------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./execute/dir_1631/ds/sub-120/sub-120_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 24s APP: Rough bias correction: Initialize 5s Estimate background 8s Initial correction 8s Refine background 4s Final correction 6s Final scaling 9s 47s Correct center-of-mass 3s Affine registration 10s SPM preprocessing 1 (estimate 1 - TPM registration): 72s SPM preprocessing 1 (estimate 2): 46s SPM preprocessing 2 (write): Write Segmentation 15s Update Segmentation 18s Update Skull-Stripping 37s Update probability maps 8s 78s Global intensity correction: 14s SANLM denoising after intensity normalization (medium): 8s Fast Optimized Shooting registration 29s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 2s Prepare segments (LASmod = 1.13) 13s Estimate local tissue thresholds (WM) 18s Estimate local tissue thresholds (GM) 24s Intensity transformation 0s SANLM denoising after LAS (medium) 22s 86s ROI segmentation (partitioning): Atlas -> subject space 7s Major structures 3s Ventricle detection 16s Blood vessel detection 9s WMH detection (WMHCstr=0.48 > WMHCstr'=0.10) 24s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 3s Final corrections 4s 68s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 30s AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.04] 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 | 0.0868 0.0000 0.0868 | 32.0000 2 | 2.50 | 0.0839 0.0013 0.0851 | 29.4886 3 | 2.50 | 0.0831 0.0018 0.0849 | 26.9772 4 | 2.50 | 0.0827 0.0021 0.0847 | 24.6107 5 | 2.50 | 0.0824 0.0022 0.0846 | 22.6548 6 | 2.50 | 0.0821 0.0023 0.0844 | 20.6989 7 | 2.50 | 0.0819 0.0023 0.0842 | 18.9688 8 | 2.50 | 0.0816 0.0024 0.0840 | 17.4455 9 | 2.50 | 0.0813 0.0025 0.0838 | 15.9223 10 | 2.50 | 0.0810 0.0026 0.0835 | 14.6627 11 | 2.50 | 0.0807 0.0026 0.0833 | 13.4764 12 | 2.50 | 0.0804 0.0027 0.0830 | 12.3015 13 | 2.50 | 0.0801 0.0027 0.0828 | 11.3776 14 | 2.50 | 0.0798 0.0028 0.0825 | 10.4537 15 | 2.25 | 0.0793 0.0029 0.0822 | 9.5920 16 | 2.25 | 0.0766 0.0042 0.0808 | 8.8725 17 | 2.25 | 0.0756 0.0046 0.0802 | 8.1530 18 | 2.25 | 0.0749 0.0048 0.0798 | 7.5234 29 | 2.00 | 0.0774 0.0023 0.0797 | 3.3283 30 | 2.00 | 0.0722 0.0045 0.0767 | 3.1221 31 | 2.00 | 0.0705 0.0054 0.0758 | 2.9160 43 | 1.75 | 0.0698 0.0030 0.0728 | 1.5785 44 | 1.75 | 0.0653 0.0054 0.0708 | 1.5194 45 | 1.75 | 0.0639 0.0063 0.0701 | 1.4626 57 | 1.50 | 0.0627 0.0045 0.0672 | 1.0900 58 | 1.50 | 0.0593 0.0068 0.0661 | 1.0730 59 | 1.50 | 0.0582 0.0075 0.0657 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 149s Prepare output 9s 158s Jacobian determinant (RMS): 0.010 0.034 0.053 0.076 0.099 | 0.105986 Template Matching: 0.087 0.225 0.211 0.192 0.175 | 0.174578 Write result maps: 20s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 45s CSF distance: 16s PBT2x thickness: 47s 114s Create initial surface 91s Topology correction: 101s Surface refinement: 94s Reduction of surface collisions with optimization: 81s Spherical mapping with areal smoothing 85s Spherical registration 273s rh: Thickness estimation (0.50 mm): WM distance: 38s CSF distance: 17s PBT2x thickness: 47s 109s Create initial surface 93s Topology correction: 106s Surface refinement: 93s Reduction of surface collisions with optimization: 79s Spherical mapping with areal smoothing 86s Spherical registration 277s Final surface processing results: Average thickness (FS): 2.3651  0.5669 mm Surface intensity / position RMSE: 0.0671 / 0.0728 Euler number / defect number / defect size: 42.0 / 22.5 / 1.67% Display thickness: /var/lib/condor/execute/dir_1631/ds/sub-120/surf/lh.thickness.sub-120_T1w Display thickness: /var/lib/condor/execute/dir_1631/ds/sub-120/surf/rh.thickness.sub-120_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_1631/ds/sub-120/sub-120_T1w.nii Surface ROI estimation: 8s Surface and thickness estimation takes: 1773s ROI estimation in native space: ROI estimation of 'cobra' atlas 8s ROI estimation of 'neuromorphometrics' atlas 27s ROI estimation of 'lpba40' atlas 8s ROI estimation of 'hammers' atlas 19s ROI estimation of 'thalamus' atlas 1s ROI estimation of 'ibsr' atlas 7s ROI estimation of 'aal3' atlas 10s ROI estimation of 'mori' atlas 16s ROI estimation of 'anatomy3' atlas 22s ROI estimation of 'julichbrain' atlas 29s 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 45s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 68s Write results 69s 294s Quality check: 5s Print 'Graphics' figure to: /var/lib/condor/execute/dir_1631/ds/sub-120/report/catreport_sub-120_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 47 minute(s) and 35 second(s). Image Quality Rating (IQR): 80.77% (B-) GM volume (GMV): 43.51% (749.44 / 1722.52 ml) GM thickness (GMT): 2.37  0.57 mm Segmentations are saved in /var/lib/condor/execute/dir_1631/ds/sub-120/mri Reports are saved in /var/lib/condor/execute/dir_1631/ds/sub-120/report Labels are saved in /var/lib/condor/execute/dir_1631/ds/sub-120/label ------------------------------------------------------------------------