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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] /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] /var/lib/condor/execute/dir_612028/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 /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 18 0.398423329778823 11.5 0.0676626563072205 0.0648740082979202 [1 1 1] [1 1 1] 1 169.92463684082 [161.328491210938 473.679992675781 1524.67895507812 2417.19506835938] [0.0667420253157616 0.19596266746521 0.630763709545135 1] T1 [75.6318539382112 255.079642294335 256.0541368505 165.075858490464] [0.0335267372429371 0.113073900341988 0.113505877554417 0.0731762498617172] 856.182312011719 0.354204893112183 0.368488788604736 0.135566100478172 0.231319919228554 [2 2 2] 2 2.77800416946411 10.5 [8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 2.77025985717773 2.2771475315094 1.03353154659271 1.81632653061224 1.09960583244471 1.575 1.35325312614441 1.29748010635376 2.49645748819056 2.16879378932178 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 20231031-005712 1639 1639 18 0.398423329778823 11.5 0.0676626563072205 0.0648740082979202 18 0.398423329778823 [219.647956862745 627.092976470588 418.151082352941 0 0] 0.251450980392157 0.00019879244810928 1777.69216746479 1264.89201568627 [0.173649571772792 0.495767993389029 0.330582434838179 0 0] [2.46413252316156 0.610803545145835] [2.44355487823486 0.714315173975083 1] [1.88396512647734 0.245843033582866 0.307572323876672;2.47514839349347 0.172196885591097 0.431124447428795;3.13329395130842 0.262883007598028 0.261303228694533] [0.911750111695084 0.294367474259289 0.512097922003985;4.04817979120643 0.335695413276324 0.487902077996015] 1.42273364534262 [0.968562711436635 6.75373551345239 3.78704085557075 0.5 0.5] 1.01987924481093 8.57328690671878 5.52969020605131 [0 1 0 10223.616 0.523346877546387] [false] [0.00148230267222971 0.00130386929959059 0.0647809132933617] [false] [759.665309803922 371.358117647059 348.310811764706 533.606737254902 1228.4910627451 7529.26447843137] [673.3518 348.520768627451 210.772768627451 432.258462745098 854.773152941176 7703.96038039216] [561.543090820312 1609.06005859375 2399.21142578125] [-34.115161895752 -34.115161895752 45.5109901428223 561.543090820312 1609.06005859375 2399.21142578125 3318.04565429688 7667.68408203125] [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 [0.0227505322545767 0.0774949193000793 0.0859683752059937 0 0] [0.0866400820582139 0 0.0866400820582139 0;0.200188718065351 0.0104452730799351 0.210633991145286 2227.43359375;0.200188718065351 0.0104452730799351 0.210633991145286 2227.43359375] [0.0499183312058449 0.103047311306 0.11415708065033] [0.0357024036347866 0.0467157326638699 0.0576671846210957] 0.11415708065033

0.0859683752059937

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 [0.0113461688160896 0.0407823175191879 0.0560419633984566 0.0641317367553711 0.0698921009898186 0.07854313403368] [0.0873487523476538 0 0.0873487523476538 0;0.222517658730159 0.0158183216956654 0.238335980425824 8097.00341796875;0.200649400385154 0.0172048175824149 0.217854217967569 12382.513671875;0.180599665483292 0.0184797955374432 0.199079461020735 19926.24609375;0.16676161843836 0.0193157841784934 0.186077402616853 33790.125;0.16676161843836 0.0193157841784934 0.186077402616853 33790.125] [0.0132524548098445 0.0469771549105644 0.0683466866612434 0.0917742252349854 0.114779278635979 0.119704194366932] [0.00344592542387545 0.0132121965289116 0.0289777256548405 0.0479715242981911 0.0657313168048859 0.0701226815581322] 0.119704194366932

