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/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 10 0.154131345325603 12 0.0575631409883499 0.0577083565294743 [1.00001159693333 1.00000000723558 1.00000000184933] [1.00001159812408 1.00000000720084 1.00000000156391] 1.00000386868768 0 [0 8236.2880859375 19326.923828125 27634.88671875] [0 0.298039495944977 0.699366867542267 1] T1 [1442.36878123721 3025.55082612789 2770.64017756108 1632.85462834387] [0.0521937645971775 0.109483018517494 0.100258782505989 0.0590867139399052] 8307.962890625 0.300633132457733 0.136924475431442 0.269577145576477 [2.00002319386665 2.00000001447116 2.00000000369865] 2.00000773737535 0.5 [1.89584374427795 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 3.57383632659912 2.29664754867554 1.12841558456421 1.40816326530612 1.0385328363314 1.6 1.15126276016235 1.15416717529297 2.18261744809548 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 20220713-030843 1639 1639 10 0.154131345325603 12 0.0575631409883499 0.0577083565294743 10 0.154131345325603 [328.21182516026 642.748903365798 521.438334559529 0 0] 0.826578221341235 0.000553858710975237 1915.54147043761 1492.39906308559 [0.219922293760806 0.430681658320592 0.349396047918602 0 0] [2.48012816985044 0.657370467244731] [2.46887278556824 0.825242921044891 1] [1.77600798712639 0.288112119521701 0.268483549160035;2.47306183608212 0.195577002086574 0.458028288674574;3.19345059522613 0.305072550703466 0.273488162165391] [0.781244608043076 0.224266768306754 0.497291102312982;4.27494370742165 0.376334744391814 0.502708897687018] 1.20071851983431 [1.79961016093401 5.58479989799914 4.12492902152662 0.5 0.5] 1.05538587109752 8.61536538804119 4.61582195716647 [0.601162037037037 1338 549 4135.19999264994 0.364175123243889] [false] [0 0 0.350841104984283] [false] [785.435430081479 471.079118679938 506.944060445698 798.418749403126 2794.65182507214 5809.55663793913] [685.675476113781 440.738652800118 323.012227554906 1707.04193086318 2253.99148701539 4957.68429556427] [9774.908203125 20598.5625 26894.921875] [0 0 252.438873291016 9774.908203125 20598.5625 26894.921875 35454.9296875 48698.5234375] [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 [0.0198993403464556 0.0767510831356049 0.0850138962268829 0 0] [0.0870150428335397 0 0.0870150428335397 0;0.201823368507559 0.0115384769325211 0.21336184544008 2460.55712890625;0.201823368507559 0.0115384769325211 0.21336184544008 2460.55712890625] [0.0441877655684948 0.101931408047676 0.113469541072845] [0.0317305214703083 0.046573493629694 0.0578092262148857] 0.113469541072845

0.0850138962268829

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 [0.00973933283239603 0.0409109145402908 0.0530307702720165 0.0614206977188587 0.0677149146795273 0.0763858780264854] [0.087539555815752 0 0.087539555815752 0;0.222173977411477 0.0180706215659341 0.240244598977411 9249.8994140625;0.203192018995098 0.0190501982042817 0.22224221719938 13710.65625;0.181610918905434 0.0203980991983006 0.202009018103735 21994.69921875;0.163858027082013 0.0230420680888877 0.1869000951709 40308.7109375;0.163858027082013 0.0230420680888877 0.1869000951709 40308.7109375] [0.0115463715046644 0.0432760193943977 0.067118227481842 0.0913735553622246 0.115400940179825 0.121753565967083] [0.00332170259207487 0.0132584804669023 0.0291080661118031 0.0490185134112835 0.0699762776494026 0.0725371763110161] 0.121753565967083

