------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./sub-season212_ses-3_acq-MPrageHiRes_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 50s APP: Rough bias correction: Initialize 8s Estimate background 8s Initial correction 11s Refine background 4s Final correction 9s Final scaling 9s 57s Correct center-of-mass 6s Affine registration 13s SPM preprocessing 1 (estimate 1 - TPM registration): 95s SPM preprocessing 1 (estimate 2): 98s SPM preprocessing 2 (write): Write Segmentation 21s Update Segmentation 25s Update Skull-Stripping 56s Update probability maps 11s 113s Global intensity correction: 20s SANLM denoising after intensity normalization (medium): 21s Fast Optimized Shooting registration 37s Local adaptive segmentation (LASstr=0.50): Prepare maps 6s Prepare partitions 4s Prepare segments (LASmod = 1.03) 20s Estimate local tissue thresholds (WM) 23s Estimate local tissue thresholds (GM) 32s Intensity transformation 0s SANLM denoising after LAS (medium) 30s 118s ROI segmentation (partitioning): Atlas -> subject space 10s Major structures 5s Ventricle detection 26s Blood vessel detection 12s WMH detection (WMHCstr=0.50 > WMHCstr'=0.04) 38s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 5s Final corrections 5s 104s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 41s AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.04] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 6s Level 1 cleanup (brain masking) 3s Level 2 cleanup (CSF correction) 2s Level 3 cleanup (CSF/WM PVE) 4s 14s 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 | 0.0793 0.0012 0.0805 | 29.4886 3 | 2.50 | 0.0785 0.0019 0.0804 | 26.9772 4 | 2.50 | 0.0781 0.0021 0.0802 | 24.6107 5 | 2.50 | 0.0778 0.0023 0.0800 | 22.6548 6 | 2.50 | 0.0775 0.0024 0.0799 | 20.6989 7 | 2.50 | 0.0772 0.0025 0.0797 | 18.9688 8 | 2.50 | 0.0769 0.0026 0.0795 | 17.4455 9 | 2.50 | 0.0766 0.0027 0.0792 | 15.9223 10 | 2.50 | 0.0762 0.0028 0.0790 | 14.6627 11 | 2.50 | 0.0759 0.0029 0.0788 | 13.4764 12 | 2.50 | 0.0756 0.0030 0.0785 | 12.3015 13 | 2.50 | 0.0752 0.0031 0.0783 | 11.3776 14 | 2.50 | 0.0749 0.0032 0.0780 | 10.4537 15 | 2.25 | 0.0735 0.0032 0.0767 | 9.5920 16 | 2.25 | 0.0706 0.0047 0.0753 | 8.8725 29 | 2.00 | 0.0715 0.0021 0.0736 | 3.3283 30 | 2.00 | 0.0652 0.0045 0.0697 | 3.1221 31 | 2.00 | 0.0630 0.0056 0.0686 | 2.9160 43 | 1.75 | 0.0617 0.0032 0.0650 | 1.5785 44 | 1.75 | 0.0576 0.0053 0.0630 | 1.5194 45 | 1.75 | 0.0562 0.0061 0.0623 | 1.4626 57 | 1.50 | 0.0544 0.0044 0.0589 | 1.0900 58 | 1.50 | 0.0515 0.0063 0.0578 | 1.0730 59 | 1.50 | 0.0506 0.0069 0.0575 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 163s Prepare output 12s 175s Jacobian determinant (RMS): 0.013 0.046 0.066 0.089 0.109 | 0.115099 Template Matching: 0.082 0.212 0.189 0.169 0.152 | 0.151774 Write result maps: 29s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 36s CSF distance: 13s PBT2x thickness: 38s 93s Create initial surface 73s Topology correction: 88s Surface refinement: 65s Reduction of surface collisions with optimization: 60s Spherical mapping with areal smoothing 72s Spherical registration 300s rh: Thickness estimation (0.50 mm): WM distance: 52s CSF distance: 14s PBT2x thickness: 41s 114s Create initial surface 80s Topology correction: 89s Surface refinement: 83s Reduction of surface collisions with optimization: 57s Spherical mapping with areal smoothing 70s Spherical registration 282s Final surface processing results: Average thickness (FS): 2.4837  0.5847 mm Surface intensity / position RMSE: 0.0654 / 0.0672 Euler number / defect number / defect size: 10.0 / 9.0 / 0.23% Display thickness: /var/lib/condor/execute/dir_21558/ds/sub-season212/surf/lh.thickness.sub-season212_ses-3_acq-MPrageHiRes_T1w Display thickness: /var/lib/condor/execute/dir_21558/ds/sub-season212/surf/rh.thickness.sub-season212_ses-3_acq-MPrageHiRes_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_21558/ds/sub-season212/sub-season212_ses-3_acq-MPrageHiRes_T1w.nii Surface ROI estimation: 7s Surface and thickness estimation takes: 1619s ROI estimation in native space: ROI estimation of 'cobra' atlas 9s ROI estimation of 'neuromorphometrics' atlas 34s ROI estimation of 'lpba40' atlas 10s ROI estimation of 'hammers' atlas 24s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 8s ROI estimation of 'aal3' atlas 14s ROI estimation of 'mori' atlas 20s ROI estimation of 'anatomy3' atlas 30s ROI estimation of 'julichbrain' atlas 40s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 16s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 29s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 64s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 98s Write results 98s 399s Quality check: 6s Print 'Graphics' figure to: /var/lib/condor/execute/dir_21558/ds/sub-season212/report/catreport_sub-season212_ses-3_acq-MPrageHiRes_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 52 minute(s) and 18 second(s). Image Quality Rating (IQR): 86.96% (B+) GM volume (GMV): 47.39% (637.20 / 1344.56 ml) GM thickness (GMT): 2.48  0.58 mm Segmentations are saved in /var/lib/condor/execute/dir_21558/ds/sub-season212/mri Reports are saved in /var/lib/condor/execute/dir_21558/ds/sub-season212/report Labels are saved in /var/lib/condor/execute/dir_21558/ds/sub-season212/label ------------------------------------------------------------------------