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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 20 0.465843648600521 14.5 0.0617500655353069 0.0600280314683914 [1 1 1] [1 1 1] 1 0 [15.6829996109009 317.769165039062 1087.82421875 1756.86218261719] [0.00892671011388302 0.180873140692711 0.619185864925385 1] T1 [14.2284759778294 202.296314224782 192.549689520511 112.895036232472] [0.0081717474386096 0.116183511912823 0.110585793852806 0.0648382604122162] 626.294128417969 0.35648450255394 0.140517711639404 0.346782118082047 [2 2 2] 2 0.5 [8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 2.73606586456299 2.3482301235199 1.3198961019516 1.91836734693878 1.11646091215013 1.725 1.2350013256073 1.20056056976318 2.22014476319813 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 20220712-170518 1639 1639 20 0.465843648600521 14.5 0.0617500655353069 0.0600280314683914 20 0.465843648600521 [347.189745098039 874.893933333333 711.209007843137 0 0] 2.5275137254902 0.00130736217202619 2426.20244098693 1933.29268627451 [0.17958467828639 0.452540859200823 0.367874462512787 0 0] [2.55131882897678 0.604473465498182] [2.53527402877808 0.761616391498786 1] [1.98047647083695 0.252247859053767 0.304561421502013;2.5710600483991 0.171862245053726 0.443619394374503;3.22657813180207 0.275886413515606 0.251819184123484] [0.92416888004375 0.337973455535913 0.527322834645669;4.23729355121163 0.370270699918007 0.472677165354331] 5.48925521494223 [1.07515586002856 5.97738612070443 4.45679709972678 0.5 0.5] 1.13073621720262 8.62399880689524 4.94416132348862 [0.131468252702193 1 1 10017.937 0.463827545280742] [false] [0.00858708750456572 0.0045748483389616 0.384672343730927] [false] [1052.50026666667 628.682145098039 832.8188 859.769882352941 2698.53831372549 6422.54323921569] [865.530788235294 597.092215686274 432.913858823529 1228.84965490196 2413.90841568627 5996.23245098039] [446.135101318359 1178.19921875 1797.40197753906] [0 0 27.2554569244385 446.135101318359 1178.19921875 1797.40197753906 2473.03540039062 5584.23046875] [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 [0.0180685706436634 0.06301149725914 0.0686606168746948 0 0] [0.0867025032669318 0 0.0867025032669318 0;0.214591384649563 0.00915262764957057 0.223744012299134 1951.77954101562;0.214591384649563 0.00915262764957057 0.223744012299134 1951.77954101562] [0.0417912118136883 0.0825518369674683 0.0926240012049675] [0.0306010227650404 0.0419380664825439 0.0524974167346954] 0.0926240012049675

0.0686606168746948

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 [0.00708295311778784 0.0261787492781878 0.0352959260344505 0.0439488440752029 0.0513401739299297 0.056566059589386] [0.0852698718027083 0 0.0852698718027083 0;0.224188507326007 0.0129122119200244 0.237100719246032 6609.4384765625;0.209661816115335 0.0151867740368717 0.224848590152207 10930.103515625;0.190461523738908 0.0181832055420617 0.20864472928097 19606.44140625;0.173242550245719 0.02195890423488 0.195201454480599 38413.875;0.173242550245719 0.02195890423488 0.195201454480599 38413.875] [0.00845256727188826 0.0293985456228256 0.044742189347744 0.0674761235713959 0.0923150554299355 0.0993109941482544] [0.00288387574255466 0.0109037347137928 0.0250550080090761 0.0450448654592037 0.0646270290017128 0.0704457983374596] 0.0993109941482544

