------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./execute/dir_23543/ds/sub-sc033/sub-sc033_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 24s APP: Rough bias correction: Initialize 7s Estimate background 6s Initial correction 6s Refine background 3s Final correction 5s Final scaling 5s 39s Correct center-of-mass 5s Affine registration 9s SPM preprocessing 1 (estimate 1 - TPM registration): 88s SPM preprocessing 1 (estimate 2): 49s SPM preprocessing 2 (write): Write Segmentation 17s Update Segmentation 18s Update Skull-Stripping 40s Update probability maps 9s 83s Global intensity correction: 16s SANLM denoising after intensity normalization (medium): 8s Fast Optimized Shooting registration 32s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 2s Prepare segments (LASmod = 1.05) 14s Estimate local tissue thresholds (WM) 18s Estimate local tissue thresholds (GM) 23s Intensity transformation 0s SANLM denoising after LAS (medium) 13s 77s ROI segmentation (partitioning): Atlas -> subject space 7s Major structures 3s Ventricle detection 13s Blood vessel detection 9s WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 25s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 3s Final corrections 5s 68s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 32s AMAP peaks: [CSF,GM,WM] = [0.360.07,0.680.07,0.980.05] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 4s Level 1 cleanup (brain masking) 3s Level 2 cleanup (CSF correction) 1s Level 3 cleanup (CSF/WM PVE) 3s 11s 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 | 0.0813 0.0000 0.0813 | 32.0000 2 | 2.50 | 0.0791 0.0010 0.0802 | 29.4886 3 | 2.50 | 0.0785 0.0016 0.0800 | 26.9772 4 | 2.50 | 0.0782 0.0018 0.0799 | 24.6107 5 | 2.50 | 0.0779 0.0019 0.0798 | 22.6548 6 | 2.50 | 0.0777 0.0020 0.0796 | 20.6989 7 | 2.50 | 0.0774 0.0021 0.0795 | 18.9688 8 | 2.50 | 0.0772 0.0022 0.0793 | 17.4455 9 | 2.50 | 0.0769 0.0022 0.0791 | 15.9223 10 | 2.50 | 0.0766 0.0023 0.0790 | 14.6627 11 | 2.50 | 0.0764 0.0024 0.0788 | 13.4764 12 | 2.50 | 0.0761 0.0025 0.0786 | 12.3015 13 | 2.50 | 0.0758 0.0026 0.0784 | 11.3776 14 | 2.50 | 0.0755 0.0026 0.0781 | 10.4537 15 | 2.25 | 0.0744 0.0027 0.0771 | 9.5920 16 | 2.25 | 0.0718 0.0041 0.0758 | 8.8725 29 | 2.00 | 0.0731 0.0018 0.0749 | 3.3283 30 | 2.00 | 0.0674 0.0042 0.0716 | 3.1221 31 | 2.00 | 0.0654 0.0051 0.0705 | 2.9160 43 | 1.75 | 0.0644 0.0029 0.0673 | 1.5785 44 | 1.75 | 0.0602 0.0051 0.0653 | 1.5194 45 | 1.75 | 0.0588 0.0059 0.0647 | 1.4626 57 | 1.50 | 0.0573 0.0043 0.0616 | 1.0900 58 | 1.50 | 0.0542 0.0063 0.0605 | 1.0730 59 | 1.50 | 0.0532 0.0069 0.0601 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 173s Prepare output 10s 183s Jacobian determinant (RMS): 0.011 0.041 0.062 0.087 0.112 | 0.118493 Template Matching: 0.081 0.215 0.196 0.176 0.160 | 0.159628 Write result maps: 26s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 28s CSF distance: 15s PBT2x thickness: 45s 94s Create initial surface 84s Topology correction: 91s Surface refinement: 81s Reduction of surface collisions with optimization: 77s Spherical mapping with areal smoothing 84s Spherical registration 298s rh: Thickness estimation (0.50 mm): WM distance: 32s CSF distance: 16s PBT2x thickness: 45s 98s Create initial surface 86s Topology correction: 97s Surface refinement: 89s Reduction of surface collisions with optimization: 73s Spherical mapping with areal smoothing 82s Spherical registration 315s Final surface processing results: Average thickness (FS): 2.7030  0.6430 mm Surface intensity / position RMSE: 0.0694 / 0.0687 Euler number / defect number / defect size: 18.0 / 15.5 / 0.94% Display thickness: /var/lib/condor/execute/dir_23543/ds/sub-sc033/surf/lh.thickness.sub-sc033_T1w Display thickness: /var/lib/condor/execute/dir_23543/ds/sub-sc033/surf/rh.thickness.sub-sc033_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_23543/ds/sub-sc033/sub-sc033_T1w.nii Surface ROI estimation: 9s Surface and thickness estimation takes: 1748s ROI estimation in native space: ROI estimation of 'cobra' atlas 9s ROI estimation of 'neuromorphometrics' atlas 34s ROI estimation of 'lpba40' atlas 9s ROI estimation of 'hammers' atlas 23s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 9s ROI estimation of 'aal3' atlas 14s ROI estimation of 'mori' atlas 20s ROI estimation of 'anatomy3' atlas 28s ROI estimation of 'julichbrain' atlas 36s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 26s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 57s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 88s Write results 89s 372s Quality check: 5s Print 'Graphics' figure to: /var/lib/condor/execute/dir_23543/ds/sub-sc033/report/catreport_sub-sc033_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 49 minute(s) and 23 second(s). Image Quality Rating (IQR): 81.25% (B-) GM volume (GMV): 53.32% (759.89 / 1425.17 ml) GM thickness (GMT): 2.70  0.64 mm Segmentations are saved in /var/lib/condor/execute/dir_23543/ds/sub-sc033/mri Reports are saved in /var/lib/condor/execute/dir_23543/ds/sub-sc033/report Labels are saved in /var/lib/condor/execute/dir_23543/ds/sub-sc033/label ------------------------------------------------------------------------