------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./execute/dir_3099/ds/sub-sc007/sub-sc007_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 33s APP: Rough bias correction: Initialize 9s Estimate background 8s Initial correction 8s Refine background 4s Final correction 6s Final scaling 6s 50s Correct center-of-mass 8s Affine registration 13s SPM preprocessing 1 (estimate 1 - TPM registration): 92s SPM preprocessing 1 (estimate 2): 72s SPM preprocessing 2 (write): Write Segmentation 22s Update Segmentation 22s Update Skull-Stripping 55s Update probability maps 12s 111s Global intensity correction: 21s SANLM denoising after intensity normalization (medium): 12s Fast Optimized Shooting registration 42s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 3s Prepare segments (LASmod = 1.00) 17s Estimate local tissue thresholds (WM) 25s Estimate local tissue thresholds (GM) 33s Intensity transformation 0s SANLM denoising after LAS (medium) 13s 102s ROI segmentation (partitioning): Atlas -> subject space 10s Major structures 4s Ventricle detection 17s Blood vessel detection 11s WMH detection (WMHCstr=0.50 > WMHCstr'=0.02) 27s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 4s Final corrections 6s 79s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 35s AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.990.05] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 5s 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 | 0.0837 0.0000 0.0837 | 32.0000 2 | 2.50 | 0.0808 0.0013 0.0820 | 29.4886 3 | 2.50 | 0.0799 0.0020 0.0818 | 26.9772 4 | 2.50 | 0.0795 0.0022 0.0817 | 24.6107 5 | 2.50 | 0.0791 0.0024 0.0815 | 22.6548 6 | 2.50 | 0.0788 0.0024 0.0813 | 20.6989 7 | 2.50 | 0.0785 0.0026 0.0811 | 18.9688 8 | 2.50 | 0.0782 0.0027 0.0808 | 17.4455 9 | 2.50 | 0.0779 0.0027 0.0806 | 15.9223 10 | 2.50 | 0.0775 0.0028 0.0803 | 14.6627 11 | 2.50 | 0.0772 0.0029 0.0801 | 13.4764 12 | 2.50 | 0.0768 0.0030 0.0798 | 12.3015 13 | 2.50 | 0.0765 0.0031 0.0796 | 11.3776 14 | 2.50 | 0.0761 0.0032 0.0793 | 10.4537 15 | 2.25 | 0.0753 0.0033 0.0785 | 9.5920 16 | 2.25 | 0.0722 0.0047 0.0769 | 8.8725 29 | 2.00 | 0.0731 0.0021 0.0753 | 3.3283 30 | 2.00 | 0.0671 0.0046 0.0716 | 3.1221 31 | 2.00 | 0.0651 0.0055 0.0706 | 2.9160 43 | 1.75 | 0.0639 0.0032 0.0671 | 1.5785 44 | 1.75 | 0.0598 0.0053 0.0651 | 1.5194 45 | 1.75 | 0.0584 0.0061 0.0645 | 1.4626 57 | 1.50 | 0.0569 0.0045 0.0613 | 1.0900 58 | 1.50 | 0.0539 0.0063 0.0603 | 1.0730 59 | 1.50 | 0.0529 0.0070 0.0599 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 205s Prepare output 13s 218s Jacobian determinant (RMS): 0.012 0.044 0.064 0.088 0.110 | 0.116511 Template Matching: 0.084 0.217 0.195 0.175 0.159 | 0.158789 Write result maps: 150s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 37s CSF distance: 18s PBT2x thickness: 53s 115s Create initial surface 98s Topology correction: 91s Surface refinement: 128s Reduction of surface collisions with optimization: 77s Spherical mapping with areal smoothing 100s Spherical registration 328s rh: Thickness estimation (0.50 mm): WM distance: 35s CSF distance: 18s PBT2x thickness: 53s 113s Create initial surface 95s Topology correction: 90s Surface refinement: 98s Reduction of surface collisions with optimization: 73s Spherical mapping with areal smoothing 102s Spherical registration 343s Final surface processing results: Average thickness (FS): 2.5205  0.6017 mm Surface intensity / position RMSE: 0.0651 / 0.0661 Euler number / defect number / defect size: 22.0 / 10.5 / 0.52% Display thickness: /var/lib/condor/execute/dir_3099/ds/sub-sc007/surf/lh.thickness.sub-sc007_T1w Display thickness: /var/lib/condor/execute/dir_3099/ds/sub-sc007/surf/rh.thickness.sub-sc007_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_3099/ds/sub-sc007/sub-sc007_T1w.nii Surface ROI estimation: 14s Surface and thickness estimation takes: 2001s ROI estimation in native space: ROI estimation of 'cobra' atlas 14s ROI estimation of 'neuromorphometrics' atlas 49s ROI estimation of 'lpba40' atlas 14s ROI estimation of 'hammers' atlas 35s ROI estimation of 'thalamus' atlas 3s ROI estimation of 'ibsr' atlas 12s ROI estimation of 'aal3' atlas 20s ROI estimation of 'mori' atlas 29s ROI estimation of 'anatomy3' atlas 42s ROI estimation of 'julichbrain' atlas 56s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 23s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 41s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 90s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 137s Write results 138s 567s Quality check: 7s Print 'Graphics' figure to: /var/lib/condor/execute/dir_3099/ds/sub-sc007/report/catreport_sub-sc007_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 63 minute(s) and 38 second(s). Image Quality Rating (IQR): 83.86% (B) GM volume (GMV): 50.32% (655.64 / 1302.95 ml) GM thickness (GMT): 2.52  0.60 mm Segmentations are saved in /var/lib/condor/execute/dir_3099/ds/sub-sc007/mri Reports are saved in /var/lib/condor/execute/dir_3099/ds/sub-sc007/report Labels are saved in /var/lib/condor/execute/dir_3099/ds/sub-sc007/label ------------------------------------------------------------------------