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-24.3356264340722] [0.364354756155512 0.0268402871276129 -0.00832502928597117] [1.07220861816501 1.01963263174015 1.12150914525407] [0.0292079588659867 0.0059490310910667 -0.0485818813403137] [-3.07182018553974 -3.04507489506492 -24.3356264340722] [0.364354756155512 0.0268402871276129 -0.00832502928597117] [1.07220861816501 1.01963263174015 1.12150914525407] [0.0292079588659867 0.0059490310910667 -0.0485818813403137] /var/lib/condor/execute/dir_16809/ds/sub-season126 sub-season126_ses-1_acq-MPrageHiRes_T1w /var/lib/condor/execute/dir_16809/ds/sub-season126/sub-season126_ses-1_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_16809/ds/sub-season126/sub-season126_ses-1_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_16809/ds/sub-season126/mri/msub-season126_ses-1_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_16809/ds/sub-season126/mri/p0sub-season126_ses-1_acq-MPrageHiRes_T1w.nii ..s/sub-season126/..son126_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 8 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 28 0.734064867032734 18 0.068381056189537 0.0738864988088608 [0.879996660799824 0.875000009050559 0.874999995868071] [0.879996659346966 0.875000005541243 0.874999997570108] 0.876668719571698 0 [9.77299976348877 289.932586669922 741.189392089844 1068.56359863281] [0.00914592202752829 0.271329283714294 0.693631529808044 1] T1 [8.71229197884645 125.520264458228 98.1962593136656 62.3179173347582] [0.00822853110730648 0.118550598621368 0.0927437916398048 0.0588576383888721] 330.395965576172 0.309196352958679 0.109799958765507 0.278636664152145 [1.75999332159965 1.75000001810112 1.74999999173614] 1.7533374391434 0.5 [8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 3.44538807868958 1.90726327896118 1.1508846282959 2.3265306122449 1.18351621675818 1.9 1.36762118339539 1.47773003578186 1.84143721830809 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 20220712-163001 1639 1639 28 0.734064867032734 18 0.068381056189537 0.0738864988088608 28 0.734064867032734 [239.816299689857 710.2762186476 518.263209058307 0 0] 1.21182593337384 0.000825294518735662 2045.22101695357 1468.35572739576 [0.163323025351076 0.483722169904514 0.352954804744409 0 0] [2.46921103444596 0.574964971957413] [2.47108745574951 0.707328620401823 1] [1.95227913921605 0.233642323499731 0.315881689864732;2.51453032845994 0.160785956104166 0.436697461282102;3.1104777933746 0.2510480268595 0.247420848853166] [0.87977387467906 0.371496789404065 0.563747228381375;4.03501272974051 0.355128499421224 0.436252771618625] 1.11051364238955 [0.783100311621345 6.53739529282532 4.1888434760131 0.5 0.5] 1.08252945187357 8.62272063648031 5.36481111204732 [0.257960932595389 1 1 7339.25289077039 0.341905728605711] [false] [0.00764550594612956 0 0.24876680970192] [false] [848.524565260466 460.644988123568 374.523139097184 1327.8903844314 3153.43514536271 4223.53516751387] [757.280859095794 435.688637686165 233.19258815935 1373.10089620371 2911.30705437695 4180.19315028245] [365.418487548828 762.920227050781 1043.14111328125] [0 0 15.268120765686 365.418487548828 762.920227050781 1043.14111328125 1382.00244140625 2865.67944335938] [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 [0.0228976365178823 0.0803206562995911 0.0884121134877205 0 0] [0.0838489570632941 0 0.0838489570632941 0;0.190381932802418 0.0104622835157012 0.200844216318119 2231.06103515625;0.190381932802418 0.0104622835157012 0.200844216318119 2231.06103515625] [0.0477731786668301 0.102902486920357 0.112522713840008] [0.0337469652295113 0.0432085730135441 0.0527929775416851] 0.112522713840008

0.0884121134877205

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 [0.0112966224551201 0.0420581996440887 0.057656928896904 0.0649215430021286 0.0705748423933983 0.0788526237010956] [0.0845721904673936 0 0.0845721904673936 0;0.216465537240537 0.0154257001678877 0.231891237408425 7896.0302734375;0.193581251945223 0.0172652747079735 0.210846526653196 12426.025390625;0.173843876475509 0.0185828611948098 0.192426737670319 20037.37890625;0.157189240107628 0.0212119963959532 0.178401236503582 37107.26953125;0.157189240107628 0.0212119963959532 0.178401236503582 37107.26953125] [0.0130456080660224 0.0474266186356544 0.0682178735733032 0.0906052216887474 0.110462561249733 0.116622976958752] [0.00342705519869924 0.0130563778802752 0.0277089960873127 0.0467983856797218 0.063236691057682 0.0684157535433769] 0.116622976958752

