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/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_2040 0 1 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] 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/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] /var/lib/condor/execute/dir_3344799/ds/code/Tian_Subcortex_S2_7T.nii 1 gm wm csf [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 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/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 22 0.996933888203413 12.5 0.0689930468797684 0.08492261916399 [0.999900817871094 1 1] [0.999900817871094 1 1] 0.999966940383411 0 [0 18.2840003967285 179.908996582031 356.286987304688] [0 0.0513181835412979 0.504955291748047 1] T1 [3.17853198545856 33.3121906044089 45.8162591808866 32.1609702087748] [0.00892126839607954 0.0934981927275658 0.128593698143959 0.0902670323848724] 119.115432739258 0.334324389696121 0.374051868915558 0.140256062150002 0.30484876036644 [1.99980163574219 2 2] 1.99993388076682 2.80638694763184 1 [1.89584374427795 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 3.06846737861633 2.34447407722473 1.21589469909668 2.02040816326531 1.24923347205085 1.625 1.37986087799072 1.69845235347748 2.52875609807745 2.21735099583527 voxel dimensions RMS error of voxel size normalized gradient slope of the white matter boundary 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 2040 /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 20231031-021247 1639 1639 22 0.996933888203413 12.5 0.0689930468797684 0.08492261916399 22 0.996933888203413 [249.771659951872 739.555049923048 556.458929234464 0 0] 0.732221487157485 0.000473688892322328 2109.63881799519 1545.78563910938 [0.16158233951234 0.478433122427731 0.359984538059929 0 0] [2.38699230465028 0.646906294507271] [2.36108040809631 0.800184557010545 1] [1.77009870361427 0.279979491771437 0.316599795267623;2.40639407151079 0.188065728235319 0.428073044746967;3.12711486235832 0.293471791567449 0.25532715998541] [0.732851714882462 0.259413499100444 0.549022983558578;4.1306662574072 0.354011331916523 0.450977016441422] 1.48991410517915 [0.751837994115303 6.44240521601528 4.31509587032919 0.5 0.5] 1.04736888923223 8.62354617615527 5.29459151965701 [0 1 0 11533.192 0.449932638030723] [false] [0.00135312566999346 0.00108568300493062 0.0419662669301033] [false] [951.717773712607 462.827957851156 510.770304316293 501.922703495848 978.868590373619 8756.85495503836] [793.260840387112 434.744174909375 265.682618967453 434.778026453534 875.434732534371 8729.55969388155] [38.5541000366211 196.233306884766 368.725494384766] [-4.19325017929077 -4.19324588775635 2.4718644618988 38.5541000366211 196.233306884766 368.725494384766 533.811157226562 899.633972167969] [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 [0.0214251689612865 0.0756286457180977 0.0835617929697037 0 0] [0.0852889068224946 0 0.0852889068224946 0;0.202286096323295 0.00986908664222525 0.21215518296552 2104.56298828125;0.202286096323295 0.00986908664222525 0.21215518296552 2104.56298828125] [0.0486927554011345 0.0994650945067406 0.11014062911272] [0.0348468534648418 0.0451556593179703 0.0558110773563385] 0.11014062911272
0.0835617929697037
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 [0.00961179099977016 0.0341722555458546 0.0469145402312279 0.0540606826543808 0.0598988868296146 0.0669510215520859] [0.0844051224696503 0 0.0844051224696503 0;0.223131547619048 0.0127824013659951 0.235913948985043 6542.99169921875;0.203647192383898 0.0155579565810699 0.219205148964968 11197.248046875;0.183830645236081 0.0179434556227464 0.201774100858828 19347.92578125;0.16714699305972 0.0210820755945198 0.18822906865424 36879.9921875;0.16714699305972 0.0210820755945198 0.18822906865424 36879.9921875] [0.0113589344546199 0.0399744771420956 0.0581489726901054 0.0807504877448082 0.102838195860386 0.109406761825085] [0.00316272140480578 0.0120077785104513 0.0261193718761206 0.0458676889538765 0.0638502165675163 0.0694702044129372] 0.109406761825085
0.0669510215520859
