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-28.2611591899471] [0.159539521075588 0.0274090084061423 -0.049311844894454] [1.09379305868946 1.01700577904885 1.1430182118965] [-0.0154254894342658 0.00133310265694647 -0.0239431946851576] [-0.99949968908703 -0.239824787059923 -28.2611591899471] [0.159539521075588 0.0274090084061423 -0.049311844894454] [1.09379305868946 1.01700577904885 1.1430182118965] [-0.0154254894342658 0.00133310265694647 -0.0239431946851576] /var/lib/condor/execute/dir_32760/ds/sub-season104 sub-season104_ses-3_acq-MPrageHiRes_T1w /var/lib/condor/execute/dir_32760/ds/sub-season104/sub-season104_ses-3_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_32760/ds/sub-season104/sub-season104_ses-3_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_32760/ds/sub-season104/mri/msub-season104_ses-3_acq-MPrageHiRes_T1w.nii /var/lib/condor/execute/dir_32760/ds/sub-season104/mri/p0sub-season104_ses-3_acq-MPrageHiRes_T1w.nii ..s/sub-season104/..son104_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 24 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 46 1.16196024460311 20 0.0763235986232758 0.0875410512089729 [0.879997842875786 0.875000007251436 0.875000013802175] [0.879997843437443 0.875000004811434 0.875000013421342] 0.876669120461051 0 [9.78999996185303 302.745971679688 802.827880859375 1148.51831054688] [0.00852402579039335 0.26359698176384 0.69901180267334 1] T1 [6.70594819052912 149.330649092976 105.973289897296 61.2159192729136] [0.00588898034766316 0.13113808631897 0.0930628404021263 0.0537581443786621] 348.662445068359 0.303575873374939 0.104635879397392 0.282553553581238 [1.75999568575157 1.75000001450287 1.75000002760435] 1.7533382409221 0.5 [8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 3.52969527244568 1.83313059806824 1.16059911251068 3.24489795918367 1.29049006115078 2 1.52647197246552 1.75082099437714 1.79632620175696 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 20220712-181145 1639 1639 46 1.16196024460311 20 0.0763235986232758 0.0875410512089729 46 1.16196024460311 [212.098544891309 715.803603627002 509.637143571868 0 0] 0.847485607439556 0.00058953909093317 1973.89801389154 1437.53929209018 [0.147542780957951 0.497936722540798 0.354520496501252 0 0] [2.58950631703182 0.677847900096468] [2.60617184638977 0.888444937973105 1] [1.92677657068391 0.303184717415676 0.288702438060664;2.62311181064386 0.196626261080873 0.426429096207393;3.33743738831722 0.308526899597662 0.284868465731943] [0.736483277634622 0.296710433594738 0.631981351981352;4.35802457300596 0.314306123966218 0.368018648018648] 1.03350033547699 [0.5 6.79268539045973 4.21696294003685 0.5 0.5] 1.05895390909332 8.62023481969396 5.56999702002818 [0.344181197030204 1 1 6486.48677835532 0.325845276057328] [false] [0.00540917133912444 0 0.175522685050964] [false] [851.144079545271 448.217968024344 313.992400328435 507.676247841369 2347.85018262637 5959.03876826466] [762.201258218052 423.236245352578 202.610270877363 419.424034439048 1277.41466029951 6806.09186624533] [360.190612792969 839.235900878906 1131.36694335938] [0 0 14.9340295791626 360.190612792969 839.235900878906 1131.36694335938 1516.955078125 3403.9755859375] [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 [0.0195298101752996 0.0696083158254623 0.0760018825531006 0 0] [0.0796609354190895 0 0.0796609354190895 0;0.188719585734685 0.0094931283060099 0.198212714040694 2024.390625;0.188719585734685 0.0094931283060099 0.198212714040694 2024.390625] [0.0431752502918243 0.0896026045084 0.0993525683879852] [0.0311007667332888 0.0423350296914577 0.0527384020388126] 0.0993525683879852

0.0760018825531006

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 [0.00904969125986099 0.0334925800561905 0.0462495721876621 0.0538092218339443 0.0600912496447563 0.0667325034737587] [0.0800483654601945 0 0.0800483654601945 0;0.210790460927961 0.0123560916514042 0.223146552579365 6324.7744140625;0.191801785818494 0.0155664506470991 0.207368236465593 11203.361328125;0.172108113143066 0.0179078372908227 0.190015950433889 19309.51953125;0.155427374435005 0.0208940775175165 0.176321451952522 36551.1171875;0.155427374435005 0.0208940775175165 0.176321451952522 36551.1171875] [0.0104591455310583 0.0378563962876797 0.055602241307497 0.0776594579219818 0.100219286978245 0.107037216424942] [0.00316510233096778 0.0121225444599986 0.0269339960068464 0.0471972450613976 0.0662422552704811 0.0714925304055214] 0.107037216424942

