------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0026003/ses-2/sub-0026003_ses-2_run-1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 44s APP: Rough bias correction: Initialize 5s Estimate background 5s Initial correction 5s Refine background 2s Final correction 4s Final scaling 4s 30s Correct center-of-mass 3s Affine registration 7s SPM preprocessing 1 (estimate 1 - TPM registration): 58s SPM preprocessing 1 (estimate 2): 44s SPM preprocessing 2 (write): Write Segmentation 14s Update Segmentation 16s Update Skull-Stripping 33s Update probability maps 7s 70s Global intensity correction: 14s SANLM denoising after intensity normalization (medium): 20s Fast Optimized Shooting registration 26s Local adaptive segmentation (LASstr=0.50): Prepare maps 3s Prepare partitions 2s Prepare segments (LASmod = 1.09) 11s Estimate local tissue thresholds (WM) 15s Estimate local tissue thresholds (GM) 22s Intensity transformation 0s SANLM denoising after LAS (medium) 38s 94s ROI segmentation (partitioning): Atlas -> subject space 6s Major structures 3s Ventricle detection 9s Blood vessel detection 8s WMH detection (WMHCstr=0.50 > WMHCstr'=0.19) 18s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 3s Final corrections 4s 50s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 30s AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05] 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 9s 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 | 0.0862 0.0000 0.0862 | 32.0000 2 | 2.50 | 0.0832 0.0013 0.0845 | 29.4886 3 | 2.50 | 0.0822 0.0020 0.0842 | 26.9772 4 | 2.50 | 0.0817 0.0023 0.0840 | 24.6107 5 | 2.50 | 0.0814 0.0025 0.0838 | 22.6548 6 | 2.50 | 0.0810 0.0026 0.0836 | 20.6989 7 | 2.50 | 0.0807 0.0027 0.0834 | 18.9688 8 | 2.50 | 0.0803 0.0029 0.0832 | 17.4455 9 | 2.50 | 0.0800 0.0029 0.0829 | 15.9223 10 | 2.50 | 0.0796 0.0031 0.0826 | 14.6627 11 | 2.50 | 0.0792 0.0032 0.0824 | 13.4764 12 | 2.50 | 0.0788 0.0033 0.0821 | 12.3015 13 | 2.50 | 0.0784 0.0034 0.0818 | 11.3776 14 | 2.50 | 0.0780 0.0035 0.0815 | 10.4537 15 | 2.25 | 0.0778 0.0036 0.0814 | 9.5920 16 | 2.25 | 0.0747 0.0052 0.0798 | 8.8725 29 | 2.00 | 0.0758 0.0023 0.0781 | 3.3283 30 | 2.00 | 0.0688 0.0051 0.0740 | 3.1221 31 | 2.00 | 0.0665 0.0063 0.0727 | 2.9160 43 | 1.75 | 0.0652 0.0036 0.0688 | 1.5785 44 | 1.75 | 0.0607 0.0060 0.0667 | 1.5194 45 | 1.75 | 0.0593 0.0068 0.0661 | 1.4626 57 | 1.50 | 0.0578 0.0050 0.0628 | 1.0900 58 | 1.50 | 0.0546 0.0071 0.0617 | 1.0730 59 | 1.50 | 0.0536 0.0077 0.0613 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 132s Prepare output 8s 140s Jacobian determinant (RMS): 0.011 0.042 0.065 0.092 0.116 | 0.123550 Template Matching: 0.086 0.224 0.199 0.178 0.161 | 0.160812 Write result maps: 28s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 42s CSF distance: 13s PBT2x thickness: 37s 96s Create initial surface 69s Topology correction: 78s Surface refinement: 68s Reduction of surface collisions with optimization: 59s Spherical mapping with areal smoothing 65s Spherical registration 245s rh: Thickness estimation (0.50 mm): WM distance: 33s CSF distance: 13s PBT2x thickness: 37s 87s Create initial surface 67s Topology correction: 77s Surface refinement: 57s Reduction of surface collisions with optimization: 55s Spherical mapping with areal smoothing 63s Spherical registration 238s Final surface processing results: Average thickness (FS): 2.4391  0.6389 mm Surface intensity / position RMSE: 0.0695 / 0.0727 Euler number / defect number / defect size: 28.0 / 18.0 / 1.06% Display thickness: /var/lib/condor/execute/dir_3011310/ds/XHCUMS/sub-0026003/ses-2/surf/lh.thickness.sub-0026003_ses-2_run-1_T1w Display thickness: /var/lib/condor/execute/dir_3011310/ds/XHCUMS/sub-0026003/ses-2/surf/rh.thickness.sub-0026003_ses-2_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_3011310/ds/XHCUMS/sub-0026003/ses-2/sub-0026003_ses-2_run-1_T1w.nii Surface ROI estimation: 7s Surface and thickness estimation takes: 1403s ROI estimation in native space: ROI estimation of 'cobra' atlas 7s ROI estimation of 'neuromorphometrics' atlas 25s ROI estimation of 'lpba40' atlas 7s ROI estimation of 'hammers' atlas 18s ROI estimation of 'thalamus' atlas 1s ROI estimation of 'ibsr' atlas 6s ROI estimation of 'aal3' atlas 10s ROI estimation of 'mori' atlas 15s ROI estimation of 'anatomy3' atlas 21s ROI estimation of 'julichbrain' atlas 28s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 20s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 45s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 68s ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s Write results 7s 290s Quality check: 9s Print 'Graphics' figure to: /var/lib/condor/execute/dir_3011310/ds/XHCUMS/sub-0026003/ses-2/report/catreport_sub-0026003_ses-2_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 40 minute(s) and 44 second(s). Image Quality Rating (IQR): 83.30% (B-) GM volume (GMV): 44.45% (669.52 / 1506.25 ml) GM thickness (GMT): 2.44  0.64 mm Segmentations are saved in /var/lib/condor/execute/dir_3011310/ds/XHCUMS/sub-0026003/ses-2/mri Reports are saved in /var/lib/condor/execute/dir_3011310/ds/XHCUMS/sub-0026003/ses-2/report Labels are saved in /var/lib/condor/execute/dir_3011310/ds/XHCUMS/sub-0026003/ses-2/label ------------------------------------------------------------------------