------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0027241/ses-2/sub-0027241_ses-2_run-1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 64s APP: Rough bias correction: Initialize 7s Estimate background 7s Initial correction 7s Refine background 3s Final correction 5s Final scaling 6s 43s Correct center-of-mass 5s Affine registration 11s SPM preprocessing 1 (estimate 1 - TPM registration): 84s SPM preprocessing 1 (estimate 2): 82s SPM preprocessing 2 (write): Write Segmentation 21s Update Segmentation 24s Update Skull-Stripping 51s Update probability maps 10s 106s Global intensity correction: 19s SANLM denoising after intensity normalization (medium): 34s Fast Optimized Shooting registration 43s Local adaptive segmentation (LASstr=0.50): Prepare maps 5s Prepare partitions 3s Prepare segments (LASmod = 1.00) 18s Estimate local tissue thresholds (WM) 24s Estimate local tissue thresholds (GM) 38s Intensity transformation 0s SANLM denoising after LAS (medium) 53s 144s ROI segmentation (partitioning): Atlas -> subject space 9s Major structures 4s Ventricle detection 22s Blood vessel detection 13s WMH detection (WMHCstr=0.50 > WMHCstr'=0.01) 30s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 4s Final corrections 5s 90s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 45s AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.67 0.08,0.99 0.04] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 6s Level 1 cleanup (brain masking) 4s Level 2 cleanup (CSF correction) 2s Level 3 cleanup (CSF/WM PVE) 4s 15s 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 | 0.0844 0.0000 0.0844 | 32.0000 2 | 2.50 | 0.0818 0.0012 0.0830 | 29.4886 3 | 2.50 | 0.0811 0.0018 0.0828 | 26.9772 4 | 2.50 | 0.0807 0.0020 0.0827 | 24.6107 5 | 2.50 | 0.0804 0.0021 0.0825 | 22.6548 6 | 2.50 | 0.0802 0.0022 0.0824 | 20.6989 7 | 2.50 | 0.0799 0.0023 0.0822 | 18.9688 8 | 2.50 | 0.0796 0.0024 0.0820 | 17.4455 9 | 2.50 | 0.0793 0.0025 0.0818 | 15.9223 10 | 2.50 | 0.0790 0.0026 0.0816 | 14.6627 11 | 2.50 | 0.0788 0.0026 0.0814 | 13.4764 12 | 2.50 | 0.0785 0.0027 0.0812 | 12.3015 13 | 2.50 | 0.0781 0.0028 0.0809 | 11.3776 14 | 2.50 | 0.0779 0.0028 0.0807 | 10.4537 15 | 2.25 | 0.0771 0.0029 0.0800 | 9.5920 16 | 2.25 | 0.0744 0.0043 0.0786 | 8.8725 29 | 2.00 | 0.0758 0.0019 0.0777 | 3.3283 30 | 2.00 | 0.0699 0.0042 0.0741 | 3.1221 31 | 2.00 | 0.0679 0.0052 0.0731 | 2.9160 43 | 1.75 | 0.0669 0.0030 0.0699 | 1.5785 44 | 1.75 | 0.0627 0.0052 0.0679 | 1.5194 45 | 1.75 | 0.0613 0.0060 0.0673 | 1.4626 57 | 1.50 | 0.0599 0.0043 0.0642 | 1.0900 58 | 1.50 | 0.0568 0.0064 0.0631 | 1.0730 59 | 1.50 | 0.0557 0.0070 0.0627 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 202s Prepare output 14s 216s Jacobian determinant (RMS): 0.011 0.040 0.058 0.081 0.103 | 0.109407 Template Matching: 0.084 0.223 0.204 0.184 0.167 | 0.167147 Write result maps: 41s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 48s CSF distance: 21s PBT2x thickness: 62s 139s Create initial surface 108s Topology correction: 122s Surface refinement: 96s Reduction of surface collisions with optimization: 88s Spherical mapping with areal smoothing 111s Spherical registration 334s rh: Thickness estimation (0.50 mm ): WM distance: 42s CSF distance: 20s PBT2x thickness: 60s 129s Create initial surface 103s Topology correction: 119s Surface refinement: 104s Reduction of surface collisions with optimization: 87s Spherical mapping with areal smoothing 112s Spherical registration 342s Final surface processing results: Average thickness (FS): 2.3870 0.6468 mm Surface intensity / position RMSE: 0.0690 / 0.0849 Euler number / defect number / defect size: 22.0 / 12.5 / 1.00% Display thickness: /var/lib/condor/execute/dir_3344799/ds/IBA_TRT/sub-0027241/ses-2/surf/lh.thickness.sub-0027241_ses-2_run-1_T1w Display thickness: /var/lib/condor/execute/dir_3344799/ds/IBA_TRT/sub-0027241/ses-2/surf/rh.thickness.sub-0027241_ses-2_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_3344799/ds/IBA_TRT/sub-0027241/ses-2/sub-0027241_ses-2_run-1_T1w.nii Surface ROI estimation: 11s Surface and thickness estimation takes: 2114s ROI estimation in native space: ROI estimation of 'cobra' atlas 10s ROI estimation of 'neuromorphometrics' atlas 39s ROI estimation of 'lpba40' atlas 11s ROI estimation of 'hammers' atlas 27s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 10s ROI estimation of 'aal3' atlas 15s ROI estimation of 'mori' atlas 23s ROI estimation of 'anatomy3' atlas 33s ROI estimation of 'julichbrain' atlas 42s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 29s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 69s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 107s ROI estimation of 'Tian_Subcortex_S2_7T' atlas 10s Write results 11s 446s Quality check: 16s Print 'Graphics' figure to: /var/lib/condor/execute/dir_3344799/ds/IBA_TRT/sub-0027241/ses-2/report/catreport_sub-0027241_ses-2_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 61 minute(s) and 56 second(s). Image Quality Rating (IQR): 82.83% (B-) GM volume (GMV): 47.84% (739.56 / 1545.79 ml) GM thickness (GMT): 2.39 0.65 mm Segmentations are saved in /var/lib/condor/execute/dir_3344799/ds/IBA_TRT/sub-0027241/ses-2/mri Reports are saved in /var/lib/condor/execute/dir_3344799/ds/IBA_TRT/sub-0027241/ses-2/report Labels are saved in /var/lib/condor/execute/dir_3344799/ds/IBA_TRT/sub-0027241/ses-2/label ------------------------------------------------------------------------