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[0.316094970693337 -0.0494597085805839 -0.0977322341670432] [1.02438619212218 1.03477448050891 1.1586546537758] [0.0277427281472685 0.0196463817629528 -0.0592993000910438] [-2.06134016945493 -20.3937452633983 -15.325311162652] [0.316094970693337 -0.0494597085805839 -0.0977322341670432] [1.02438619212218 1.03477448050891 1.1586546537758] [0.0277427281472685 0.0196463817629528 -0.0592993000910438] /var/lib/condor/execute/dir_2937729/ds/sub-wlsubj062 sub-wlsubj062_ses-anat_acq-highres_run-01_T1w /var/lib/condor/execute/dir_2937729/ds/sub-wlsubj062/sub-wlsubj062_ses-anat_acq-highres_run-01_T1w.nii /var/lib/condor/execute/dir_2937729/ds/sub-wlsubj062/sub-wlsubj062_ses-anat_acq-highres_run-01_T1w.nii /var/lib/condor/execute/dir_2937729/ds/sub-wlsubj062/mri/msub-wlsubj062_ses-anat_acq-highres_run-01_T1w.nii /var/lib/condor/execute/dir_2937729/ds/sub-wlsubj062/mri/p0sub-wlsubj062_ses-anat_acq-highres_run-01_T1w.nii ..s/sub-wlsubj062/.._ses-anat_acq-highres_run-01_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 20 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 8 0.107512667052155 9 0.0656073987483978 0.0608814433217049 [0.800000979164593 0.800000012737503 0.800000000197966] [0.800000981774701 0.800000011723598 0.800000002814389] 0.800000330700152 0 [4.73099994659424 141.200744628906 354.352783203125 500.7490234375] [0.0094478465616703 0.281979084014893 0.70764547586441 1] T1 [3.92287214455975 60.8332095467636 48.1442110664035 24.5422119071891] [0.00790872890502214 0.122643142938614 0.0970614105463028 0.049478467553854] 147.792556762695 0.295142978429794 0.11182851344347 0.351380735635757 [1.60000195832919 1.60000002547501 1.60000000039593] 1.6000006614003 0.5 [8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 3.65618848800659 1.93638408184052 1.33130145072937 1.30612244897959 1.02687816676304 1.45 1.31214797496796 1.21762883663177 1.81985496339668 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 20220712-154406 1639 1639 8 0.107512667052155 9 0.0656073987483978 0.0608814433217049 8 0.107512667052155 [310.58686121725 692.371609503589 544.219167239255 0 0] 1.28397110492627 0.000829879564843728 1999.30550502427 1547.17763796009 [0.200744150895788 0.447506215521871 0.351749633582341 0 0] [2.4957834551239 0.598641384627118] [2.48022556304932 0.730969301160556 1] [1.94577975079471 0.235003067179187 0.314105195079786;2.5278667654964 0.170577245606579 0.435170329465318;3.17265793759817 0.268510770239731 0.250724475454896] [0.879132652758057 0.391966663315309 0.521300448430493;4.09187744880076 0.321603263739785 0.478699551569507] 1.49899991655762 [1.45517512384677 5.88696507761981 4.1671988789932 0.5 0.5] 1.08298795648437 8.62141565916675 4.85109372950742 [0.269232259114583 1 1 6896.39818438586 0.485750828576513] [false] [0.00591114535927773 0.00460187764838338 0.0709441155195236] [false] [810.907447166072 500.851251519511 517.656692621377 643.94359951343 2246.22248507642 5305.60676415783] [713.27012625979 475.624010313539 323.380401856071 510.596932676286 1438.13699869538 5976.2629046721] [144.395797729492 365.367004394531 494.275787353516] [0 0 6.25316143035889 144.395797729492 365.367004394531 494.275787353516 669.2158203125 1713.88659667969] [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 [0.0210253410041332 0.074954979121685 0.0824093222618103 0 0] [0.0840074982629771 0 0.0840074982629771 0;0.195546785608775 0.0102762792433868 0.205823064852162 2191.39599609375;0.195546785608775 0.0102762792433868 0.205823064852162 2191.39599609375] [0.0454724244773388 0.0976754203438759 0.107424378395081] [0.0322844609618187 0.0427724942564964 0.0524042658507824] 0.107424378395081

