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../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 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/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 10 0.535040847298987 7.5 0.0593376792967319 0.0602942854166031 [0.999987337201291 0.999999997523243 0.999999968772942] [0.999987335858233 0.999999996276145 0.999999969891876] 0.999995767850261 0 [174.162002563477 21888.8203125 48935.43359375 69592.9375] [0.00250258157029748 0.314526468515396 0.703166663646698 1] T1 [9350.14558113272 7670.76837017026 6987.78668426642 3809.13520704705] [0.134691894054413 0.110499911010265 0.100661337375641 0.0548718310892582] 20709.33203125 0.297578066587448 0.130955338478088 0.254484623670578 [1.99997467440258 1.99999999504649 1.99999993754588] 1.99999153570052 0.5 [8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 3.61966228485107 2.2109580039978 1.09098374843597 1.40816326530612 1.13376021182475 1.375 1.18675363063812 1.20588564872742 2.12353560374783 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 20220713-013709 1639 1639 10 0.535040847298987 7.5 0.0593376792967319 0.0602942854166031 10 0.535040847298987 [294.865196938523 545.242590161713 468.886916599075 0 0] 0.831663949223186 0.000635345541790846 1680.03158204213 1308.99470369931 [0.225260802129461 0.416535367653375 0.358203830217164 0 0] [2.31180684800379 0.579203384206698] [2.30728888511658 0.718801345218795 1] [1.72235042615457 0.249759038692321 0.272488881273606;2.31745734875471 0.162677462913923 0.467358995180023;2.92519339727699 0.260175074654301 0.260152123546371] [0.807733840886294 0.229082705399161 0.518253793710139;3.96501140958015 0.431250066491595 0.481746206289861] 1.19478627333548 [1.89548854399176 5.33073576963676 4.28311476683125 0.5 0.5] 1.06353455417908 8.47278164878071 4.44756193343315 [0.566258198302469 12642 3883 4496.97790338569 0.396684026342394] [false] [0 0 0.16806735098362] [false] [656.62827381053 427.030310844985 406.460019108141 502.861136170256 2942.28812862551 5966.40999066428] [579.2751815407 402.979984866712 277.624627626298 831.051376609559 2335.67074133864 5941.28555675655] [23861.38671875 51719.12890625 67742.7890625] [0 0 611.542785644531 23861.38671875 51719.12890625 67742.7890625 89683.4921875 126781.703125] [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 [0.0232058148831129 0.088877446949482 0.0993279963731766 0 0] [0.0870250260748831 0 0.0870250260748831 0;0.197866561175251 0.0123860415290384 0.21025260270429 2641.29858398438;0.197866561175251 0.0123860415290384 0.21025260270429 2641.29858398438] [0.049008771777153 0.115826576948166 0.129271507263184] [0.0346985831856728 0.0534644275903702 0.0658428817987442] 0.129271507263184

0.0993279963731766

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 [0.0111437765881419 0.0429822988808155 0.0620075725018978 0.0708000957965851 0.0766767784953117 0.0876076966524124] [0.0863594041758807 0 0.0863594041758807 0;0.223005021367521 0.0156443242521368 0.238649345619658 8007.9384765625;0.199937831035192 0.0186669882796869 0.218604819314879 13434.85546875;0.178397270122937 0.0203675164116753 0.198764786534613 21961.72265625;0.161033054077708 0.0230786910039026 0.18411174508161 40372.77734375;0.161033054077708 0.0230786910039026 0.18411174508161 40372.77734375] [0.0126361912116408 0.0482616983354092 0.0732587575912476 0.102538838982582 0.128481477499008 0.137431770563126] [0.00368599616922438 0.0148581257089972 0.0314641669392586 0.0541537441313267 0.0743210315704346 0.0809987410902977] 0.137431770563126

