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[0.297817204371196 0.0367444362146447 0.0420473410528133] [1.05618231135212 1.05174904663612 1.1252432602766] [0.00340287070718985 -0.00332250809664152 -0.0490372221832174] [-1.86909502065765 -16.0818214803155 10.8591834571913] [0.297817204371196 0.0367444362146447 0.0420473410528133] [1.05618231135212 1.05174904663612 1.1252432602766] [0.00340287070718985 -0.00332250809664152 -0.0490372221832174] /var/lib/condor/execute/dir_18373/ds/sub-sc034 sub-sc034_T1w /var/lib/condor/execute/dir_18373/ds/sub-sc034/sub-sc034_T1w.nii /var/lib/condor/execute/dir_18373/ds/sub-sc034/sub-sc034_T1w.nii /var/lib/condor/execute/dir_18373/ds/sub-sc034/mri/msub-sc034_T1w.nii /var/lib/condor/execute/dir_18373/ds/sub-sc034/mri/p0sub-sc034_T1w.nii ..73/ds/sub-sc034/sub-sc034_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 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 /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 26 0.793280209407548 13 0.0720575153827667 0.081629142165184 [1.00000001075889 1.00000001546649 0.999999990976777] [1.00000001344365 1.00000001990576 0.999999991075484] 1.00000000573405 0 [0 37908.53515625 176266.890625 342939.03125] [0 0.11054015904665 0.513988971710205 1] T1 [2629.73495334353 34742.5322282887 43129.069944239 32528.0599437776] [0.00766822881996632 0.101308189332485 0.125763088464737 0.0948508530855179] 115272.4921875 0.336131155490875 0.164444878697395 0.308282554149628 [2.00000002151778 2.00000003093298 1.99999998195355] 2.0000000114681 0.5 [1.89584374427795 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 3.0413658618927 2.69171524047852 1.22441112995148 2.22448979591837 1.19832005235189 1.65 1.44115030765533 1.63258290290833 2.4958749687803 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 20220711-184459 1639 1639 26 0.793280209407548 13 0.0720575153827667 0.081629142165184 26 0.793280209407548 [211.79285615341 723.334758843845 496.75239644685 0 0] 0.732588253187508 0.000511626845358826 2010.5018041672 1431.8800114441 [0.147912432927818 0.505164366471136 0.346923200601045 0 0] [2.48665682387272 0.597315029498268] [2.47756719589233 0.729833237741957 1] [1.92855122201758 0.238820892863752 0.299627596173443;2.5081754104187 0.167487376893098 0.438195169249202;3.14584120756978 0.257959915498191 0.262177234577356] [0.863685595975279 0.348857773274289 0.554717332588246;4.0870039810124 0.357914759325462 0.445282667411754] 1.02417577244407 [0.506329614364556 6.92249221392127 4.08051725217394 0.5 0.5] 1.05116268453588 8.62181688245642 5.67122358084046 [0.700769255050505 2093 743 3791.85206522803 0.50914895744057] [false] [0 0 0.218980386853218] [false] [882.026684288506 435.044614547487 360.795248028072 1013.08536984254 4211.5277930622 6689.34993985725] [780.029089640362 411.010547293791 187.18372614057 102.020445629093 26.0570869109514 11165.837794293] [46881.390625 198265 348300.8125] [0 0 20487.515625 46881.390625 198265 348300.8125 499010.53125 1013530.0625] [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 [0.0208769906312227 0.0753695666790009 0.0831234902143478 0 0] [0.0822708111564938 0 0.0822708111564938 0;0.19037438583832 0.0100642761834959 0.200438662021816 2146.18676757812;0.19037438583832 0.0100642761834959 0.200438662021816 2146.18676757812] [0.0463985837996006 0.0989909172058105 0.109447941184044] [0.0332718528807163 0.0456381738185883 0.0560233257710934] 0.109447941184044

0.0831234902143478

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 [0.00998143013566732 0.0368355847895145 0.0516239628195763 0.0592791512608528 0.065299317240715 0.0737194716930389] [0.0841303852846253 0 0.0841303852846253 0;0.217659004884005 0.014241701007326 0.231900705891331 7289.970703125;0.196221739563881 0.0168290460715536 0.213050785635435 12112.06640625;0.176592704577324 0.0184945688854482 0.195087273462772 19942.17578125;0.160377025820403 0.0212141780060971 0.1815912038265 37111.0859375;0.160377025820403 0.0212141780060971 0.1815912038265 37111.0859375] [0.0117681501433253 0.0427582673728466 0.0640469864010811 0.090363398194313 0.114416375756264 0.121063493192196] [0.00333579885773361 0.0131437135860324 0.0289975050836802 0.0499116592109203 0.0682492405176163 0.0736644119024277] 0.121063493192196

