------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0027273/ses-1/sub-0027273_ses-1_run-1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 59s APP: Rough bias correction: Initialize 5s Estimate background 5s Initial correction 4s Refine background 3s Final correction 4s Final scaling 4s 31s Correct center-of-mass 4s Affine registration 7s SPM preprocessing 1 (estimate 1 - TPM registration): 66s SPM preprocessing 1 (estimate 2): 47s SPM preprocessing 2 (write): Write Segmentation 15s Update Segmentation 17s Update Skull-Stripping 35s Update probability maps 8s 75s Global intensity correction: 14s SANLM denoising after intensity normalization (medium): 26s Fast Optimized Shooting registration 30s Local adaptive segmentation (LASstr=0.50): Prepare maps 3s Prepare partitions 3s Prepare segments (LASmod = 1.00) 13s Estimate local tissue thresholds (WM) 15s Estimate local tissue thresholds (GM) 22s Intensity transformation 0s SANLM denoising after LAS (medium) 34s 93s ROI segmentation (partitioning): Atlas -> subject space 7s Major structures 3s Ventricle detection 13s Blood vessel detection 9s WMH detection (WMHCstr=0.50 > WMHCstr'=0.04) 21s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 3s Final corrections 4s 61s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 30s AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05] 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) 3s 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 | 0.0871 0.0000 0.0871 | 32.0000 2 | 2.50 | 0.0840 0.0013 0.0853 | 29.4886 3 | 2.50 | 0.0832 0.0020 0.0851 | 26.9772 4 | 2.50 | 0.0827 0.0022 0.0849 | 24.6107 5 | 2.50 | 0.0824 0.0024 0.0848 | 22.6548 6 | 2.50 | 0.0821 0.0025 0.0846 | 20.6989 7 | 2.50 | 0.0818 0.0026 0.0844 | 18.9688 8 | 2.50 | 0.0815 0.0027 0.0842 | 17.4455 9 | 2.50 | 0.0811 0.0028 0.0839 | 15.9223 10 | 2.50 | 0.0808 0.0029 0.0837 | 14.6627 11 | 2.50 | 0.0805 0.0030 0.0834 | 13.4764 12 | 2.50 | 0.0801 0.0030 0.0831 | 12.3015 13 | 2.50 | 0.0797 0.0032 0.0829 | 11.3776 14 | 2.50 | 0.0794 0.0032 0.0826 | 10.4537 15 | 2.25 | 0.0785 0.0033 0.0818 | 9.5920 16 | 2.25 | 0.0755 0.0048 0.0803 | 8.8725 17 | 2.25 | 0.0744 0.0053 0.0796 | 8.1530 29 | 2.00 | 0.0757 0.0024 0.0781 | 3.3283 30 | 2.00 | 0.0702 0.0047 0.0750 | 3.1221 31 | 2.00 | 0.0683 0.0057 0.0740 | 2.9160 43 | 1.75 | 0.0674 0.0032 0.0706 | 1.5785 44 | 1.75 | 0.0632 0.0055 0.0686 | 1.5194 45 | 1.75 | 0.0617 0.0063 0.0680 | 1.4626 57 | 1.50 | 0.0604 0.0046 0.0650 | 1.0900 58 | 1.50 | 0.0572 0.0067 0.0639 | 1.0730 59 | 1.50 | 0.0562 0.0073 0.0635 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 171s Prepare output 10s 181s Jacobian determinant (RMS): 0.012 0.045 0.068 0.094 0.119 | 0.125703 Template Matching: 0.087 0.223 0.205 0.185 0.169 | 0.168570 Write result maps: 31s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 35s CSF distance: 16s PBT2x thickness: 45s 103s Create initial surface 86s Topology correction: 92s Surface refinement: 83s Reduction of surface collisions with optimization: 71s Spherical mapping with areal smoothing 86s Spherical registration 307s rh: Thickness estimation (0.50 mm): WM distance: 28s CSF distance: 15s PBT2x thickness: 43s 92s Create initial surface 83s Topology correction: 89s Surface refinement: 77s Reduction of surface collisions with optimization: 66s Spherical mapping with areal smoothing 82s Spherical registration 298s Final surface processing results: Average thickness (FS): 2.5666  0.6125 mm Surface intensity / position RMSE: 0.0661 / 0.0609 Euler number / defect number / defect size: 12.0 / 8.5 / 0.56% Display thickness: /var/lib/condor/execute/dir_2615109/ds/UWM/sub-0027273/ses-1/surf/lh.thickness.sub-0027273_ses-1_run-1_T1w Display thickness: /var/lib/condor/execute/dir_2615109/ds/UWM/sub-0027273/ses-1/surf/rh.thickness.sub-0027273_ses-1_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_2615109/ds/UWM/sub-0027273/ses-1/sub-0027273_ses-1_run-1_T1w.nii Surface ROI estimation: 8s Surface and thickness estimation takes: 1708s ROI estimation in native space: ROI estimation of 'cobra' atlas 7s ROI estimation of 'neuromorphometrics' atlas 26s ROI estimation of 'lpba40' atlas 8s ROI estimation of 'hammers' atlas 18s ROI estimation of 'thalamus' atlas 1s ROI estimation of 'ibsr' atlas 6s ROI estimation of 'aal3' atlas 11s ROI estimation of 'mori' atlas 16s ROI estimation of 'anatomy3' atlas 24s ROI estimation of 'julichbrain' atlas 30s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 22s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 53s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 79s ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s Write results 8s 320s Quality check: 11s Print 'Graphics' figure to: /var/lib/condor/execute/dir_2615109/ds/UWM/sub-0027273/ses-1/report/catreport_sub-0027273_ses-1_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 47 minute(s) and 54 second(s). Image Quality Rating (IQR): 81.95% (B-) GM volume (GMV): 50.02% (711.47 / 1422.35 ml) GM thickness (GMT): 2.57  0.61 mm Segmentations are saved in /var/lib/condor/execute/dir_2615109/ds/UWM/sub-0027273/ses-1/mri Reports are saved in /var/lib/condor/execute/dir_2615109/ds/UWM/sub-0027273/ses-1/report Labels are saved in /var/lib/condor/execute/dir_2615109/ds/UWM/sub-0027273/ses-1/label ------------------------------------------------------------------------