0.0876076966524124

------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./dir_11915/ds/sub-035/sub-035_ses-t0_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 17s APP: Rough bias correction: Initialize 5s Estimate background 6s Initial correction 6s Refine background 3s Final correction 4s Final scaling 5s 35s Correct center-of-mass 7s Affine registration 11s SPM preprocessing 1 (estimate 1 - TPM registration): 74s SPM preprocessing 1 (estimate 2): 50s SPM preprocessing 2 (write): Write Segmentation 15s Update Segmentation 17s Update Skull-Stripping 38s Update probability maps 8s 78s Global intensity correction: 15s SANLM denoising after intensity normalization (medium): 18s Fast Optimized Shooting registration 32s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 2s Prepare segments (LASmod = 1.06) 13s Estimate local tissue thresholds (WM) 15s Estimate local tissue thresholds (GM) 20s Intensity transformation 0s SANLM denoising after LAS (medium) 29s 86s ROI segmentation (partitioning): Atlas -> subject space 7s Major structures 3s Ventricle detection 12s Blood vessel detection 8s WMH detection (WMHCstr=0.50 > WMHCstr'=0.18) 23s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 3s Final corrections 4s 61s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 32s AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.08,0.98 0.05] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 4s Level 1 cleanup (brain masking) 3s Level 2 cleanup (CSF correction) 1s Level 3 cleanup (CSF/WM PVE) 3s 11s 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 | 0.0864 0.0000 0.0864 | 32.0000 2 | 2.50 | 0.0833 0.0013 0.0846 | 29.4886 3 | 2.50 | 0.0824 0.0020 0.0844 | 26.9772 4 | 2.50 | 0.0819 0.0023 0.0842 | 24.6107 5 | 2.50 | 0.0816 0.0025 0.0840 | 22.6548 6 | 2.50 | 0.0812 0.0026 0.0838 | 20.6989 7 | 2.50 | 0.0809 0.0027 0.0836 | 18.9688 8 | 2.50 | 0.0805 0.0028 0.0833 | 17.4455 9 | 2.50 | 0.0802 0.0029 0.0831 | 15.9223 10 | 2.50 | 0.0798 0.0031 0.0828 | 14.6627 11 | 2.50 | 0.0794 0.0032 0.0825 | 13.4764 12 | 2.50 | 0.0790 0.0032 0.0822 | 12.3015 13 | 2.50 | 0.0786 0.0034 0.0819 | 11.3776 14 | 2.50 | 0.0782 0.0035 0.0816 | 10.4537 15 | 2.25 | 0.0776 0.0036 0.0811 | 9.5920 16 | 2.25 | 0.0743 0.0052 0.0795 | 8.8725 29 | 2.00 | 0.0755 0.0024 0.0779 | 3.3283 30 | 2.00 | 0.0689 0.0051 0.0740 | 3.1221 31 | 2.00 | 0.0666 0.0062 0.0729 | 2.9160 43 | 1.75 | 0.0654 0.0036 0.0690 | 1.5785 44 | 1.75 | 0.0609 0.0060 0.0669 | 1.5194 45 | 1.75 | 0.0595 0.0068 0.0663 | 1.4626 57 | 1.50 | 0.0579 0.0050 0.0628 | 1.0900 58 | 1.50 | 0.0547 0.0070 0.0618 | 1.0730 59 | 1.50 | 0.0537 0.0077 0.0614 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 167s Prepare output 10s 176s Jacobian determinant (RMS): 0.013 0.048 0.073 0.103 0.128 | 0.137432 Template Matching: 0.086 0.223 0.200 0.178 0.161 | 0.161033 Write result maps: 23s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 30s CSF distance: 14s PBT2x thickness: 38s 88s Create initial surface 71s Topology correction: 69s Surface refinement: 59s Reduction of surface collisions with optimization: 49s Spherical mapping with areal smoothing 65s Spherical registration 289s rh: Thickness estimation (0.50 mm ): WM distance: 41s CSF distance: 12s PBT2x thickness: 35s 93s Create initial surface 69s Topology correction: 70s Surface refinement: 56s Reduction of surface collisions with optimization: 52s Spherical mapping with areal smoothing 67s Spherical registration 281s Final surface processing results: Average thickness (FS): 2.3118 0.5791 mm Surface intensity / position RMSE: 0.0593 / 0.0603 Euler number / defect number / defect size: 10.0 / 7.5 / 0.54% Display thickness: /var/lib/condor/execute/dir_11915/ds/sub-035/surf/lh.thickness.sub-035_ses-t0_T1w Display thickness: /var/lib/condor/execute/dir_11915/ds/sub-035/surf/rh.thickness.sub-035_ses-t0_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_11915/ds/sub-035/sub-035_ses-t0_T1w.nii Surface ROI estimation: 8s Surface and thickness estimation takes: 1458s ROI estimation in native space: ROI estimation of 'cobra' atlas 7s ROI estimation of 'neuromorphometrics' atlas 26s ROI estimation of 'lpba40' atlas 7s ROI estimation of 'hammers' atlas 18s ROI estimation of 'thalamus' atlas 1s ROI estimation of 'ibsr' atlas 6s ROI estimation of 'aal3' atlas 11s ROI estimation of 'mori' atlas 16s ROI estimation of 'anatomy3' atlas 23s ROI estimation of 'julichbrain' atlas 31s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 13s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 23s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 51s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 85s Write results 86s 318s Quality check: 6s Print 'Graphics' figure to: /var/lib/condor/execute/dir_11915/ds/sub-035/report/catreport_sub-035_ses-t0_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 44 minute(s) and 10 second(s). Image Quality Rating (IQR): 83.76% (B) GM volume (GMV): 41.65% (545.24 / 1308.99 ml) GM thickness (GMT): 2.31 0.58 mm Segmentations are saved in /var/lib/condor/execute/dir_11915/ds/sub-035/mri Reports are saved in /var/lib/condor/execute/dir_11915/ds/sub-035/report Labels are saved in /var/lib/condor/execute/dir_11915/ds/sub-035/label ------------------------------------------------------------------------