0.0824093222618103

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 [0.0101706478744745 0.0371848829090595 0.0518376566469669 0.0590775869786739 0.0644181743264198 0.072346106171608] [0.0838821143871107 0 0.0838821143871107 0;0.215978952991453 0.0141520852411477 0.230131038232601 7244.0986328125;0.192496334471289 0.0165437458620601 0.209040080333349 11906.732421875;0.172613739854137 0.0180381818374677 0.190651921691605 19450.06640625;0.155716999370624 0.0205485301208504 0.176265529491475 35946.6328125;0.155716999370624 0.0205485301208504 0.176265529491475 35946.6328125] [0.0121109457686543 0.0438773483037949 0.0643630623817444 0.0879172757267952 0.109180927276611 0.115623809397221] [0.00334871048107743 0.0128687573596835 0.0273849479854107 0.0463164411485195 0.0633926466107368 0.0683046579360962] 0.115623809397221

0.072346106171608

------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./sub-wlsubj062_ses-anat_acq-highres_run-01_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 68s APP: Rough bias correction: Initialize 13s Estimate background 11s Initial correction 13s Refine background 7s Final correction 12s Final scaling 13s 82s Correct center-of-mass 4s Affine registration 17s SPM preprocessing 1 (estimate 1 - TPM registration): 157s SPM preprocessing 1 (estimate 2): 67s SPM preprocessing 2 (write): Write Segmentation 34s Update Segmentation 44s Update Skull-Stripping 99s Update probability maps 18s 196s Global intensity correction: 33s SANLM denoising after intensity normalization (medium): 23s Fast Optimized Shooting registration 63s Local adaptive segmentation (LASstr=0.50): Prepare maps 11s Prepare partitions 5s Prepare segments (LASmod = 1.01) 33s Estimate local tissue thresholds (WM) 38s Estimate local tissue thresholds (GM) 54s Intensity transformation 0s SANLM denoising after LAS (medium) 53s 202s ROI segmentation (partitioning): Atlas -> subject space 21s Major structures 9s Ventricle detection 27s Blood vessel detection 26s WMH detection (WMHCstr=0.50 > WMHCstr'=0.12) 70s Manual stroke lesion detection 0s Closing of deep structures 5s Side alignment 10s Final corrections 10s 177s Blood vessel correction (BVCstr=0.50): 3s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 59s 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) 10s Level 1 cleanup (brain masking) 6s Level 2 cleanup (CSF correction) 3s Level 3 cleanup (CSF/WM PVE) 6s 25s 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 | 0.0839 0.0000 0.0839 | 32.0000 2 | 2.50 | 0.0810 0.0013 0.0822 | 29.4886 3 | 2.50 | 0.0801 0.0019 0.0821 | 26.9772 4 | 2.50 | 0.0797 0.0021 0.0819 | 24.6107 5 | 2.50 | 0.0794 0.0023 0.0817 | 22.6548 6 | 2.50 | 0.0791 0.0024 0.0815 | 20.6989 7 | 2.50 | 0.0788 0.0025 0.0813 | 18.9688 8 | 2.50 | 0.0785 0.0026 0.0811 | 17.4455 9 | 2.50 | 0.0782 0.0027 0.0809 | 15.9223 10 | 2.50 | 0.0778 0.0028 0.0807 | 14.6627 11 | 2.50 | 0.0775 0.0029 0.0804 | 13.4764 12 | 2.50 | 0.0772 0.0030 0.0801 | 12.3015 13 | 2.50 | 0.0768 0.0031 0.0799 | 