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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] /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_3719195/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 28 1.12255126483697 15 0.0684447959065437 0.0827742218971252 [1.00000002221413 1.00000000039182 1.00000001032621] [1.0000000811075 1.00000000065194 1.00000001045591] 1.00000001097739 0 [4.8439998626709 113.925003051758 266.808990478516 385.2080078125] [0.0125750238075852 0.295749306678772 0.692636132240295 1] T1 [7.46287331176028 45.5668461497239 37.3030869479141 24.2803607368072] [0.0196203459054232 0.119797997176647 0.0980720743536949 0.0638345405459404] 119.906845092773 0.311278164386749 0.302901029586792 0.142270743846893 0.293013632297516 [2.00000004442826 2.00000000078364 2.00000002065241] 2.00000002195477 2.44337248802185 1 [8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 3.41416072845459 2.3733959197998 1.18654179573059 2.3265306122449 1.28063781620924 1.75 1.36889588832855 1.6554844379425 2.32176357820777 2.23892682314552 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 20231031-010142 1639 1639 28 1.12255126483697 15 0.0684447959065437 0.0827742218971252 28 1.12255126483697 [304.388996696785 707.740473107664 446.774684336733 0 0] 0.221027471362515 0.000151502393584332 1953.18335586894 1458.90415414118 [0.208642216716403 0.485117868160634 0.306239915122963 0 0] [2.55034708456075 0.673933353303817] [2.56158471107483 0.836021910714179 1] [1.88012986855304 0.290657734016526 0.283913106645863;2.57563370950719 0.197032152857146 0.431232589429533;3.30036694173234 0.295968315071895 0.284854303924603] [0.745745427475818 0.298486304739084 0.6206995963867;4.23716675791222 0.296052741445751 0.3793004036133] 1.08221903936213 [1.5970225703377 6.56246171265507 3.349854797467 0.5 0.5] 1.01515023935843 8.61891703360885 5.36964863454778 [0 1 0 11534.3363798505 0.389928522935387] [false] [0.00143010192550719 0.00121145695447922 0.0182279124855995] [false] [808.028152943961 398.205660250081 551.841137162726 392.320436177961 907.496413096853 8968.89523883441] [699.105350742746 372.153316671185 349.205130241285 315.416868301959 757.104544326455 9041.37634355749] [134.999893188477 284.335296630859 375.273193359375] [-5.47609996795654 -5.47609519958496 3.00151634216309 134.999893188477 284.335296630859 375.273193359375 495.409851074219 1012.52191162109] [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 [0.0218591243028641 0.0756331533193588 0.0849350690841675 0 0] [0.0895394473707452 0 0.0895394473707452 0;0.213606780602866 0.0117519625953409 0.225358743198207 2506.08251953125;0.213606780602866 0.0117519625953409 0.225358743198207 2506.08251953125] [0.0444227457046509 0.105994656682014 0.120027638971806] [0.0311085507273674 0.0527363158762455 0.0651712045073509] 0.120027638971806

0.0849350690841675

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 [0.00924278702586889 0.0342370569705963 0.0437086559832096 0.0530980341136456 0.0609367713332176 0.0684918835759163] [0.0863263160105008 0 0.0863263160105008 0;0.224387332112332 0.0149108592796093 0.239298191391941 7632.49609375;0.20951989736867 0.0168374071633862 0.226357304532056 12118.083984375;0.188475562636329 0.0195281290487233 0.208003691685053 21056.634765625;0.17036986317227 0.022854297774663 0.193224160946933 39980.234375;0.17036986317227 0.022854297774663 0.193224160946933 39980.234375] [0.0108248703181744 0.0374605469405651 0.0580168031156063 0.084031768143177 0.109644211828709 0.11578942835331] [0.0031223960686475 0.0124014858156443 0.0293580796569586 0.0506413727998734 0.0690798684954643 0.0745939463376999] 0.11578942835331

