------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./execute/dir_28845/ds/sub-105/sub-105_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 105s APP: Rough bias correction: Initialize 6s Estimate background 11s Initial correction 8s Refine background 5s Final correction 6s Final scaling 9s 50s Correct center-of-mass 3s Affine registration 11s SPM preprocessing 1 (estimate 1 - TPM registration): 61s SPM preprocessing 1 (estimate 2): 60s SPM preprocessing 2 (write): Write Segmentation 15s Update Segmentation 18s Update Skull-Stripping 41s Update probability maps 9s 84s Global intensity correction: 16s SANLM denoising after intensity normalization (medium): 24s Fast Optimized Shooting registration 33s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 2s Prepare segments (LASmod = 1.00) 15s Estimate local tissue thresholds (WM) 20s Estimate local tissue thresholds (GM) 27s Intensity transformation 0s SANLM denoising after LAS (medium) 36s 107s ROI segmentation (partitioning): Atlas -> subject space 7s Major structures 4s Ventricle detection 18s Blood vessel detection 11s WMH detection (WMHCstr=0.48 > WMHCstr'=0.19) 26s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 4s Final corrections 4s 76s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 34s AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.990.04] Final cleanup (gcutstr=0.24): 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 | 0.0870 0.0000 0.0870 | 32.0000 2 | 2.50 | 0.0838 0.0013 0.0851 | 29.4886 3 | 2.50 | 0.0828 0.0021 0.0848 | 26.9772 4 | 2.50 | 0.0823 0.0023 0.0846 | 24.6107 5 | 2.50 | 0.0819 0.0025 0.0844 | 22.6548 6 | 2.50 | 0.0816 0.0027 0.0842 | 20.6989 7 | 2.50 | 0.0812 0.0028 0.0840 | 18.9688 8 | 2.50 | 0.0808 0.0029 0.0838 | 17.4455 9 | 2.50 | 0.0805 0.0030 0.0835 | 15.9223 10 | 2.50 | 0.0801 0.0031 0.0832 | 14.6627 11 | 2.50 | 0.0797 0.0032 0.0829 | 13.4764 12 | 2.50 | 0.0793 0.0033 0.0826 | 12.3015 13 | 2.50 | 0.0789 0.0034 0.0823 | 11.3776 14 | 2.50 | 0.0785 0.0035 0.0820 | 10.4537 15 | 2.25 | 0.0791 0.0036 0.0827 | 9.5920 16 | 2.25 | 0.0758 0.0052 0.0810 | 8.8725 17 | 2.25 | 0.0745 0.0058 0.0803 | 8.1530 29 | 2.00 | 0.0764 0.0027 0.0791 | 3.3283 30 | 2.00 | 0.0704 0.0052 0.0756 | 3.1221 31 | 2.00 | 0.0682 0.0062 0.0745 | 2.9160 43 | 1.75 | 0.0672 0.0036 0.0708 | 1.5785 44 | 1.75 | 0.0627 0.0060 0.0687 | 1.5194 45 | 1.75 | 0.0611 0.0069 0.0680 | 1.4626 57 | 1.50 | 0.0598 0.0050 0.0649 | 1.0900 58 | 1.50 | 0.0565 0.0072 0.0637 | 1.0730 59 | 1.50 | 0.0554 0.0079 0.0632 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 164s Prepare output 10s 174s Jacobian determinant (RMS): 0.011 0.041 0.062 0.085 0.108 | 0.115154 Template Matching: 0.087 0.223 0.205 0.183 0.166 | 0.166122 Write result maps: 23s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 40s CSF distance: 18s PBT2x thickness: 50s 114s Create initial surface 94s Topology correction: 100s Surface refinement: 79s Reduction of surface collisions with optimization: 74s Spherical mapping with areal smoothing 94s Spherical registration 283s rh: Thickness estimation (0.50 mm): WM distance: 53s CSF distance: 16s PBT2x thickness: 47s 123s Create initial surface 90s Topology correction: 96s Surface refinement: 104s Reduction of surface collisions with optimization: 73s Spherical mapping with areal smoothing 86s Spherical registration 287s Final surface processing results: Average thickness (FS): 2.4678  0.5876 mm Surface intensity / position RMSE: 0.0641 / 0.0649 Euler number / defect number / defect size: 24.0 / 16.0 / 0.61% Display thickness: /var/lib/condor/execute/dir_28845/ds/sub-105/surf/lh.thickness.sub-105_T1w Display thickness: /var/lib/condor/execute/dir_28845/ds/sub-105/surf/rh.thickness.sub-105_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_28845/ds/sub-105/sub-105_T1w.nii Surface ROI estimation: 8s Surface and thickness estimation takes: 1795s ROI estimation in native space: ROI estimation of 'cobra' atlas 8s ROI estimation of 'neuromorphometrics' atlas 28s ROI estimation of 'lpba40' atlas 8s ROI estimation of 'hammers' atlas 20s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 7s ROI estimation of 'aal3' atlas 11s ROI estimation of 'mori' atlas 16s ROI estimation of 'anatomy3' atlas 23s ROI estimation of 'julichbrain' atlas 30s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 47s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 70s Write results 71s 303s Quality check: 5s Print 'Graphics' figure to: /var/lib/condor/execute/dir_28845/ds/sub-105/report/catreport_sub-105_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 50 minute(s) and 58 second(s). Image Quality Rating (IQR): 81.99% (B-) GM volume (GMV): 41.25% (726.30 / 1760.87 ml) GM thickness (GMT): 2.47  0.59 mm Segmentations are saved in /var/lib/condor/execute/dir_28845/ds/sub-105/mri Reports are saved in /var/lib/condor/execute/dir_28845/ds/sub-105/report Labels are saved in /var/lib/condor/execute/dir_28845/ds/sub-105/label ------------------------------------------------------------------------