210122663956] [0.943355182930956 0.412019512678192 0.532487822810403;4.08950295569223 0.351460347372779 0.467512177189597] 1.64699337119834 [0.5 6.67137144424863 4.35887492378172 0.5 0.5] 1.05433359966354 8.62371824095924 5.47794248534793 [0.235485008784703 1 1 7561.56741756174 0.332987487622851] [false] [0.00708739226683974 0 0.222820609807968] [false] [925.423607477202 500.958169446535 344.681132933971 818.714403366366 2662.46959788969 5316.58839895078] [831.282015653056 473.976133909033 211.772305644172 1265.15156529291 2321.77244346654 4786.75270664794] [400.971893310547 881.012512207031 1183.685546875] [0 0 19.5282859802246 400.971893310547 881.012512207031 1183.685546875 1575.04235839844 2964.49877929688] [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 [0.021118177101016 0.0750022903084755 0.0821364894509315 0 0] [0.081204314000991 0 0.081204314000991 0;0.185257983808758 0.00968718442882524 0.194945168237583 2065.77270507812;0.185257983808758 0.00968718442882524 0.194945168237583 2065.77270507812] [0.0463035441935062 0.0960628241300583 0.105165973305702] [0.0331899859011173 0.0417297929525375 0.0512371771037579] 0.105165973305702

0.0821364894509315

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 [0.0103588048368692 0.0384414494037628 0.0530784130096436 0.0604050606489182 0.0650252625346184 0.0728262066841125] [0.0823926729430749 0 0.0823926729430749 0;0.20976076007326 0.0140881820436508 0.223848942116911 7211.38818359375;0.188582746466642 0.0160071502016605 0.204589896668303 11520.5380859375;0.170110298584216 0.0173940124221903 0.187504311006407 18755.4765625;0.157038398625092 0.0181623153138618 0.175200713938953 31772.30078125;0.157038398625092 0.0181623153138618 0.175200713938953 31772.30078125] [0.0120372101664543 0.0438198894262314 0.0638512894511223 0.0875388011336327 0.110017918050289 0.114849880337715] [0.00331308203749359 0.0127156060189009 0.0272105075418949 0.0467989444732666 0.0645895823836327 0.0687049776315689] 0.114849880337715

0.0728262066841125

------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./sub-season127_ses-3_acq-MPrageHiRes_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 38s APP: Rough bias correction: Initialize 10s Estimate background 11s Initial correction 32s Refine background 5s Final correction 22s Final scaling 14s 104s Correct center-of-mass 6s Affine registration 17s SPM preprocessing 1 (estimate 1 - TPM registration): 139s SPM preprocessing 1 (estimate 2): 111s SPM preprocessing 2 (write): Write Segmentation 26s Update Segmentation 32s Update Skull-Stripping 69s Update probability maps 13s 141s 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 = 1.00) 28s Estimate local tissue thresholds (WM) 33s Estimate local tissue thresholds (GM) 48s Intensity transformation 0s SANLM denoising after LAS (medium) 38s 164s 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) 50s Manual stroke lesion detection 0s Closing of deep structures 3s Side alignment 6s Final corrections 7s 130s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 57s 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 | 0.0824 0.0000 0.0824 | 32.0000 2 | 2.50 | 0.0792 0.0013 0.0805 | 29.4886 3 | 2.50 | 0.0783 0.0020 0.0803 | 26.9772 4 | 2.50 | 0.0779 0.0022 0.0801 | 24.6107 5 | 2.50 | 0.0775 0.0024 0.0799 | 22.6548 6 | 2.50 | 0.0772 0.0025 0.0797 | 20.6989 7 | 2.50 | 0.0769 0.0026 0.0794 | 18.9688 8 | 2.50 | 0.0765 0.0027 0.0792 | 17.4455 9 | 2.50 | 0.0762 0.0027 0.0790 | 15.9223 10 | 2.50 | 0.0759 0.0029 0.0787 | 14.6627 11 | 2.50 | 0.0755 0.0029 0.0785 | 13.4764 12 | 2.50 | 0.0752 0.0030 0.0782 | 12.3015 13 | 2.50 | 0.0748 0.0031 0.0779 | 11.3776 14 | 2.50 | 0.0745 0.0032 0.0776 | 10.4537 15 | 2.25 | 0.0727 0.0032 0.0760 | 9.5920 16 | 2.25 | 0.0699 0.0047 0.0746 | 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 | 0.0629 0.0053 0.0682 | 2.9160 43 | 1.75 | 0.0618 0.0031 0.0648 | 1.5785 44 | 1.75 | 0.0579 0.0051 0.0630 | 1.5194 45 | 1.75 | 0.0567 0.0058 0.0625 | 1.4626 57 | 1.50 | 0.0552 0.0042 0.0594 | 1.0900 58 | 1.50 | 0.0523 0.0061 0.0584 | 1.0730 Shooting registration with 2.50:-0.25:1.50 mm takes: 162s Prepare output 16s 178s Jacobian determinant (RMS): 0.012 0.044 0.064 0.088 0.110 | 0.114850 Template Matching: 0.082 0.210 0.189 0.170 0.157 | 0.157038 Write result maps: 40s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 67s CSF distance: 20s PBT2x thickness: 59s 153s Create initial surface 103s Topology correction: 114s Surface refinement: 98s Reduction of surface collisions with optimization: 89s Spherical mapping with areal smoothing 99s Spherical registration 322s rh: Thickness estimation (0.50 mm ): WM distance: 48s CSF distance: 20s PBT2x thickness: 60s 136s Create initial surface 103s Topology correction: 107s Surface refinement: 119s Reduction of surface collisions with optimization: 82s Spherical mapping with areal smoothing 97s Spherical registration 290s Final surface processing results: Average thickness (FS): 2.5723 0.5909 mm Surface intensity / position RMSE: 0.0678 / 0.0662 Euler number / defect number / defect size: 12.0 / 18.0 / 0.29% Display thickness: /var/lib/condor/execute/dir_377798/ds/sub-season127/surf/lh.thickness.sub-season127_ses-3_acq-MPrageHiRes_T1w Display thickness: /var/lib/condor/execute/dir_377798/ds/sub-season127/surf/rh.thickness.sub-season127_ses-3_acq-MPrageHiRes_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_377798/ds/sub-season127/sub-season127_ses-3_acq-MPrageHiRes_T1w.nii Surface ROI estimation: 8s Surface and thickness estimation takes: 2033s ROI estimation in native space: ROI estimation of 'cobra' atlas 12s ROI estimation of 'neuromorphometrics' atlas 42s ROI estimation of 'lpba40' atlas 12s ROI estimation of 'hammers' atlas 30s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 10s ROI estimation of 'aal3' atlas 18s ROI estimation of 'mori' atlas 26s ROI estimation of 'anatomy3' atlas 31s ROI estimation of 'julichbrain' atlas 41s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 16s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 27s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 64s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 95s Write results 96s 427s Quality check: 8s Print 'Graphics' figure to: /var/lib/condor/execute/dir_377798/ds/sub-season127/report/catreport_sub-season127_ses-3_acq-MPrageHiRes_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 64 minute(s) and 1 second(s). Image Quality Rating (IQR): 86.72% (B+) GM volume (GMV): 49.12% (770.40 / 1568.46 ml) GM thickness (GMT): 2.57 0.59 mm Segmentations are saved in /var/lib/condor/execute/dir_377798/ds/sub-season127/mri Reports are saved in /var/lib/condor/execute/dir_377798/ds/sub-season127/report Labels are saved in /var/lib/condor/execute/dir_377798/ds/sub-season127/label ------------------------------------------------------------------------