0.0788526237010956

------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./sub-season126_ses-1_acq-MPrageHiRes_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 72s APP: Rough bias correction: Initialize 6s Estimate background 5s Initial correction 15s Refine background 3s Final correction 11s Final scaling 9s 56s Correct center-of-mass 4s Affine registration 8s SPM preprocessing 1 (estimate 1 - TPM registration): 78s SPM preprocessing 1 (estimate 2): 80s SPM preprocessing 2 (write): Write Segmentation 16s Update Segmentation 19s Update Skull-Stripping 42s Update probability maps 8s 85s Global intensity correction: 15s SANLM denoising after intensity normalization (medium): 14s Fast Optimized Shooting registration 29s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 2s Prepare segments (LASmod = 1.00) 14s Estimate local tissue thresholds (WM) 17s Estimate local tissue thresholds (GM) 24s Intensity transformation 0s SANLM denoising after LAS (medium) 27s 92s ROI segmentation (partitioning): Atlas -> subject space 8s Major structures 4s Ventricle detection 13s Blood vessel detection 10s WMH detection (WMHCstr=0.50 > WMHCstr'=0.02) 28s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 4s Final corrections 5s 74s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 28s 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) 4s Level 1 cleanup (brain masking) 3s Level 2 cleanup (CSF correction) 2s 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 | 0.0846 0.0000 0.0846 | 32.0000 2 | 2.50 | 0.0813 0.0013 0.0827 | 29.4886 3 | 2.50 | 0.0804 0.0021 0.0824 | 26.9772 4 | 2.50 | 0.0799 0.0023 0.0822 | 24.6107 5 | 2.50 | 0.0795 0.0025 0.0820 | 22.6548 6 | 2.50 | 0.0792 0.0026 0.0818 | 20.6989 7 | 2.50 | 0.0788 0.0027 0.0816 | 18.9688 8 | 2.50 | 0.0785 0.0029 0.0813 | 17.4455 9 | 2.50 | 0.0781 0.0029 0.0810 | 15.9223 10 | 2.50 | 0.0777 0.0031 0.0808 | 14.6627 11 | 2.50 | 0.0773 0.0032 0.0805 | 13.4764 12 | 2.50 | 0.0769 0.0032 0.0802 | 12.3015 13 | 2.50 | 0.0765 0.0034 0.0799 | 11.3776 14 | 2.50 | 0.0762 0.0034 0.0796 | 10.4537 15 | 2.25 | 0.0754 0.0036 0.0790 | 9.5920 16 | 2.25 | 0.0722 0.0051 0.0773 | 8.8725 29 | 2.00 | 0.0727 0.0023 0.0751 | 3.3283 30 | 2.00 | 0.0666 0.0048 0.0714 | 3.1221 31 | 2.00 | 0.0645 0.0058 0.0703 | 2.9160 43 | 1.75 | 0.0634 0.0033 0.0667 | 1.5785 44 | 1.75 | 0.0593 0.0055 0.0648 | 1.5194 45 | 1.75 | 0.0579 0.0062 0.0641 | 1.4626 57 | 1.50 | 0.0563 0.0045 0.0609 | 1.0900 58 | 1.50 | 0.0534 0.0064 0.0598 | 1.0730 59 | 1.50 | 0.0524 0.0071 0.0595 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 134s Prepare output 9s 143s Jacobian determinant (RMS): 0.013 0.047 0.068 0.091 0.110 | 0.116623 Template Matching: 0.085 0.216 0.194 0.174 0.157 | 0.157189 Write result maps: 25s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 31s CSF distance: 12s PBT2x thickness: 36s 84s Create initial surface 58s Topology correction: 65s Surface refinement: 75s Reduction of surface collisions with optimization: 43s Spherical mapping with areal smoothing 61s Spherical registration 178s rh: Thickness estimation (0.50 mm ): WM distance: 31s CSF distance: 13s PBT2x thickness: 36s 85s Create initial surface 58s Topology correction: 65s Surface refinement: 72s Reduction of surface collisions with optimization: 44s Spherical mapping with areal smoothing 60s Spherical registration 164s Final surface processing results: Average thickness (FS): 2.4692 0.5750 mm Surface intensity / position RMSE: 0.0684 / 0.0739 Euler number / defect number / defect size: 28.0 / 18.0 / 0.73% Display thickness: /var/lib/condor/execute/dir_16809/ds/sub-season126/surf/lh.thickness.sub-season126_ses-1_acq-MPrageHiRes_T1w Display thickness: /var/lib/condor/execute/dir_16809/ds/sub-season126/surf/rh.thickness.sub-season126_ses-1_acq-MPrageHiRes_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_16809/ds/sub-season126/sub-season126_ses-1_acq-MPrageHiRes_T1w.nii Surface ROI estimation: 5s Surface and thickness estimation takes: 1193s ROI estimation in native space: ROI estimation of 'cobra' atlas 13s ROI estimation of 'neuromorphometrics' atlas 47s ROI estimation of 'lpba40' atlas 14s ROI estimation of 'hammers' atlas 34s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 12s ROI estimation of 'aal3' atlas 19s ROI estimation of 'mori' atlas 28s ROI estimation of 'anatomy3' atlas 40s ROI estimation of 'julichbrain' atlas 53s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 19s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 24s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 87s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 126s Write results 126s 519s Quality check: 5s Print 'Graphics' figure to: /var/lib/condor/execute/dir_16809/ds/sub-season126/report/catreport_sub-season126_ses-1_acq-MPrageHiRes_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 43 minute(s) and 47 second(s). Image Quality Rating (IQR): 86.59% (B) GM volume (GMV): 48.37% (710.28 / 1468.36 ml) GM thickness (GMT): 2.47 0.57 mm Segmentations are saved in /var/lib/condor/execute/dir_16809/ds/sub-season126/mri Reports are saved in /var/lib/condor/execute/dir_16809/ds/sub-season126/report Labels are saved in /var/lib/condor/execute/dir_16809/ds/sub-season126/label ------------------------------------------------------------------------