0.0737194716930389

------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./execute/dir_18373/ds/sub-sc034/sub-sc034_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 26s APP: Rough bias correction: Initialize 7s Estimate background 6s Initial correction 6s Refine background 3s Final correction 5s Final scaling 6s 38s Correct center-of-mass 3s Affine registration 9s SPM preprocessing 1 (estimate 1 - TPM registration): 77s SPM preprocessing 1 (estimate 2): 55s SPM preprocessing 2 (write): Write Segmentation 17s Update Segmentation 18s Update Skull-Stripping 41s Update probability maps 8s 85s Global intensity correction: 16s SANLM denoising after intensity normalization (medium): 8s Fast Optimized Shooting registration 34s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 2s Prepare segments (LASmod = 1.00) 14s Estimate local tissue thresholds (WM) 19s Estimate local tissue thresholds (GM) 24s Intensity transformation 0s SANLM denoising after LAS (medium) 9s 75s ROI segmentation (partitioning): Atlas -> subject space 7s Major structures 3s Ventricle detection 18s Blood vessel detection 9s WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 25s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 3s Final corrections 5s 72s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 32s AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.08,0.99 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 | 0.0841 0.0000 0.0841 | 32.0000 2 | 2.50 | 0.0811 0.0013 0.0824 | 29.4886 3 | 2.50 | 0.0802 0.0019 0.0822 | 26.9772 4 | 2.50 | 0.0798 0.0022 0.0820 | 24.6107 5 | 2.50 | 0.0795 0.0024 0.0818 | 22.6548 6 | 2.50 | 0.0792 0.0025 0.0816 | 20.6989 7 | 2.50 | 0.0789 0.0026 0.0814 | 18.9688 8 | 2.50 | 0.0785 0.0027 0.0812 | 17.4455 9 | 2.50 | 0.0782 0.0027 0.0810 | 15.9223 10 | 2.50 | 0.0779 0.0029 0.0807 | 14.6627 11 | 2.50 | 0.0775 0.0029 0.0805 | 13.4764 12 | 2.50 | 0.0772 0.0030 0.0802 | 12.3015 13 | 2.50 | 0.0768 0.0031 0.0800 | 11.3776 14 | 2.50 | 0.0765 0.0032 0.0797 | 10.4537 15 | 2.25 | 0.0755 0.0033 0.0788 | 9.5920 16 | 2.25 | 0.0726 0.0047 0.0773 | 8.8725 29 | 2.00 | 0.0737 0.0021 0.0758 | 3.3283 30 | 2.00 | 0.0675 0.0046 0.0721 | 3.1221 31 | 2.00 | 0.0654 0.0056 0.0710 | 2.9160 43 | 1.75 | 0.0644 0.0032 0.0676 | 1.5785 44 | 1.75 | 0.0602 0.0054 0.0656 | 1.5194 45 | 1.75 | 0.0589 0.0062 0.0650 | 1.4626 57 | 1.50 | 0.0575 0.0045 0.0620 | 1.0900 58 | 1.50 | 0.0544 0.0064 0.0609 | 1.0730 59 | 1.50 | 0.0535 0.0071 0.0605 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 160s Prepare output 10s 170s Jacobian determinant (RMS): 0.012 0.043 0.064 0.090 0.114 | 0.121063 Template Matching: 0.084 0.218 0.196 0.177 0.160 | 0.160377 Write result maps: 24s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 30s CSF distance: 13s PBT2x thickness: 41s 90s Create initial surface 79s Topology correction: 94s Surface refinement: 84s Reduction of surface collisions with optimization: 74s Spherical mapping with areal smoothing 95s Spherical registration 306s rh: Thickness estimation (0.50 mm ): WM distance: 26s CSF distance: 15s PBT2x thickness: 44s 91s Create initial surface 84s Topology correction: 97s Surface refinement: 84s Reduction of surface collisions with optimization: 69s Spherical mapping with areal smoothing 90s Spherical registration 297s Final surface processing results: Average thickness (FS): 2.4867 0.5968 mm Surface intensity / position RMSE: 0.0721 / 0.0816 Euler number / defect number / defect size: 26.0 / 13.0 / 0.79% Display thickness: /var/lib/condor/execute/dir_18373/ds/sub-sc034/surf/lh.thickness.sub-sc034_T1w Display thickness: /var/lib/condor/execute/dir_18373/ds/sub-sc034/surf/rh.thickness.sub-sc034_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_18373/ds/sub-sc034/sub-sc034_T1w.nii Surface ROI estimation: 10s Surface and thickness estimation takes: 1728s ROI estimation in native space: ROI estimation of 'cobra' atlas 9s ROI estimation of 'neuromorphometrics' atlas 33s ROI estimation of 'lpba40' atlas 9s ROI estimation of 'hammers' atlas 22s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 8s ROI estimation of 'aal3' atlas 13s ROI estimation of 'mori' atlas 20s ROI estimation of 'anatomy3' atlas 28s ROI estimation of 'julichbrain' atlas 37s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 26s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 58s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 88s Write results 89s 370s Quality check: 5s Print 'Graphics' figure to: /var/lib/condor/execute/dir_18373/ds/sub-sc034/report/catreport_sub-sc034_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 48 minute(s) and 41 second(s). Image Quality Rating (IQR): 80.04% (B-) GM volume (GMV): 50.52% (723.33 / 1431.88 ml) GM thickness (GMT): 2.49 0.60 mm Segmentations are saved in /var/lib/condor/execute/dir_18373/ds/sub-sc034/mri Reports are saved in /var/lib/condor/execute/dir_18373/ds/sub-sc034/report Labels are saved in /var/lib/condor/execute/dir_18373/ds/sub-sc034/label ------------------------------------------------------------------------