0.0763858780264854

------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./dir_12014/ds/sub-013/sub-013_ses-t1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 11s APP: Rough bias correction: Initialize 5s Estimate background 6s Initial correction 6s Refine background 3s Final correction 5s Final scaling 6s 36s Correct center-of-mass 5s Affine registration 9s SPM preprocessing 1 (estimate 1 - TPM registration): 65s SPM preprocessing 1 (estimate 2): 52s SPM preprocessing 2 (write): Write Segmentation 13s Update Segmentation 16s Update Skull-Stripping 34s Update probability maps 7s 69s Global intensity correction: 13s SANLM denoising after intensity normalization (medium): 5s Fast Optimized Shooting registration 27s Local adaptive segmentation (LASstr=0.50): Prepare maps 3s Prepare partitions 2s Prepare segments (LASmod = 1.05) 12s Estimate local tissue thresholds (WM) 14s Estimate local tissue thresholds (GM) 18s Intensity transformation 0s SANLM denoising after LAS (medium) 12s 64s ROI segmentation (partitioning): Atlas -> subject space 6s Major structures 3s Ventricle detection 11s Blood vessel detection 8s WMH detection (WMHCstr=0.50 > WMHCstr'=0.14) 22s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 3s Final corrections 3s 58s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 29s AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.08,0.98 0.05] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 4s Level 1 cleanup (brain masking) 2s Level 2 cleanup (CSF correction) 1s Level 3 cleanup (CSF/WM PVE) 2s 9s 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 | 0.0875 0.0000 0.0875 | 32.0000 2 | 2.50 | 0.0846 0.0013 0.0859 | 29.4886 3 | 2.50 | 0.0837 0.0020 0.0856 | 26.9772 4 | 2.50 | 0.0832 0.0022 0.0854 | 24.6107 5 | 2.50 | 0.0828 0.0024 0.0853 | 22.6548 6 | 2.50 | 0.0825 0.0025 0.0850 | 20.6989 7 | 2.50 | 0.0822 0.0027 0.0848 | 18.9688 8 | 2.50 | 0.0818 0.0028 0.0846 | 17.4455 9 | 2.50 | 0.0815 0.0029 0.0844 | 15.9223 10 | 2.50 | 0.0811 0.0030 0.0841 | 14.6627 11 | 2.50 | 0.0808 0.0031 0.0839 | 13.4764 12 | 2.50 | 0.0804 0.0032 0.0836 | 12.3015 13 | 2.50 | 0.0800 0.0033 0.0833 | 11.3776 14 | 2.50 | 0.0796 0.0034 0.0830 | 10.4537 15 | 2.25 | 0.0798 0.0035 0.0833 | 9.5920 16 | 2.25 | 0.0765 0.0051 0.0816 | 8.8725 17 | 2.25 | 0.0750 0.0057 0.0807 | 8.1530 18 | 2.25 | 0.0741 0.0060 0.0801 | 7.5234 29 | 2.00 | 0.0755 0.0029 0.0784 | 3.3283 30 | 2.00 | 0.0697 0.0054 0.0751 | 3.1221 31 | 2.00 | 0.0677 0.0064 0.0741 | 2.9160 43 | 1.75 | 0.0665 0.0036 0.0701 | 1.5785 44 | 1.75 | 0.0620 0.0060 0.0680 | 1.5194 45 | 1.75 | 0.0605 0.0068 0.0673 | 1.4626 57 | 1.50 | 0.0588 0.0050 0.0638 | 1.0900 58 | 1.50 | 0.0557 0.0071 0.0627 | 1.0730 59 | 1.50 | 0.0546 0.0077 0.0623 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 142s Prepare output 8s 150s Jacobian determinant (RMS): 0.012 0.043 0.067 0.091 0.115 | 0.121754 Template Matching: 0.088 0.222 0.203 0.182 0.164 | 0.163858 Write result maps: 19s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 38s CSF distance: 13s PBT2x thickness: 37s 94s Create initial surface 73s Topology correction: 78s Surface refinement: 67s Reduction of surface collisions with optimization: 55s Spherical mapping with areal smoothing 64s Spherical registration 238s rh: Thickness estimation (0.50 mm ): WM distance: 35s CSF distance: 12s PBT2x thickness: 36s 88s Create initial surface 67s Topology correction: 76s Surface refinement: 66s Reduction of surface collisions with optimization: 54s Spherical mapping with areal smoothing 63s Spherical registration 243s Final surface processing results: Average thickness (FS): 2.4802 0.6573 mm Surface intensity / position RMSE: 0.0576 / 0.0577 Euler number / defect number / defect size: 10.0 / 12.0 / 0.15% Display thickness: /var/lib/condor/execute/dir_12014/ds/sub-013/surf/lh.thickness.sub-013_ses-t1_T1w Display thickness: /var/lib/condor/execute/dir_12014/ds/sub-013/surf/rh.thickness.sub-013_ses-t1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_12014/ds/sub-013/sub-013_ses-t1_T1w.nii Surface ROI estimation: 7s Surface and thickness estimation takes: 1397s ROI estimation in native space: ROI estimation of 'cobra' atlas 6s ROI estimation of 'neuromorphometrics' atlas 21s ROI estimation of 'lpba40' atlas 6s ROI estimation of 'hammers' atlas 15s ROI estimation of 'thalamus' atlas 1s ROI estimation of 'ibsr' atlas 5s ROI estimation of 'aal3' atlas 9s ROI estimation of 'mori' atlas 14s ROI estimation of 'anatomy3' atlas 20s ROI estimation of 'julichbrain' atlas 26s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 19s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 42s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 63s Write results 63s 260s Quality check: 4s Print 'Graphics' figure to: /var/lib/condor/execute/dir_12014/ds/sub-013/report/catreport_sub-013_ses-t1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 39 minute(s) and 7 second(s). Image Quality Rating (IQR): 83.17% (B-) GM volume (GMV): 43.07% (642.75 / 1492.40 ml) GM thickness (GMT): 2.48 0.66 mm Segmentations are saved in /var/lib/condor/execute/dir_12014/ds/sub-013/mri Reports are saved in /var/lib/condor/execute/dir_12014/ds/sub-013/report Labels are saved in /var/lib/condor/execute/dir_12014/ds/sub-013/label ------------------------------------------------------------------------