------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./condor/execute/dir_52137/ds/sub-06/sub-06_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 63s APP: Rough bias correction: Initialize 8s Estimate background 10s Initial correction 10s Refine background 4s Final correction 7s Final scaling 7s 54s Correct center-of-mass 6s Affine registration 12s SPM preprocessing 1 (estimate 1 - TPM registration): 94s SPM preprocessing 1 (estimate 2): 74s SPM preprocessing 2 (write): Write Segmentation 23s Update Segmentation 25s Update Skull-Stripping 53s Update probability maps 10s 111s Global intensity correction: 19s SANLM denoising after intensity normalization (medium): 14s Fast Optimized Shooting registration 42s Local adaptive segmentation (LASstr=0.50): Prepare maps 5s Prepare partitions 3s Prepare segments (LASmod = 1.00) 19s Estimate local tissue thresholds (WM) 25s Estimate local tissue thresholds (GM) 36s Intensity transformation 0s SANLM denoising after LAS (medium) 38s 131s ROI segmentation (partitioning): Atlas -> subject space 9s Major structures 4s Ventricle detection 21s Blood vessel detection 13s WMH detection (WMHCstr=0.50 > WMHCstr'=0.04) 32s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 5s Final corrections 6s 93s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 40s AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.07,0.990.04] 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 | 0.0820 0.0000 0.0820 | 32.0000 2 | 2.50 | 0.0797 0.0010 0.0807 | 29.4886 3 | 2.50 | 0.0790 0.0016 0.0806 | 26.9772 4 | 2.50 | 0.0787 0.0018 0.0805 | 24.6107 5 | 2.50 | 0.0785 0.0019 0.0804 | 22.6548 6 | 2.50 | 0.0782 0.0020 0.0802 | 20.6989 7 | 2.50 | 0.0780 0.0020 0.0800 | 18.9688 8 | 2.50 | 0.0778 0.0021 0.0799 | 17.4455 9 | 2.50 | 0.0775 0.0022 0.0797 | 15.9223 10 | 2.50 | 0.0772 0.0023 0.0795 | 14.6627 11 | 2.50 | 0.0770 0.0023 0.0793 | 13.4764 12 | 2.50 | 0.0767 0.0024 0.0791 | 12.3015 13 | 2.50 | 0.0764 0.0025 0.0789 | 11.3776 14 | 2.50 | 0.0762 0.0025 0.0787 | 10.4537 15 | 2.25 | 0.0751 0.0026 0.0777 | 9.5920 16 | 2.25 | 0.0724 0.0040 0.0764 | 8.8725 29 | 2.00 | 0.0742 0.0018 0.0760 | 3.3283 30 | 2.00 | 0.0680 0.0043 0.0723 | 3.1221 31 | 2.00 | 0.0660 0.0053 0.0713 | 2.9160 43 | 1.75 | 0.0650 0.0030 0.0681 | 1.5785 44 | 1.75 | 0.0605 0.0055 0.0659 | 1.5194 45 | 1.75 | 0.0590 0.0063 0.0653 | 1.4626 57 | 1.50 | 0.0575 0.0046 0.0620 | 1.0900 58 | 1.50 | 0.0542 0.0067 0.0609 | 1.0730 59 | 1.50 | 0.0531 0.0073 0.0604 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 204s Prepare output 15s 219s Jacobian determinant (RMS): 0.011 0.038 0.056 0.078 0.100 | 0.106721 Template Matching: 0.082 0.217 0.198 0.177 0.159 | 0.159261 Write result maps: 29s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 40s CSF distance: 21s PBT2x thickness: 60s 129s Create initial surface 105s Topology correction: 132s Surface refinement: 168s Reduction of surface collisions with optimization: 162s Spherical mapping with areal smoothing 108s Spherical registration 318s rh: Thickness estimation (0.50 mm): WM distance: 49s CSF distance: 20s PBT2x thickness: 57s 132s Create initial surface 97s Topology correction: 111s Surface refinement: 123s Reduction of surface collisions with optimization: 82s Spherical mapping with areal smoothing 101s Spherical registration 303s Final surface processing results: Average thickness (FS): 2.5717  0.6339 mm Surface intensity / position RMSE: 0.0663 / 0.0753 Euler number / defect number / defect size: 18.0 / 18.0 / 1.06% Display thickness: /var/lib/condor/execute/dir_52137/ds/sub-06/surf/lh.thickness.sub-06_T1w Display thickness: /var/lib/condor/execute/dir_52137/ds/sub-06/surf/rh.thickness.sub-06_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_52137/ds/sub-06/sub-06_T1w.nii Surface ROI estimation: 10s Surface and thickness estimation takes: 2185s ROI estimation in native space: ROI estimation of 'cobra' atlas 9s ROI estimation of 'neuromorphometrics' atlas 32s ROI estimation of 'lpba40' atlas 9s ROI estimation of 'hammers' atlas 21s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 8s ROI estimation of 'aal3' atlas 12s ROI estimation of 'mori' atlas 19s ROI estimation of 'anatomy3' atlas 34s ROI estimation of 'julichbrain' atlas 42s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 31s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 72s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 84s Write results 85s 393s Quality check: 6s Print 'Graphics' figure to: /var/lib/condor/execute/dir_52137/ds/sub-06/report/catreport_sub-06_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 61 minute(s) and 34 second(s). Image Quality Rating (IQR): 83.55% (B) GM volume (GMV): 47.26% (717.10 / 1517.20 ml) GM thickness (GMT): 2.57  0.63 mm Segmentations are saved in /var/lib/condor/execute/dir_52137/ds/sub-06/mri Reports are saved in /var/lib/condor/execute/dir_52137/ds/sub-06/report Labels are saved in /var/lib/condor/execute/dir_52137/ds/sub-06/label ------------------------------------------------------------------------