------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./execute/dir_2771311/ds/sub-26/sub-26_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 81s APP: Rough bias correction: Initialize 7s Estimate background 14s Initial correction 10s Refine background 5s Final correction 7s Final scaling 8s 58s Correct center-of-mass 6s Affine registration 10s SPM preprocessing 1 (estimate 1 - TPM registration): 74s SPM preprocessing 1 (estimate 2): 66s SPM preprocessing 2 (write): Write Segmentation 20s Update Segmentation 21s Update Skull-Stripping 47s Update probability maps 10s 99s Global intensity correction: 18s SANLM denoising after intensity normalization (medium): 11s Fast Optimized Shooting registration 41s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 2s Prepare segments (LASmod = 1.02) 16s Estimate local tissue thresholds (WM) 26s Estimate local tissue thresholds (GM) 37s Intensity transformation 0s SANLM denoising after LAS (medium) 42s 132s ROI segmentation (partitioning): Atlas -> subject space 8s Major structures 4s Ventricle detection 16s Blood vessel detection 11s WMH detection (WMHCstr=0.48 > WMHCstr'=0.01) 28s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 4s Final corrections 5s 78s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 37s AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.07,0.990.05] Final cleanup (gcutstr=0.24): Level 1 cleanup (ROI estimation) 5s Level 1 cleanup (brain masking) 3s Level 2 cleanup (CSF correction) 2s Level 3 cleanup (CSF/WM PVE) 3s 13s 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 | 0.0840 0.0000 0.0840 | 32.0000 2 | 2.50 | 0.0811 0.0012 0.0824 | 29.4886 3 | 2.50 | 0.0803 0.0019 0.0822 | 26.9772 4 | 2.50 | 0.0799 0.0021 0.0820 | 24.6107 5 | 2.50 | 0.0795 0.0022 0.0818 | 22.6548 6 | 2.50 | 0.0793 0.0023 0.0816 | 20.6989 7 | 2.50 | 0.0790 0.0024 0.0814 | 18.9688 8 | 2.50 | 0.0786 0.0025 0.0812 | 17.4455 9 | 2.50 | 0.0783 0.0026 0.0809 | 15.9223 10 | 2.50 | 0.0780 0.0027 0.0807 | 14.6627 11 | 2.50 | 0.0777 0.0028 0.0804 | 13.4764 12 | 2.50 | 0.0773 0.0028 0.0802 | 12.3015 13 | 2.50 | 0.0770 0.0029 0.0799 | 11.3776 14 | 2.50 | 0.0766 0.0030 0.0796 | 10.4537 15 | 2.25 | 0.0756 0.0031 0.0787 | 9.5920 16 | 2.25 | 0.0727 0.0045 0.0771 | 8.8725 29 | 2.00 | 0.0739 0.0020 0.0759 | 3.3283 30 | 2.00 | 0.0677 0.0045 0.0722 | 3.1221 31 | 2.00 | 0.0655 0.0055 0.0710 | 2.9160 43 | 1.75 | 0.0645 0.0032 0.0676 | 1.5785 44 | 1.75 | 0.0602 0.0054 0.0656 | 1.5194 45 | 1.75 | 0.0588 0.0061 0.0650 | 1.4626 57 | 1.50 | 0.0573 0.0045 0.0618 | 1.0900 58 | 1.50 | 0.0543 0.0064 0.0607 | 1.0730 59 | 1.50 | 0.0533 0.0070 0.0603 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 200s Prepare output 13s 213s Jacobian determinant (RMS): 0.011 0.041 0.060 0.083 0.105 | 0.112455 Template Matching: 0.084 0.218 0.197 0.176 0.160 | 0.160014 Write result maps: 29s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 35s CSF distance: 19s PBT2x thickness: 58s 119s Create initial surface 103s Topology correction: 112s Surface refinement: 82s Reduction of surface collisions with optimization: 78s Spherical mapping with areal smoothing 99s Spherical registration 339s rh: Thickness estimation (0.50 mm): WM distance: 32s CSF distance: 17s PBT2x thickness: 53s 110s Create initial surface 95s Topology correction: 105s Surface refinement: 89s Reduction of surface collisions with optimization: 75s Spherical mapping with areal smoothing 96s Spherical registration 318s Final surface processing results: Average thickness (FS): 2.5766  0.6175 mm Surface intensity / position RMSE: 0.0657 / 0.0651 Euler number / defect number / defect size: 12.0 / 14.0 / 0.30% Display thickness: /var/lib/condor/execute/dir_2771311/ds/sub-26/surf/lh.thickness.sub-26_T1w Display thickness: /var/lib/condor/execute/dir_2771311/ds/sub-26/surf/rh.thickness.sub-26_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_2771311/ds/sub-26/sub-26_T1w.nii Surface ROI estimation: 9s Surface and thickness estimation takes: 1926s 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 22s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 8s ROI estimation of 'aal3' atlas 13s ROI estimation of 'mori' atlas 20s ROI estimation of 'anatomy3' atlas 28s ROI estimation of 'julichbrain' atlas 37s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 26s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 60s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 80s Write results 81s 362s Quality check: 5s Print 'Graphics' figure to: /var/lib/condor/execute/dir_2771311/ds/sub-26/report/catreport_sub-26_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 55 minute(s) and 55 second(s). Image Quality Rating (IQR): 84.43% (B) GM volume (GMV): 49.47% (701.70 / 1418.51 ml) GM thickness (GMT): 2.58  0.62 mm Segmentations are saved in /var/lib/condor/execute/dir_2771311/ds/sub-26/mri Reports are saved in /var/lib/condor/execute/dir_2771311/ds/sub-26/report Labels are saved in /var/lib/condor/execute/dir_2771311/ds/sub-26/label ------------------------------------------------------------------------