------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./execute/dir_9674/ds/sub-sc016/sub-sc016_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 41s APP: Rough bias correction: Initialize 9s Estimate background 9s Initial correction 8s Refine background 4s Final correction 6s Final scaling 6s 52s Correct center-of-mass 3s Affine registration 13s SPM preprocessing 1 (estimate 1 - TPM registration): 105s SPM preprocessing 1 (estimate 2): 78s SPM preprocessing 2 (write): Write Segmentation 24s Update Segmentation 25s Update Skull-Stripping 57s Update probability maps 12s 118s Global intensity correction: 22s SANLM denoising after intensity normalization (medium): 13s Fast Optimized Shooting registration 44s Local adaptive segmentation (LASstr=0.50): Prepare maps 5s Prepare partitions 3s Prepare segments (LASmod = 1.08) 20s Estimate local tissue thresholds (WM) 26s Estimate local tissue thresholds (GM) 37s Intensity transformation 0s SANLM denoising after LAS (medium) 13s 108s ROI segmentation (partitioning): Atlas -> subject space 10s Major structures 5s Ventricle detection 15s Blood vessel detection 14s WMH detection (WMHCstr=0.50 > WMHCstr'=0.15) 31s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 5s Final corrections 6s 87s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 40s AMAP peaks: [CSF,GM,WM] = [0.360.07,0.680.07,0.980.04] 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) 3s 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 | 0.0855 0.0000 0.0855 | 32.0000 2 | 2.50 | 0.0831 0.0011 0.0843 | 29.4886 3 | 2.50 | 0.0825 0.0017 0.0841 | 26.9772 4 | 2.50 | 0.0821 0.0019 0.0840 | 24.6107 5 | 2.50 | 0.0819 0.0020 0.0838 | 22.6548 6 | 2.50 | 0.0816 0.0021 0.0837 | 20.6989 7 | 2.50 | 0.0814 0.0021 0.0835 | 18.9688 8 | 2.50 | 0.0811 0.0022 0.0833 | 17.4455 9 | 2.50 | 0.0809 0.0023 0.0831 | 15.9223 10 | 2.50 | 0.0806 0.0024 0.0830 | 14.6627 11 | 2.50 | 0.0803 0.0024 0.0827 | 13.4764 12 | 2.50 | 0.0800 0.0025 0.0825 | 12.3015 13 | 2.50 | 0.0797 0.0026 0.0823 | 11.3776 14 | 2.50 | 0.0794 0.0026 0.0821 | 10.4537 15 | 2.25 | 0.0773 0.0027 0.0800 | 9.5920 16 | 2.25 | 0.0744 0.0041 0.0785 | 8.8725 29 | 2.00 | 0.0749 0.0018 0.0767 | 3.3283 30 | 2.00 | 0.0690 0.0043 0.0733 | 3.1221 31 | 2.00 | 0.0671 0.0052 0.0724 | 2.9160 43 | 1.75 | 0.0659 0.0030 0.0689 | 1.5785 44 | 1.75 | 0.0617 0.0053 0.0670 | 1.5194 45 | 1.75 | 0.0604 0.0060 0.0664 | 1.4626 57 | 1.50 | 0.0586 0.0043 0.0629 | 1.0900 58 | 1.50 | 0.0556 0.0063 0.0619 | 1.0730 59 | 1.50 | 0.0546 0.0069 0.0616 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 207s Prepare output 14s 221s Jacobian determinant (RMS): 0.010 0.038 0.059 0.086 0.111 | 0.118559 Template Matching: 0.086 0.223 0.201 0.181 0.164 | 0.163950 Write result maps: 68s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 55s CSF distance: 23s PBT2x thickness: 68s 155s Create initial surface 117s Topology correction: 119s Surface refinement: 132s Reduction of surface collisions with optimization: 89s Spherical mapping with areal smoothing 116s Spherical registration 338s rh: Thickness estimation (0.50 mm): WM distance: 44s CSF distance: 22s PBT2x thickness: 62s 136s Create initial surface 158s Topology correction: 133s Surface refinement: 157s Reduction of surface collisions with optimization: 82s Spherical mapping with areal smoothing 103s Spherical registration 339s Final surface processing results: Average thickness (FS): 2.6557  0.6384 mm Surface intensity / position RMSE: 0.0574 / 0.0552 Euler number / defect number / defect size: 6.0 / 8.5 / 0.06% Display thickness: /var/lib/condor/execute/dir_9674/ds/sub-sc016/surf/lh.thickness.sub-sc016_T1w Display thickness: /var/lib/condor/execute/dir_9674/ds/sub-sc016/surf/rh.thickness.sub-sc016_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_9674/ds/sub-sc016/sub-sc016_T1w.nii Surface ROI estimation: 119s Surface and thickness estimation takes: 2489s ROI estimation in native space: ROI estimation of 'cobra' atlas 14s ROI estimation of 'neuromorphometrics' atlas 48s ROI estimation of 'lpba40' atlas 15s ROI estimation of 'hammers' atlas 36s ROI estimation of 'thalamus' atlas 3s ROI estimation of 'ibsr' atlas 13s ROI estimation of 'aal3' atlas 22s ROI estimation of 'mori' atlas 32s ROI estimation of 'anatomy3' atlas 46s ROI estimation of 'julichbrain' atlas 58s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 24s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 43s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 95s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 136s Write results 137s 585s Quality check: 7s Print 'Graphics' figure to: /var/lib/condor/execute/dir_9674/ds/sub-sc016/report/catreport_sub-sc016_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 70 minute(s) and 18 second(s). Image Quality Rating (IQR): 84.39% (B) GM volume (GMV): 46.94% (744.51 / 1586.07 ml) GM thickness (GMT): 2.66  0.64 mm Segmentations are saved in /var/lib/condor/execute/dir_9674/ds/sub-sc016/mri Reports are saved in /var/lib/condor/execute/dir_9674/ds/sub-sc016/report Labels are saved in /var/lib/condor/execute/dir_9674/ds/sub-sc016/label ------------------------------------------------------------------------