------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./execute/dir_29720/ds/sub-12/sub-12_ses-01_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 59s APP: Rough bias correction: Initialize 5s Estimate background 4s Initial correction 5s Refine background 3s Final correction 5s Final scaling 5s 32s Correct center-of-mass 2s Affine registration 8s SPM preprocessing 1 (estimate 1 - TPM registration): 71s SPM preprocessing 1 (estimate 2): 42s SPM preprocessing 2 (write): Write Segmentation 12s Update Segmentation 14s Update Skull-Stripping 31s Update probability maps 6s 64s Global intensity correction: 11s SANLM denoising after intensity normalization (medium): 7s Fast Optimized Shooting registration 25s Local adaptive segmentation (LASstr=0.50): Prepare maps 3s Prepare partitions 2s Prepare segments (LASmod = 1.00) 10s Estimate local tissue thresholds (WM) 13s Estimate local tissue thresholds (GM) 18s Intensity transformation 0s SANLM denoising after LAS (medium) 17s 66s ROI segmentation (partitioning): Atlas -> subject space 6s Major structures 3s Ventricle detection 10s Blood vessel detection 7s WMH detection (WMHCstr=0.50 > WMHCstr'=0.13) 22s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 3s Final corrections 3s 55s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 21s AMAP peaks: [CSF,GM,WM] = [0.360.05,0.670.07,0.980.05] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 3s Level 1 cleanup (brain masking) 2s Level 2 cleanup (CSF correction) 1s Level 3 cleanup (CSF/WM PVE) 2s 8s 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 | 0.0861 0.0000 0.0861 | 32.0000 2 | 2.50 | 0.0838 0.0011 0.0849 | 29.4886 3 | 2.50 | 0.0831 0.0016 0.0848 | 26.9772 4 | 2.50 | 0.0828 0.0018 0.0846 | 24.6107 5 | 2.50 | 0.0825 0.0020 0.0845 | 22.6548 6 | 2.50 | 0.0823 0.0021 0.0843 | 20.6989 7 | 2.50 | 0.0820 0.0022 0.0842 | 18.9688 8 | 2.50 | 0.0817 0.0023 0.0840 | 17.4455 9 | 2.50 | 0.0815 0.0023 0.0838 | 15.9223 10 | 2.50 | 0.0812 0.0025 0.0836 | 14.6627 11 | 2.50 | 0.0809 0.0025 0.0834 | 13.4764 12 | 2.50 | 0.0806 0.0026 0.0832 | 12.3015 13 | 2.50 | 0.0802 0.0027 0.0830 | 11.3776 14 | 2.50 | 0.0799 0.0028 0.0827 | 10.4537 15 | 2.25 | 0.0809 0.0028 0.0837 | 9.5920 16 | 2.25 | 0.0779 0.0043 0.0822 | 8.8725 17 | 2.25 | 0.0766 0.0049 0.0815 | 8.1530 18 | 2.25 | 0.0758 0.0052 0.0810 | 7.5234 19 | 2.25 | 0.0752 0.0053 0.0805 | 6.9630 20 | 2.25 | 0.0746 0.0054 0.0800 | 6.4027 29 | 2.00 | 0.0773 0.0030 0.0803 | 3.3283 30 | 2.00 | 0.0723 0.0053 0.0775 | 3.1221 31 | 2.00 | 0.0704 0.0062 0.0766 | 2.9160 43 | 1.75 | 0.0697 0.0035 0.0732 | 1.5785 44 | 1.75 | 0.0647 0.0062 0.0709 | 1.5194 45 | 1.75 | 0.0631 0.0071 0.0702 | 1.4626 57 | 1.50 | 0.0619 0.0051 0.0670 | 1.0900 58 | 1.50 | 0.0582 0.0075 0.0658 | 1.0730 59 | 1.50 | 0.0570 0.0083 0.0653 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 166s Prepare output 8s 174s Jacobian determinant (RMS): 0.010 0.038 0.061 0.085 0.111 | 0.118315 Template Matching: 0.086 0.224 0.211 0.189 0.171 | 0.171059 Write result maps: 24s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 35s CSF distance: 15s PBT2x thickness: 42s 98s Create initial surface 72s Topology correction: 80s Surface refinement: 63s Reduction of surface collisions with optimization: 51s Spherical mapping with areal smoothing 69s Spherical registration 189s rh: Thickness estimation (0.50 mm): WM distance: 46s CSF distance: 14s PBT2x thickness: 41s 107s Create initial surface 64s Topology correction: 75s Surface refinement: 70s Reduction of surface collisions with optimization: 59s Spherical mapping with areal smoothing 73s Spherical registration 179s Final surface processing results: Average thickness (FS): 2.5386  0.6711 mm Surface intensity / position RMSE: 0.0732 / 0.1011 Euler number / defect number / defect size: 16.0 / 11.5 / 1.44% Display thickness: /var/lib/condor/execute/dir_29720/ds/sub-12/surf/lh.thickness.sub-12_ses-01_T1w Display thickness: /var/lib/condor/execute/dir_29720/ds/sub-12/surf/rh.thickness.sub-12_ses-01_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_29720/ds/sub-12/sub-12_ses-01_T1w.nii Surface ROI estimation: 7s Surface and thickness estimation takes: 1329s ROI estimation in native space: ROI estimation of 'cobra' atlas 10s ROI estimation of 'neuromorphometrics' atlas 39s ROI estimation of 'lpba40' atlas 11s ROI estimation of 'hammers' atlas 27s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 9s ROI estimation of 'aal3' atlas 15s ROI estimation of 'mori' atlas 21s ROI estimation of 'anatomy3' atlas 31s ROI estimation of 'julichbrain' atlas 40s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 18s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 68s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 102s Write results 102s 409s Quality check: 4s Print 'Graphics' figure to: /var/lib/condor/execute/dir_29720/ds/sub-12/report/catreport_sub-12_ses-01_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 41 minute(s) and 12 second(s). Image Quality Rating (IQR): 82.13% (B-) GM volume (GMV): 47.37% (808.56 / 1706.95 ml) GM thickness (GMT): 2.54  0.67 mm Segmentations are saved in /var/lib/condor/execute/dir_29720/ds/sub-12/mri Reports are saved in /var/lib/condor/execute/dir_29720/ds/sub-12/report Labels are saved in /var/lib/condor/execute/dir_29720/ds/sub-12/label ------------------------------------------------------------------------