0.0667325034737587

------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./sub-season104_ses-3_acq-MPrageHiRes_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 37s APP: Rough bias correction: Initialize 11s Estimate background 12s Initial correction 11s Refine background 6s Final correction 10s Final scaling 12s 73s Correct center-of-mass 5s Affine registration 17s SPM preprocessing 1 (estimate 1 - TPM registration): 8s Use initial fine affine registration. 141s SPM preprocessing 1 (estimate 2): 129s SPM preprocessing 2 (write): Write Segmentation 30s Update Segmentation 35s Update Skull-Stripping 75s Update probability maps 15s 155s Global intensity correction: 29s SANLM denoising after intensity normalization (medium): 13s Fast Optimized Shooting registration 53s Local adaptive segmentation (LASstr=0.50): Prepare maps 9s Prepare partitions 4s Prepare segments (LASmod = 1.03) 30s Estimate local tissue thresholds (WM) 31s Estimate local tissue thresholds (GM) 42s Intensity transformation 0s SANLM denoising after LAS (medium) 35s 157s ROI segmentation (partitioning): Atlas -> subject space 16s Major structures 8s Ventricle detection 29s Blood vessel detection 18s WMH detection (WMHCstr=0.50 > WMHCstr'=0.02) 50s Manual stroke lesion detection 0s Closing of deep structures 3s Side alignment 7s Final corrections 8s 137s Blood vessel correction (BVCstr=0.50): 3s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 69s 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) 9s 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 | 0.0800 0.0000 0.0800 | 32.0000 2 | 2.50 | 0.0778 0.0011 0.0789 | 29.4886 3 | 2.50 | 0.0771 0.0016 0.0787 | 26.9772 4 | 2.50 | 0.0768 0.0018 0.0786 | 24.6107 5 | 2.50 | 0.0765 0.0019 0.0785 | 22.6548 6 | 2.50 | 0.0763 0.0020 0.0783 | 20.6989 7 | 2.50 | 0.0760 0.0021 0.0782 | 18.9688 8 | 2.50 | 0.0758 0.0022 0.0780 | 17.4455 9 | 2.50 | 0.0755 0.0023 0.0778 | 15.9223 10 | 2.50 | 0.0752 0.0024 0.0776 | 14.6627 11 | 2.50 | 0.0750 0.0024 0.0774 | 13.4764 12 | 2.50 | 0.0747 0.0025 0.0772 | 12.3015 13 | 2.50 | 0.0744 0.0026 0.0770 | 11.3776 14 | 2.50 | 0.0741 0.0026 0.0768 | 10.4537 15 | 2.25 | 0.0731 0.0027 0.0758 | 9.5920 16 | 2.25 | 0.0703 0.0041 0.0744 | 8.8725 29 | 2.00 | 0.0718 0.0019 0.0736 | 3.3283 30 | 2.00 | 0.0659 0.0042 0.0702 | 3.1221 31 | 2.00 | 0.0639 0.0052 0.0691 | 2.9160 43 | 1.75 | 0.0630 0.0030 0.0660 | 1.5785 44 | 1.75 | 0.0588 0.0052 0.0640 | 1.5194 45 | 1.75 | 0.0574 0.0060 0.0633 | 1.4626 57 | 1.50 | 0.0559 0.0043 0.0603 | 1.0900 58 | 1.50 | 0.0528 0.0063 0.0592 | 1.0730 59 | 1.50 | 0.0518 0.0070 0.0588 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 247s Prepare output 15s 262s Jacobian determinant (RMS): 0.010 0.038 0.056 0.078 0.100 | 0.107037 Template Matching: 0.080 0.211 0.192 0.172 0.155 | 0.155427 Write result maps: 42s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 65s CSF distance: 20s PBT2x thickness: 62s 157s Create initial surface 111s Topology correction: 130s Surface refinement: 147s Reduction of surface collisions with optimization: 98s Spherical mapping with areal smoothing 109s Spherical registration 281s rh: Thickness estimation (0.50 mm ): WM distance: 47s CSF distance: 18s PBT2x thickness: 57s 132s Create initial surface 102s Topology correction: 111s Surface refinement: 100s Reduction of surface collisions with optimization: 94s Spherical mapping with areal smoothing 97s Spherical registration 256s Final surface processing results: Average thickness (FS): 2.5893 0.6774 mm Surface intensity / position RMSE: 0.0763 / 0.0875 Euler number / defect number / defect size: 46.0 / 20.0 / 1.16% Display thickness: /var/lib/condor/execute/dir_32760/ds/sub-season104/surf/lh.thickness.sub-season104_ses-3_acq-MPrageHiRes_T1w Display thickness: /var/lib/condor/execute/dir_32760/ds/sub-season104/surf/rh.thickness.sub-season104_ses-3_acq-MPrageHiRes_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_32760/ds/sub-season104/sub-season104_ses-3_acq-MPrageHiRes_T1w.nii Surface ROI estimation: 8s Surface and thickness estimation takes: 2046s ROI estimation in native space: ROI estimation of 'cobra' atlas 18s ROI estimation of 'neuromorphometrics' atlas 66s ROI estimation of 'lpba40' atlas 19s ROI estimation of 'hammers' atlas 47s ROI estimation of 'thalamus' atlas 4s ROI estimation of 'ibsr' atlas 17s ROI estimation of 'aal3' atlas 27s ROI estimation of 'mori' atlas 40s ROI estimation of 'anatomy3' atlas 59s ROI estimation of 'julichbrain' atlas 77s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 29s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 37s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 124s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 186s Write results 187s 751s Quality check: 7s Print 'Graphics' figure to: /var/lib/condor/execute/dir_32760/ds/sub-season104/report/catreport_sub-season104_ses-3_acq-MPrageHiRes_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 71 minute(s) and 47 second(s). Image Quality Rating (IQR): 87.04% (B+) GM volume (GMV): 49.79% (715.80 / 1437.54 ml) GM thickness (GMT): 2.59 0.68 mm Segmentations are saved in /var/lib/condor/execute/dir_32760/ds/sub-season104/mri Reports are saved in /var/lib/condor/execute/dir_32760/ds/sub-season104/report Labels are saved in /var/lib/condor/execute/dir_32760/ds/sub-season104/label ------------------------------------------------------------------------