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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/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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[0.0270363669842482 0.116256453096867 0.0921548083424568 0.0574729666113853] 105.307983398438 0.296352535486221 0.292933225631714 0.155448123812675 0.359804719686508 [2 2 2] 2 2.39251637458801 10.5 [1.89584374427795 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 3.63804531097412 2.5625627040863 1.35219430923462 2.73469387755102 1.4002786604594 1.7 1.40370154380798 1.76260888576508 2.38956151428729 2.38807443898012 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 20231031-015500 1639 1639 36 1.60111464183762 14 0.0701850801706314 0.0881304442882538 36 1.60111464183762 [288.558843137255 784.112807843137 603.696705882353 0 0] 0.537545098039216 0.000320660489586674 2222.7395857005 1676.36835686275 [0.172133315423157 0.46774493483674 0.360121749740103 0 0] [2.56832714803033 0.666691757049883] [2.60153698921204 0.820397457687691 1] [1.88127162628239 0.284033946870965 0.273333370341792;2.59464997550956 0.19477258116903 0.421968590921455;3.27746535640699 0.287036429595489 0.304698038736753] [0.794423610985775 0.29536984916962 0.621329340321105;4.21261512510387 0.322319266683809 0.378670659678895] 2.61886265681013 [0.941331095961878 6.2504478239357 4.31756016056219 0.5 0.5] 1.03206604895867 8.62393612825593 5.14379105629614 [0 1 0 11534.336 0.3727289553641] [false] [0.00165779003873467 0.00134805729612708 0.353421628475189] [false] [956.043133333333 536.953823529412 570.645854901961 1910.20050980392 1242.70330588235 7392.60590980392] [794.330074509804 497.946721568627 337.709909803922 754.682231372549 1048.19184705882 8103.25658431373] [132.779403686523 262.859313964844 344.864013671875] [-5.71474981307983 -0.651824951171875 2.68452286720276 132.779403686523 262.859313964844 344.864013671875 450.906311035156 954.129150390625] [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 [0.0201772730797529 0.073627881705761 0.0815395712852478 0 0] [0.0874268164296969 0 0.0874268164296969 0;0.206476584774535 0.0116308013073393 0.218107386081874 2480.2451171875;0.206476584774535 0.0116308013073393 0.218107386081874 2480.2451171875] [0.047423217445612 0.0987782180309296 0.110898643732071] [0.0344314649701118 0.0484537109732628 0.0599831715226173] 0.110898643732071
0.0815395712852478
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 [0.00831342674791813 0.0350697301328182 0.0450686551630497 0.0541058219969273 0.0608553737401962 0.0678819045424461] [0.0867769008411709 0 0.0867769008411709 0;0.223667643467643 0.0166112904456654 0.240278933913309 8502.904296875;0.208822222465375 0.0189116445189187 0.227733866984294 13610.9375;0.186373921654276 0.021585471722928 0.207959393377204 23275.009765625;0.16786892068096 0.0250483455526129 0.192917266233573 43818.3984375;0.16786892068096 0.0250483455526129 0.192917266233573 43818.3984375] [0.00992405880242586 0.0364003330469131 0.0585384629666805 0.0826016962528229 0.106496937572956 0.113050043582916] [0.00335175707004964 0.0129800094291568 0.029304314404726 0.0500547662377357 0.0691832676529884 0.0742664411664009] 0.113050043582916
0.0678819045424461
------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0025767/ses-1/sub-0025767_ses-1_run-1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 36s APP: Rough bias correction: Initialize 5s Estimate background 4s Initial correction 5s 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): 55s SPM preprocessing 1 (estimate 2): 47s SPM preprocessing 2 (write): Write Segmentation 13s Update Segmentation 16s Update Skull-Stripping 32s Update probability maps 7s 67s Global intensity correction: 12s SANLM denoising after intensity normalization (medium): 22s Fast Optimized Shooting registration 25s Local adaptive segmentation (LASstr=0.50): Prepare maps 3s Prepare partitions 2s Prepare segments (LASmod = 1.03) 11s Estimate local tissue thresholds (WM) 14s Estimate local tissue thresholds (GM) 21s Intensity transformation 0s SANLM denoising after LAS (medium) 36s 90s ROI segmentation (partitioning): Atlas -> subject space 6s Major structures 3s Ventricle detection 10s Blood vessel detection 8s WMH detection (WMHCstr=0.50 > WMHCstr'=0.09) 18s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 3s Final corrections 4s 52s 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 0.06,0.68 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 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 | 0.0868 0.0000 0.0868 | 32.0000 2 | 2.50 | 0.0841 0.0012 0.0853 | 29.4886 3 | 2.50 | 0.0833 0.0018 0.0852 | 26.9772 4 | 2.50 | 0.0829 0.0020 0.0850 | 24.6107 5 | 2.50 | 0.0826 0.0022 0.0848 | 22.6548 6 | 2.50 | 0.0824 0.0023 0.0846 | 20.6989 7 | 2.50 | 0.0821 0.0024 0.0844 | 18.9688 8 | 2.50 | 0.0818 0.0025 0.0842 | 17.4455 9 | 2.50 | 0.0815 0.0025 0.0840 | 15.9223 10 | 2.50 | 0.0811 0.0026 0.0838 | 14.6627 11 | 2.50 | 0.0808 0.0027 0.0836 | 13.4764 12 | 2.50 | 0.0805 0.0028 0.0833 | 12.3015 13 | 2.50 | 0.0802 0.0029 0.0831 | 11.3776 14 | 2.50 | 0.0799 0.0029 0.0828 | 10.4537 15 | 2.25 | 0.0805 0.0030 0.0835 | 9.5920 16 | 2.25 | 0.0773 0.0046 0.0819 | 8.8725 17 | 2.25 | 0.0760 0.0052 0.0812 | 8.1530 18 | 2.25 | 0.0752 0.0054 0.0806 | 7.5234 19 | 2.25 | 0.0746 0.0055 0.0801 | 6.9630 29 | 2.00 | 0.0772 0.0028 0.0800 | 3.3283 30 | 2.00 | 0.0716 0.0053 0.0769 | 3.1221 31 | 2.00 | 0.0696 0.0063 0.0759 | 2.9160 43 | 1.75 | 0.0689 0.0036 0.0724 | 1.5785 44 | 1.75 | 0.0638 0.0063 0.0701 | 1.5194 45 | 1.75 | 0.0621 0.0072 0.0693 | 1.4626 57 | 1.50 | 0.0608 0.0052 0.0660 | 1.0900 58 | 1.50 | 0.0572 0.0076 0.0648 | 1.0730 59 | 1.50 | 0.0560 0.0083 0.0643 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 140s Prepare output 8s 148s Jacobian determinant (RMS): 0.010 0.036 0.059 0.083 0.106 | 0.113050 Template Matching: 0.087 0.224 0.209 0.186 0.168 | 0.167869 Write result maps: 33s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 27s CSF distance: 13s PBT2x thickness: 37s 83s Create initial surface 66s Topology correction: 84s Surface refinement: 89s Reduction of surface collisions with optimization: 68s Spherical mapping with areal smoothing 114s Spherical registration 226s rh: Thickness estimation (0.50 mm ): WM distance: 25s CSF distance: 13s PBT2x thickness: 37s 80s Create initial surface 63s Topology correction: 81s Surface refinement: 75s Reduction of surface collisions with optimization: 63s Spherical mapping with areal smoothing 76s Spherical registration 230s Final surface processing results: Average thickness (FS): 2.5685 0.6655 mm Surface intensity / position RMSE: 0.0702 / 0.0881 Euler number / defect number / defect size: 36.0 / 14.0 / 1.60% Display thickness: /var/lib/condor/execute/dir_3435141/ds/SWU_4/sub-0025767/ses-1/surf/lh.thickness.sub-0025767_ses-1_run-1_T1w Display thickness: /var/lib/condor/execute/dir_3435141/ds/SWU_4/sub-0025767/ses-1/surf/rh.thickness.sub-0025767_ses-1_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_3435141/ds/SWU_4/sub-0025767/ses-1/sub-0025767_ses-1_run-1_T1w.nii Surface ROI estimation: 8s Surface and thickness estimation takes: 1480s ROI estimation in native space: ROI estimation of 'cobra' atlas 9s ROI estimation of 'neuromorphometrics' atlas 39s ROI estimation of 'lpba40' atlas 12s ROI estimation of 'hammers' atlas 27s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 9s ROI estimation of 'aal3' atlas 14s ROI estimation of 'mori' atlas 22s ROI estimation of 'anatomy3' atlas 32s ROI estimation of 'julichbrain' atlas 49s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 21s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 44s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 97s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 176s ROI estimation of 'Tian_Subcortex_S2_7T' atlas 17s Write results 18s 570s Quality check: 12s Print 'Graphics' figure to: /var/lib/condor/execute/dir_3435141/ds/SWU_4/sub-0025767/ses-1/report/catreport_sub-0025767_ses-1_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 49 minute(s) and 5 second(s). Image Quality Rating (IQR): 81.12% (B-) GM volume (GMV): 46.77% (784.11 / 1676.37 ml) GM thickness (GMT): 2.57 0.67 mm Segmentations are saved in /var/lib/condor/execute/dir_3435141/ds/SWU_4/sub-0025767/ses-1/mri Reports are saved in /var/lib/condor/execute/dir_3435141/ds/SWU_4/sub-0025767/ses-1/report Labels are saved in /var/lib/condor/execute/dir_3435141/ds/SWU_4/sub-0025767/ses-1/label ------------------------------------------------------------------------