0.0684918835759163

------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0025804/ses-2/sub-0025804_ses-2_run-1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 35s APP: Rough bias correction: Initialize 5s Estimate background 4s Initial correction 4s Refine background 2s Final correction 4s Final scaling 4s 29s Correct center-of-mass 3s Affine registration 7s SPM preprocessing 1 (estimate 1 - TPM registration): 57s SPM preprocessing 1 (estimate 2): 44s SPM preprocessing 2 (write): Write Segmentation 13s Update Segmentation 15s Update Skull-Stripping 32s Update probability maps 7s 68s Global intensity correction: 13s SANLM denoising after intensity normalization (medium): 19s Fast Optimized Shooting registration 25s Local adaptive segmentation (LASstr=0.50): Prepare maps 2s Prepare partitions 2s Prepare segments (LASmod = 1.08) 10s Estimate local tissue thresholds (WM) 14s Estimate local tissue thresholds (GM) 20s Intensity transformation 0s SANLM denoising after LAS (medium) 35s 86s ROI segmentation (partitioning): Atlas -> subject space 6s Major structures 2s Ventricle detection 10s Blood vessel detection 7s WMH detection (WMHCstr=0.50 > WMHCstr'=0.18) 14s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 2s Final corrections 4s 47s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 26s 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) 3s Level 1 cleanup (brain masking) 2s Level 2 cleanup (CSF correction) 1s Level 3 cleanup (CSF/WM PVE) 2s 8s 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 | 0.0863 0.0000 0.0863 | 32.0000 2 | 2.50 | 0.0839 0.0012 0.0851 | 29.4886 3 | 2.50 | 0.0832 0.0017 0.0850 | 26.9772 4 | 2.50 | 0.0829 0.0019 0.0848 | 24.6107 5 | 2.50 | 0.0826 0.0021 0.0847 | 22.6548 6 | 2.50 | 0.0824 0.0021 0.0845 | 20.6989 7 | 2.50 | 0.0821 0.0022 0.0843 | 18.9688 8 | 2.50 | 0.0819 0.0023 0.0842 | 17.4455 9 | 2.50 | 0.0816 0.0024 0.0840 | 15.9223 10 | 2.50 | 0.0813 0.0025 0.0838 | 14.6627 11 | 2.50 | 0.0810 0.0025 0.0836 | 13.4764 12 | 2.50 | 0.0808 0.0026 0.0833 | 12.3015 13 | 2.50 | 0.0804 0.0027 0.0831 | 11.3776 14 | 2.50 | 0.0802 0.0027 0.0829 | 10.4537 15 | 2.25 | 0.0798 0.0028 0.0826 | 9.5920 16 | 2.25 | 0.0768 0.0042 0.0810 | 8.8725 17 | 2.25 | 0.0756 0.0047 0.0803 | 8.1530 18 | 2.25 | 0.0748 0.0050 0.0798 | 7.5234 29 | 2.00 | 0.0771 0.0024 0.0794 | 3.3283 30 | 2.00 | 0.0717 0.0047 0.0764 | 3.1221 31 | 2.00 | 0.0698 0.0056 0.0755 | 2.9160 43 | 1.75 | 0.0690 0.0032 0.0722 | 1.5785 44 | 1.75 | 0.0644 0.0057 0.0700 | 1.5194 45 | 1.75 | 0.0628 0.0065 0.0693 | 1.4626 57 | 1.50 | 0.0613 0.0047 0.0660 | 1.0900 58 | 1.50 | 0.0579 0.0069 0.0648 | 1.0730 59 | 1.50 | 0.0568 0.0076 0.0644 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 141s Prepare output 7s 149s Jacobian determinant (RMS): 0.011 0.037 0.058 0.084 0.110 | 0.115789 Template Matching: 0.086 0.224 0.210 0.188 0.170 | 0.170370 Write result maps: 28s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 30s CSF distance: 11s PBT2x thickness: 33s 79s Create initial surface 61s Topology correction: 79s Surface refinement: 58s Reduction of surface collisions with optimization: 50s Spherical mapping with areal smoothing 62s Spherical registration 217s rh: Thickness estimation (0.50 mm ): WM distance: 24s CSF distance: 12s PBT2x thickness: 33s 73s Create initial surface 60s Topology correction: 69s Surface refinement: 49s Reduction of surface collisions with optimization: 48s Spherical mapping with areal smoothing 62s Spherical registration 202s Final surface processing results: Average thickness (FS): 2.5508 0.6717 mm Surface intensity / position RMSE: 0.0684 / 0.0828 Euler number / defect number / defect size: 28.0 / 15.0 / 1.12% Display thickness: /var/lib/condor/execute/dir_3719195/ds/SWU_4/sub-0025804/ses-2/surf/lh.thickness.sub-0025804_ses-2_run-1_T1w Display thickness: /var/lib/condor/execute/dir_3719195/ds/SWU_4/sub-0025804/ses-2/surf/rh.thickness.sub-0025804_ses-2_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_3719195/ds/SWU_4/sub-0025804/ses-2/sub-0025804_ses-2_run-1_T1w.nii Surface ROI estimation: 8s Surface and thickness estimation takes: 1246s ROI estimation in native space: ROI estimation of 'cobra' atlas 15s ROI estimation of 'neuromorphometrics' atlas 61s ROI estimation of 'lpba40' atlas 24s ROI estimation of 'hammers' atlas 61s ROI estimation of 'thalamus' atlas 5s ROI estimation of 'ibsr' atlas 21s ROI estimation of 'aal3' atlas 35s ROI estimation of 'mori' atlas 52s ROI estimation of 'anatomy3' atlas 73s ROI estimation of 'julichbrain' atlas 89s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 35s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 65s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 105s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 117s ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s Write results 9s 769s Quality check: 9s Print 'Graphics' figure to: /var/lib/condor/execute/dir_3719195/ds/SWU_4/sub-0025804/ses-2/report/catreport_sub-0025804_ses-2_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 46 minute(s) and 9 second(s). Image Quality Rating (IQR): 82.61% (B-) GM volume (GMV): 48.51% (707.74 / 1458.90 ml) GM thickness (GMT): 2.55 0.67 mm Segmentations are saved in /var/lib/condor/execute/dir_3719195/ds/SWU_4/sub-0025804/ses-2/mri Reports are saved in /var/lib/condor/execute/dir_3719195/ds/SWU_4/sub-0025804/ses-2/report Labels are saved in /var/lib/condor/execute/dir_3719195/ds/SWU_4/sub-0025804/ses-2/label ------------------------------------------------------------------------