------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./sub-NC250_ses-20190814_acq-highres_run-02_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 53s APP: Rough bias correction: Initialize 8s Estimate background 10s Initial correction 8s Refine background 5s Final correction 7s Final scaling 8s 53s Correct center-of-mass 4s Affine registration 13s SPM preprocessing 1 (estimate 1 - TPM registration): 90s SPM preprocessing 1 (estimate 2): 91s SPM preprocessing 2 (write): Write Segmentation 22s Update Segmentation 24s Update Skull-Stripping 52s Update probability maps 10s 108s Global intensity correction: 20s SANLM denoising after intensity normalization (medium): 11s Fast Optimized Shooting registration 45s Local adaptive segmentation (LASstr=0.50): Prepare maps 5s Prepare partitions 3s Prepare segments (LASmod = 1.15) 20s Estimate local tissue thresholds (WM) 22s Estimate local tissue thresholds (GM) 28s Intensity transformation 0s SANLM denoising after LAS (medium) 27s 109s ROI segmentation (partitioning): Atlas -> subject space 11s Major structures 5s Ventricle detection 20s Blood vessel detection 11s WMH detection (WMHCstr=0.50 > WMHCstr'=0.05) 28s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 4s Final corrections 6s 88s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 49s AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05] 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 16s 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 | 0.0867 0.0000 0.0867 | 32.0000 2 | 2.50 | 0.0838 0.0013 0.0850 | 29.4886 3 | 2.50 | 0.0829 0.0019 0.0848 | 26.9772 4 | 2.50 | 0.0825 0.0021 0.0847 | 24.6107 5 | 2.50 | 0.0822 0.0023 0.0845 | 22.6548 6 | 2.50 | 0.0819 0.0023 0.0843 | 20.6989 7 | 2.50 | 0.0816 0.0024 0.0841 | 18.9688 8 | 2.50 | 0.0813 0.0025 0.0839 | 17.4455 9 | 2.50 | 0.0810 0.0026 0.0836 | 15.9223 10 | 2.50 | 0.0807 0.0027 0.0834 | 14.6627 11 | 2.50 | 0.0804 0.0028 0.0832 | 13.4764 12 | 2.50 | 0.0801 0.0028 0.0829 | 12.3015 13 | 2.50 | 0.0798 0.0029 0.0826 | 11.3776 14 | 2.50 | 0.0794 0.0029 0.0824 | 10.4537 15 | 2.25 | 0.0791 0.0030 0.0821 | 9.5920 16 | 2.25 | 0.0762 0.0044 0.0806 | 8.8725 17 | 2.25 | 0.0751 0.0049 0.0800 | 8.1530 18 | 2.25 | 0.0744 0.0051 0.0795 | 7.5234 29 | 2.00 | 0.0766 0.0024 0.0790 | 3.3283 30 | 2.00 | 0.0713 0.0047 0.0761 | 3.1221 31 | 2.00 | 0.0696 0.0056 0.0752 | 2.9160 43 | 1.75 | 0.0690 0.0032 0.0722 | 1.5785 44 | 1.75 | 0.0645 0.0055 0.0701 | 1.5194 45 | 1.75 | 0.0631 0.0064 0.0695 | 1.4626 57 | 1.50 | 0.0622 0.0046 0.0668 | 1.0900 58 | 1.50 | 0.0588 0.0068 0.0657 | 1.0730 59 | 1.50 | 0.0578 0.0075 0.0653 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 237s Prepare output 12s 249s Jacobian determinant (RMS): 0.011 0.039 0.059 0.081 0.105 | 0.110663 Template Matching: 0.087 0.223 0.209 0.189 0.173 | 0.173289 Write result maps: 37s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 39s CSF distance: 20s PBT2x thickness: 64s 135s Create initial surface 120s Topology correction: 150s Surface refinement: 170s Reduction of surface collisions with optimization: 205s Spherical mapping with areal smoothing 119s Spherical registration 280s rh: Thickness estimation (0.50 mm): WM distance: 39s CSF distance: 20s PBT2x thickness: 65s 135s Create initial surface 121s Topology correction: 146s Surface refinement: 141s Reduction of surface collisions with optimization: 112s Spherical mapping with areal smoothing 116s Spherical registration 289s Final surface processing results: Average thickness (FS): 2.3066  0.6969 mm Surface intensity / position RMSE: 0.0961 / 0.1411 Euler number / defect number / defect size: 182.0 / 61.0 / 5.81% Display thickness: /var/lib/condor/execute/dir_28111/ds/sub-NC250/surf/lh.thickness.sub-NC250_ses-20190814_acq-highres_run-02_T1w Display thickness: /var/lib/condor/execute/dir_28111/ds/sub-NC250/surf/rh.thickness.sub-NC250_ses-20190814_acq-highres_run-02_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_28111/ds/sub-NC250/sub-NC250_ses-20190814_acq-highres_run-02_T1w.nii Surface ROI estimation: 10s Surface and thickness estimation takes: 2365s ROI estimation in native space: ROI estimation of 'cobra' atlas 17s ROI estimation of 'neuromorphometrics' atlas 57s ROI estimation of 'lpba40' atlas 17s ROI estimation of 'hammers' atlas 43s ROI estimation of 'thalamus' atlas 3s ROI estimation of 'ibsr' atlas 16s ROI estimation of 'aal3' atlas 26s ROI estimation of 'mori' atlas 39s ROI estimation of 'anatomy3' atlas 54s ROI estimation of 'julichbrain' atlas 74s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 28s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 42s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 116s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 153s Write results 154s 688s Quality check: 7s Print 'Graphics' figure to: /var/lib/condor/execute/dir_28111/ds/sub-NC250/report/catreport_sub-NC250_ses-20190814_acq-highres_run-02_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 70 minute(s) and 7 second(s). Image Quality Rating (IQR): 66.89% (D+) GM volume (GMV): 47.33% (723.33 / 1528.39 ml) GM thickness (GMT): 2.31  0.70 mm Segmentations are saved in /var/lib/condor/execute/dir_28111/ds/sub-NC250/mri Reports are saved in /var/lib/condor/execute/dir_28111/ds/sub-NC250/report Labels are saved in /var/lib/condor/execute/dir_28111/ds/sub-NC250/label ------------------------------------------------------------------------