------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./condor/execute/dir_11451/ds/sub-15/sub-15_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 42s APP: Rough bias correction: Initialize 3s Estimate background 5s Initial correction 4s Refine background 2s Final correction 4s Final scaling 4s 26s Correct center-of-mass 2s Affine registration 7s SPM preprocessing 1 (estimate 1 - TPM registration): 57s SPM preprocessing 1 (estimate 2): 34s SPM preprocessing 2 (write): Write Segmentation 10s Update Segmentation 16s Update Skull-Stripping 27s Update probability maps 5s 58s Global intensity correction: 9s SANLM denoising after intensity normalization (medium): 10s Fast Optimized Shooting registration 27s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 1s Prepare segments (LASmod = 1.06) 14s Estimate local tissue thresholds (WM) 13s Estimate local tissue thresholds (GM) 20s Intensity transformation 0s SANLM denoising after LAS (medium) 16s 70s ROI segmentation (partitioning): Atlas -> subject space 6s Major structures 3s Ventricle detection 15s Blood vessel detection 9s WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 27s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 4s Final corrections 3s 68s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 34s AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 4s Level 1 cleanup (brain masking) 2s Level 2 cleanup (CSF correction) 1s Level 3 cleanup (CSF/WM PVE) 2s 10s 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 | 0.0807 0.0000 0.0807 | 32.0000 2 | 2.50 | 0.0793 0.0008 0.0801 | 29.4886 3 | 2.50 | 0.0789 0.0012 0.0801 | 26.9772 4 | 2.50 | 0.0787 0.0013 0.0800 | 24.6107 5 | 2.50 | 0.0786 0.0014 0.0800 | 22.6548 6 | 2.50 | 0.0784 0.0015 0.0799 | 20.6989 7 | 2.50 | 0.0783 0.0015 0.0798 | 18.9688 8 | 2.50 | 0.0781 0.0016 0.0797 | 17.4455 9 | 2.50 | 0.0780 0.0016 0.0796 | 15.9223 10 | 2.50 | 0.0778 0.0017 0.0795 | 14.6627 11 | 2.50 | 0.0776 0.0018 0.0794 | 13.4764 12 | 2.50 | 0.0775 0.0018 0.0793 | 12.3015 13 | 2.50 | 0.0773 0.0019 0.0792 | 11.3776 14 | 2.50 | 0.0771 0.0019 0.0790 | 10.4537 15 | 2.25 | 0.0761 0.0019 0.0780 | 9.5920 16 | 2.25 | 0.0737 0.0031 0.0768 | 8.8725 29 | 2.00 | 0.0755 0.0014 0.0769 | 3.3283 30 | 2.00 | 0.0699 0.0036 0.0735 | 3.1221 31 | 2.00 | 0.0681 0.0045 0.0726 | 2.9160 43 | 1.75 | 0.0674 0.0026 0.0699 | 1.5785 44 | 1.75 | 0.0630 0.0049 0.0679 | 1.5194 45 | 1.75 | 0.0616 0.0057 0.0673 | 1.4626 57 | 1.50 | 0.0603 0.0041 0.0643 | 1.0900 58 | 1.50 | 0.0571 0.0061 0.0632 | 1.0730 59 | 1.50 | 0.0560 0.0068 0.0629 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 157s Prepare output 8s 165s Jacobian determinant (RMS): 0.008 0.027 0.043 0.067 0.092 | 0.098820 Template Matching: 0.081 0.221 0.204 0.185 0.168 | 0.168132 Write result maps: 14s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 34s CSF distance: 15s PBT2x thickness: 45s 100s Create initial surface 83s Topology correction: 101s Surface refinement: 91s Reduction of surface collisions with optimization: 79s Spherical mapping with areal smoothing 115s Spherical registration 278s rh: Thickness estimation (0.50 mm): WM distance: 38s CSF distance: 14s PBT2x thickness: 40s 98s Create initial surface 84s Topology correction: 102s Surface refinement: 114s Reduction of surface collisions with optimization: 83s Spherical mapping with areal smoothing 92s Spherical registration 299s Final surface processing results: Average thickness (FS): 2.4940  0.5878 mm Surface intensity / position RMSE: 0.0639 / 0.0648 Euler number / defect number / defect size: 12.0 / 8.5 / 0.20% Display thickness: /var/lib/condor/execute/dir_11451/ds/sub-15/surf/lh.thickness.sub-15_T1w Display thickness: /var/lib/condor/execute/dir_11451/ds/sub-15/surf/rh.thickness.sub-15_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_11451/ds/sub-15/sub-15_T1w.nii Surface ROI estimation: 8s Surface and thickness estimation takes: 1801s ROI estimation in native space: ROI estimation of 'cobra' atlas 4s ROI estimation of 'neuromorphometrics' atlas 15s ROI estimation of 'lpba40' atlas 4s ROI estimation of 'hammers' atlas 10s ROI estimation of 'thalamus' atlas 1s ROI estimation of 'ibsr' atlas 4s ROI estimation of 'aal3' atlas 6s ROI estimation of 'mori' atlas 9s ROI estimation of 'anatomy3' atlas 12s ROI estimation of 'julichbrain' atlas 16s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 6s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 11s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 25s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 38s Write results 39s 163s Quality check: 5s Print 'Graphics' figure to: /var/lib/condor/execute/dir_11451/ds/sub-15/report/catreport_sub-15_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 44 minute(s) and 48 second(s). Image Quality Rating (IQR): 82.93% (B-) GM volume (GMV): 47.63% (756.55 / 1588.35 ml) GM thickness (GMT): 2.49  0.59 mm Segmentations are saved in /var/lib/condor/execute/dir_11451/ds/sub-15/mri Reports are saved in /var/lib/condor/execute/dir_11451/ds/sub-15/report Labels are saved in /var/lib/condor/execute/dir_11451/ds/sub-15/label ------------------------------------------------------------------------