0.056566059589386

------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./condor/execute/dir_13235/ds/sub-24/sub-24_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 52s APP: Rough bias correction: Initialize 6s Estimate background 8s Initial correction 7s Refine background 3s Final correction 5s Final scaling 7s 42s Correct center-of-mass 5s Affine registration 9s SPM preprocessing 1 (estimate 1 - TPM registration): 74s SPM preprocessing 1 (estimate 2): 72s SPM preprocessing 2 (write): Write Segmentation 17s Update Segmentation 22s Update Skull-Stripping 48s Update probability maps 8s 95s Global intensity correction: 16s SANLM denoising after intensity normalization (medium): 11s Fast Optimized Shooting registration 31s Local adaptive segmentation (LASstr=0.50): Prepare maps 5s Prepare partitions 2s Prepare segments (LASmod = 1.00) 17s Estimate local tissue thresholds (WM) 20s Estimate local tissue thresholds (GM) 28s Intensity transformation 0s SANLM denoising after LAS (medium) 40s 115s ROI segmentation (partitioning): Atlas -> subject space 8s Major structures 4s Ventricle detection 18s Blood vessel detection 12s WMH detection (WMHCstr=0.50 > WMHCstr'=0.10) 33s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 5s Final corrections 4s 88s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 39s AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.04] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 5s Level 1 cleanup (brain masking) 3s Level 2 cleanup (CSF correction) 2s Level 3 cleanup (CSF/WM PVE) 3s 13s 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 | 0.0853 0.0000 0.0853 | 32.0000 2 | 2.50 | 0.0828 0.0011 0.0839 | 29.4886 3 | 2.50 | 0.0821 0.0017 0.0838 | 26.9772 4 | 2.50 | 0.0817 0.0019 0.0836 | 24.6107 5 | 2.50 | 0.0815 0.0020 0.0835 | 22.6548 6 | 2.50 | 0.0812 0.0021 0.0833 | 20.6989 7 | 2.50 | 0.0810 0.0022 0.0832 | 18.9688 8 | 2.50 | 0.0807 0.0022 0.0830 | 17.4455 9 | 2.50 | 0.0805 0.0023 0.0828 | 15.9223 10 | 2.50 | 0.0802 0.0024 0.0826 | 14.6627 11 | 2.50 | 0.0800 0.0024 0.0824 | 13.4764 12 | 2.50 | 0.0797 0.0025 0.0821 | 12.3015 13 | 2.50 | 0.0794 0.0025 0.0819 | 11.3776 14 | 2.50 | 0.0791 0.0026 0.0817 | 10.4537 15 | 2.25 | 0.0784 0.0026 0.0810 | 9.5920 16 | 2.25 | 0.0757 0.0039 0.0796 | 8.8725 17 | 2.25 | 0.0747 0.0043 0.0790 | 8.1530 29 | 2.00 | 0.0770 0.0019 0.0789 | 3.3283 30 | 2.00 | 0.0716 0.0042 0.0758 | 3.1221 31 | 2.00 | 0.0699 0.0051 0.0749 | 2.9160 43 | 1.75 | 0.0693 0.0028 0.0722 | 1.5785 44 | 1.75 | 0.0649 0.0052 0.0701 | 1.5194 45 | 1.75 | 0.0635 0.0061 0.0695 | 1.4626 57 | 1.50 | 0.0623 0.0043 0.0666 | 1.0900 58 | 1.50 | 0.0589 0.0066 0.0655 | 1.0730 59 | 1.50 | 0.0577 0.0073 0.0651 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 163s Prepare output 11s 173s Jacobian determinant (RMS): 0.008 0.029 0.045 0.067 0.092 | 0.099311 Template Matching: 0.085 0.224 0.210 0.190 0.173 | 0.173243 Write result maps: 24s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 51s CSF distance: 21s PBT2x thickness: 55s 135s Create initial surface 110s Topology correction: 119s Surface refinement: 96s Reduction of surface collisions with optimization: 99s Spherical mapping with areal smoothing 132s Spherical registration 295s rh: Thickness estimation (0.50 mm ): WM distance: 49s CSF distance: 19s PBT2x thickness: 53s 127s Create initial surface 95s Topology correction: 106s Surface refinement: 102s Reduction of surface collisions with optimization: 91s Spherical mapping with areal smoothing 96s Spherical registration 286s Final surface processing results: Average thickness (FS): 2.5513 0.6044 mm Surface intensity / position RMSE: 0.0618 / 0.0600 Euler number / defect number / defect size: 20.0 / 14.5 / 0.47% Display thickness: /var/lib/condor/execute/dir_13235/ds/sub-24/surf/lh.thickness.sub-24_T1w Display thickness: /var/lib/condor/execute/dir_13235/ds/sub-24/surf/rh.thickness.sub-24_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_13235/ds/sub-24/sub-24_T1w.nii Surface ROI estimation: 8s Surface and thickness estimation takes: 1991s ROI estimation in native space: ROI estimation of 'cobra' atlas 7s ROI estimation of 'neuromorphometrics' atlas 26s ROI estimation of 'lpba40' atlas 8s 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 15s ROI estimation of 'anatomy3' atlas 22s ROI estimation of 'julichbrain' atlas 30s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 48s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 72s Write results 72s 299s Quality check: 6s Print 'Graphics' figure to: /var/lib/condor/execute/dir_13235/ds/sub-24/report/catreport_sub-24_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 53 minute(s) and 58 second(s). Image Quality Rating (IQR): 82.80% (B-) GM volume (GMV): 45.25% (874.89 / 1933.29 ml) GM thickness (GMT): 2.55 0.60 mm Segmentations are saved in /var/lib/condor/execute/dir_13235/ds/sub-24/mri Reports are saved in /var/lib/condor/execute/dir_13235/ds/sub-24/report Labels are saved in /var/lib/condor/execute/dir_13235/ds/sub-24/label ------------------------------------------------------------------------