11.3776 14 | 2.50 | 0.0765 0.0031 0.0796 | 10.4537 15 | 2.25 | 0.0750 0.0032 0.0782 | 9.5920 16 | 2.25 | 0.0720 0.0047 0.0767 | 8.8725 29 | 2.00 | 0.0723 0.0021 0.0744 | 3.3283 30 | 2.00 | 0.0662 0.0045 0.0707 | 3.1221 31 | 2.00 | 0.0642 0.0055 0.0697 | 2.9160 43 | 1.75 | 0.0629 0.0032 0.0660 | 1.5785 44 | 1.75 | 0.0589 0.0053 0.0641 | 1.5194 45 | 1.75 | 0.0575 0.0060 0.0636 | 1.4626 57 | 1.50 | 0.0557 0.0044 0.0601 | 1.0900 58 | 1.50 | 0.0528 0.0062 0.0591 | 1.0730 59 | 1.50 | 0.0519 0.0068 0.0588 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 242s Prepare output 17s 259s Jacobian determinant (RMS): 0.012 0.044 0.064 0.088 0.109 | 0.115624 Template Matching: 0.084 0.216 0.192 0.173 0.156 | 0.155717 Write result maps: 56s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 60s CSF distance: 22s PBT2x thickness: 63s 153s Create initial surface 96s Topology correction: 111s Surface refinement: 93s Reduction of surface collisions with optimization: 73s Spherical mapping with areal smoothing 104s Spherical registration 304s rh: Thickness estimation (0.50 mm ): WM distance: 69s CSF distance: 21s PBT2x thickness: 59s 158s Create initial surface 98s Topology correction: 110s Surface refinement: 128s Reduction of surface collisions with optimization: 72s Spherical mapping with areal smoothing 103s Spherical registration 290s Final surface processing results: Average thickness (FS): 2.4958 0.5984 mm Surface intensity / position RMSE: 0.0656 / 0.0609 Euler number / defect number / defect size: 8.0 / 9.0 / 0.11% Display thickness: /var/lib/condor/execute/dir_2937729/ds/sub-wlsubj062/surf/lh.thickness.sub-wlsubj062_ses-anat_acq-highres_run-01_T1w Display thickness: /var/lib/condor/execute/dir_2937729/ds/sub-wlsubj062/surf/rh.thickness.sub-wlsubj062_ses-anat_acq-highres_run-01_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_2937729/ds/sub-wlsubj062/sub-wlsubj062_ses-anat_acq-highres_run-01_T1w.nii Surface ROI estimation: 9s Surface and thickness estimation takes: 2036s ROI estimation in native space: ROI estimation of 'cobra' atlas 28s ROI estimation of 'neuromorphometrics' atlas 106s ROI estimation of 'lpba40' atlas 31s ROI estimation of 'hammers' atlas 75s ROI estimation of 'thalamus' atlas 5s ROI estimation of 'ibsr' atlas 26s ROI estimation of 'aal3' atlas 41s ROI estimation of 'mori' atlas 62s ROI estimation of 'anatomy3' atlas 90s ROI estimation of 'julichbrain' atlas 118s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 44s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 60s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 194s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 284s Write results 285s 1167s Quality check: 11s Print 'Graphics' figure to: /var/lib/condor/execute/dir_2937729/ds/sub-wlsubj062/report/catreport_sub-wlsubj062_ses-anat_acq-highres_run-01_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 81 minute(s) and 17 second(s). Image Quality Rating (IQR): 86.80% (B+) GM volume (GMV): 44.75% (692.37 / 1547.18 ml) GM thickness (GMT): 2.50 0.60 mm Segmentations are saved in /var/lib/condor/execute/dir_2937729/ds/sub-wlsubj062/mri Reports are saved in /var/lib/condor/execute/dir_2937729/ds/sub-wlsubj062/report Labels are saved in /var/lib/condor/execute/dir_2937729/ds/sub-wlsubj062/label ------------------------------------------------------------------------