0.07854313403368

------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0027271/ses-2/sub-0027271_ses-2_run-1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 50s APP: Rough bias correction: Initialize 5s Estimate background 5s Initial correction 5s Refine background 3s Final correction 4s Final scaling 4s 31s Correct center-of-mass 5s Affine registration 7s SPM preprocessing 1 (estimate 1 - TPM registration): 67s SPM preprocessing 1 (estimate 2): 41s SPM preprocessing 2 (write): Write Segmentation 14s Update Segmentation 16s Update Skull-Stripping 34s Update probability maps 7s 72s Global intensity correction: 13s SANLM denoising after intensity normalization (medium): 22s Fast Optimized Shooting registration 29s Local adaptive segmentation (LASstr=0.50): Prepare maps 3s Prepare partitions 2s Prepare segments (LASmod = 1.00) 12s Estimate local tissue thresholds (WM) 15s Estimate local tissue thresholds (GM) 23s Intensity transformation 0s SANLM denoising after LAS (medium) 35s 92s ROI segmentation (partitioning): Atlas -> subject space 6s Major structures 3s Ventricle detection 11s Blood vessel detection 8s WMH detection (WMHCstr=0.50 > WMHCstr'=0.06) 19s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 3s Final corrections 4s 55s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 28s AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 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 | 0.0873 0.0000 0.0873 | 32.0000 2 | 2.50 | 0.0838 0.0014 0.0853 | 29.4886 3 | 2.50 | 0.0828 0.0022 0.0850 | 26.9772 4 | 2.50 | 0.0823 0.0025 0.0848 | 24.6107 5 | 2.50 | 0.0819 0.0027 0.0846 | 22.6548 6 | 2.50 | 0.0815 0.0028 0.0843 | 20.6989 7 | 2.50 | 0.0812 0.0029 0.0841 | 18.9688 8 | 2.50 | 0.0808 0.0030 0.0838 | 17.4455 9 | 2.50 | 0.0804 0.0031 0.0835 | 15.9223 10 | 2.50 | 0.0800 0.0032 0.0833 | 14.6627 11 | 2.50 | 0.0796 0.0033 0.0830 | 13.4764 12 | 2.50 | 0.0793 0.0034 0.0827 | 12.3015 13 | 2.50 | 0.0788 0.0035 0.0824 | 11.3776 14 | 2.50 | 0.0784 0.0036 0.0820 | 10.4537 15 | 2.25 | 0.0774 0.0037 0.0811 | 9.5920 16 | 2.25 | 0.0742 0.0053 0.0794 | 8.8725 29 | 2.00 | 0.0750 0.0024 0.0773 | 3.3283 30 | 2.00 | 0.0689 0.0048 0.0737 | 3.1221 31 | 2.00 | 0.0669 0.0057 0.0726 | 2.9160 43 | 1.75 | 0.0656 0.0033 0.0690 | 1.5785 44 | 1.75 | 0.0616 0.0054 0.0670 | 1.5194 45 | 1.75 | 0.0602 0.0062 0.0664 | 1.4626 57 | 1.50 | 0.0586 0.0045 0.0631 | 1.0900 58 | 1.50 | 0.0556 0.0064 0.0620 | 1.0730 Shooting registration with 2.50:-0.25:1.50 mm takes: 145s Prepare output 10s 155s Jacobian determinant (RMS): 0.013 0.047 0.068 0.092 0.115 | 0.119704 Template Matching: 0.087 0.223 0.201 0.181 0.167 | 0.166762 Write result maps: 31s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 29s CSF distance: 14s PBT2x thickness: 41s 90s Create initial surface 79s Topology correction: 75s Surface refinement: 88s Reduction of surface collisions with optimization: 60s Spherical mapping with areal smoothing 85s Spherical registration 305s rh: Thickness estimation (0.50 mm ): WM distance: 27s CSF distance: 14s PBT2x thickness: 39s 85s Create initial surface 76s Topology correction: 71s Surface refinement: 90s Reduction of surface collisions with optimization: 56s Spherical mapping with areal smoothing 68s Spherical registration 291s Final surface processing results: Average thickness (FS): 2.4641 0.6105 mm Surface intensity / position RMSE: 0.0677 / 0.0649 Euler number / defect number / defect size: 18.0 / 11.5 / 0.40% Display thickness: /var/lib/condor/execute/dir_612028/ds/UWM/sub-0027271/ses-2/surf/lh.thickness.sub-0027271_ses-2_run-1_T1w Display thickness: /var/lib/condor/execute/dir_612028/ds/UWM/sub-0027271/ses-2/surf/rh.thickness.sub-0027271_ses-2_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_612028/ds/UWM/sub-0027271/ses-2/sub-0027271_ses-2_run-1_T1w.nii Surface ROI estimation: 8s Surface and thickness estimation takes: 1607s ROI estimation in native space: ROI estimation of 'cobra' atlas 8s ROI estimation of 'neuromorphometrics' atlas 28s ROI estimation of 'lpba40' atlas 8s ROI estimation of 'hammers' atlas 19s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 7s ROI estimation of 'aal3' atlas 10s ROI estimation of 'mori' atlas 16s ROI estimation of 'anatomy3' atlas 22s ROI estimation of 'julichbrain' atlas 29s 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 46s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 70s ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s Write results 7s 304s Quality check: 10s Print 'Graphics' figure to: /var/lib/condor/execute/dir_612028/ds/UWM/sub-0027271/ses-2/report/catreport_sub-0027271_ses-2_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 44 minute(s) and 53 second(s). Image Quality Rating (IQR): 83.31% (B-) GM volume (GMV): 49.58% (627.09 / 1264.89 ml) GM thickness (GMT): 2.46 0.61 mm Segmentations are saved in /var/lib/condor/execute/dir_612028/ds/UWM/sub-0027271/ses-2/mri Reports are saved in /var/lib/condor/execute/dir_612028/ds/UWM/sub-0027271/ses-2/report Labels are saved in /var/lib/condor/execute/dir_612028/ds/UWM/sub-0027271/ses-2/label ------------------------------------------------------------------------