------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0026004/ses-1/sub-0026004_ses-1_run-1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 51s APP: Rough bias correction: Initialize 6s Estimate background 6s Initial correction 5s Refine background 3s Final correction 5s Final scaling 4s 34s Correct center-of-mass 4s Affine registration 9s SPM preprocessing 1 (estimate 1 - TPM registration): 75s SPM preprocessing 1 (estimate 2): 67s SPM preprocessing 2 (write): Write Segmentation 17s Update Segmentation 20s Update Skull-Stripping 40s Update probability maps 8s 85s Global intensity correction: 17s SANLM denoising after intensity normalization (medium): 27s Fast Optimized Shooting registration 31s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 2s Prepare segments (LASmod = 1.00) 14s Estimate local tissue thresholds (WM) 18s Estimate local tissue thresholds (GM) 27s Intensity transformation 0s SANLM denoising after LAS (medium) 48s 117s ROI segmentation (partitioning): Atlas -> subject space 8s Major structures 4s Ventricle detection 15s Blood vessel detection 10s WMH detection (WMHCstr=0.50 > WMHCstr'=0.05) 27s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 4s Final corrections 4s 73s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 37s 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) 3s Level 2 cleanup (CSF correction) 1s Level 3 cleanup (CSF/WM PVE) 3s 11s 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 | 0.0871 0.0000 0.0871 | 32.0000 2 | 2.50 | 0.0836 0.0014 0.0850 | 29.4886 3 | 2.50 | 0.0826 0.0021 0.0848 | 26.9772 4 | 2.50 | 0.0821 0.0024 0.0845 | 24.6107 5 | 2.50 | 0.0817 0.0026 0.0843 | 22.6548 6 | 2.50 | 0.0814 0.0027 0.0841 | 20.6989 7 | 2.50 | 0.0810 0.0028 0.0838 | 18.9688 8 | 2.50 | 0.0806 0.0030 0.0836 | 17.4455 9 | 2.50 | 0.0802 0.0030 0.0833 | 15.9223 10 | 2.50 | 0.0798 0.0032 0.0830 | 14.6627 11 | 2.50 | 0.0794 0.0033 0.0827 | 13.4764 12 | 2.50 | 0.0790 0.0033 0.0824 | 12.3015 13 | 2.50 | 0.0786 0.0035 0.0821 | 11.3776 14 | 2.50 | 0.0782 0.0035 0.0818 | 10.4537 15 | 2.25 | 0.0792 0.0036 0.0829 | 9.5920 16 | 2.25 | 0.0758 0.0054 0.0812 | 8.8725 17 | 2.25 | 0.0744 0.0060 0.0804 | 8.1530 29 | 2.00 | 0.0769 0.0027 0.0796 | 3.3283 30 | 2.00 | 0.0705 0.0054 0.0760 | 3.1221 31 | 2.00 | 0.0683 0.0065 0.0748 | 2.9160 43 | 1.75 | 0.0674 0.0037 0.0711 | 1.5785 44 | 1.75 | 0.0626 0.0063 0.0689 | 1.5194 45 | 1.75 | 0.0609 0.0072 0.0681 | 1.4626 57 | 1.50 | 0.0596 0.0053 0.0649 | 1.0900 58 | 1.50 | 0.0560 0.0076 0.0637 | 1.0730 59 | 1.50 | 0.0548 0.0083 0.0631 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 170s Prepare output 11s 181s Jacobian determinant (RMS): 0.011 0.041 0.062 0.088 0.136 | 0.123913 Template Matching: 0.087 0.223 0.205 0.183 0.164 | 0.164357 Write result maps: 33s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 43s CSF distance: 17s PBT2x thickness: 48s 114s Create initial surface 91s Topology correction: 104s Surface refinement: 96s Reduction of surface collisions with optimization: 80s Spherical mapping with areal smoothing 88s Spherical registration 304s rh: Thickness estimation (0.50 mm): WM distance: 48s CSF distance: 16s PBT2x thickness: 46s 116s Create initial surface 88s Topology correction: 105s Surface refinement: 127s Reduction of surface collisions with optimization: 84s Spherical mapping with areal smoothing 94s Spherical registration 321s Final surface processing results: Average thickness (FS): 2.4616  0.6221 mm Surface intensity / position RMSE: 0.0654 / 0.0686 Euler number / defect number / defect size: 32.0 / 16.5 / 0.99% Display thickness: /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-1/surf/lh.thickness.sub-0026004_ses-1_run-1_T1w Display thickness: /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-1/surf/rh.thickness.sub-0026004_ses-1_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-1/sub-0026004_ses-1_run-1_T1w.nii Surface ROI estimation: 9s Surface and thickness estimation takes: 1914s ROI estimation in native space: ROI estimation of 'cobra' atlas 8s ROI estimation of 'neuromorphometrics' atlas 31s 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 19s ROI estimation of 'anatomy3' atlas 27s ROI estimation of 'julichbrain' atlas 36s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 28s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 62s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 95s ROI estimation of 'Tian_Subcortex_S2_7T' atlas 9s Write results 10s 385s Quality check: 13s Print 'Graphics' figure to: /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-1/report/catreport_sub-0026004_ses-1_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 54 minute(s) and 53 second(s). Image Quality Rating (IQR): 82.45% (B-) GM volume (GMV): 45.06% (758.56 / 1683.60 ml) GM thickness (GMT): 2.46  0.62 mm Segmentations are saved in /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-1/mri Reports are saved in /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-1/report Labels are saved in /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-1/label ------------------------------------------------------------------------