------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./execute/dir_19497/ds/sub-140/sub-140_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 69s APP: Rough bias correction: Initialize 7s Estimate background 10s Initial correction 11s Refine background 5s Final correction 8s Final scaling 9s 58s Correct center-of-mass 5s Affine registration 12s SPM preprocessing 1 (estimate 1 - TPM registration): 85s SPM preprocessing 1 (estimate 2): 56s SPM preprocessing 2 (write): Write Segmentation 21s Update Segmentation 21s Update Skull-Stripping 50s Update probability maps 11s 102s Global intensity correction: 19s SANLM denoising after intensity normalization (medium): 11s Fast Optimized Shooting registration 42s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 3s Prepare segments (LASmod = 1.14) 16s Estimate local tissue thresholds (WM) 27s Estimate local tissue thresholds (GM) 36s Intensity transformation 0s SANLM denoising after LAS (medium) 18s 107s ROI segmentation (partitioning): Atlas -> subject space 9s Major structures 4s Ventricle detection 16s Blood vessel detection 11s WMH detection (WMHCstr=0.48 > WMHCstr'=0.02) 26s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 4s Final corrections 5s 75s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 36s AMAP peaks: [CSF,GM,WM] = [0.360.07,0.680.07,0.990.04] Final cleanup (gcutstr=0.24): Level 1 cleanup (ROI estimation) 5s Level 1 cleanup (brain masking) 3s Level 2 cleanup (CSF correction) 2s Level 3 cleanup (CSF/WM PVE) 3s 13s 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 | 0.0851 0.0000 0.0851 | 32.0000 2 | 2.50 | 0.0826 0.0011 0.0837 | 29.4886 3 | 2.50 | 0.0819 0.0017 0.0836 | 26.9772 4 | 2.50 | 0.0815 0.0019 0.0834 | 24.6107 5 | 2.50 | 0.0812 0.0021 0.0833 | 22.6548 6 | 2.50 | 0.0809 0.0022 0.0831 | 20.6989 7 | 2.50 | 0.0806 0.0023 0.0829 | 18.9688 8 | 2.50 | 0.0803 0.0024 0.0827 | 17.4455 9 | 2.50 | 0.0800 0.0025 0.0825 | 15.9223 10 | 2.50 | 0.0797 0.0026 0.0823 | 14.6627 11 | 2.50 | 0.0794 0.0027 0.0821 | 13.4764 12 | 2.50 | 0.0791 0.0028 0.0818 | 12.3015 13 | 2.50 | 0.0787 0.0029 0.0816 | 11.3776 14 | 2.50 | 0.0784 0.0030 0.0814 | 10.4537 15 | 2.25 | 0.0782 0.0030 0.0812 | 9.5920 16 | 2.25 | 0.0752 0.0045 0.0797 | 8.8725 17 | 2.25 | 0.0739 0.0051 0.0791 | 8.1530 29 | 2.00 | 0.0754 0.0024 0.0778 | 3.3283 30 | 2.00 | 0.0694 0.0049 0.0743 | 3.1221 31 | 2.00 | 0.0673 0.0059 0.0732 | 2.9160 43 | 1.75 | 0.0661 0.0034 0.0695 | 1.5785 44 | 1.75 | 0.0617 0.0058 0.0674 | 1.5194 45 | 1.75 | 0.0602 0.0066 0.0667 | 1.4626 57 | 1.50 | 0.0586 0.0048 0.0634 | 1.0900 58 | 1.50 | 0.0555 0.0068 0.0623 | 1.0730 59 | 1.50 | 0.0544 0.0075 0.0619 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 204s Prepare output 13s 217s Jacobian determinant (RMS): 0.011 0.043 0.067 0.094 0.119 | 0.126727 Template Matching: 0.085 0.222 0.202 0.180 0.163 | 0.163138 Write result maps: 31s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 36s CSF distance: 18s PBT2x thickness: 56s 117s Create initial surface 103s Topology correction: 106s Surface refinement: 106s Reduction of surface collisions with optimization: 72s Spherical mapping with areal smoothing 97s Spherical registration 340s rh: Thickness estimation (0.50 mm): WM distance: 46s CSF distance: 18s PBT2x thickness: 55s 126s Create initial surface 97s Topology correction: 107s Surface refinement: 89s Reduction of surface collisions with optimization: 72s Spherical mapping with areal smoothing 97s Spherical registration 339s Final surface processing results: Average thickness (FS): 2.5660  0.5953 mm Surface intensity / position RMSE: 0.0619 / 0.0621 Euler number / defect number / defect size: 8.0 / 8.5 / 0.30% Display thickness: /var/lib/condor/execute/dir_19497/ds/sub-140/surf/lh.thickness.sub-140_T1w Display thickness: /var/lib/condor/execute/dir_19497/ds/sub-140/surf/rh.thickness.sub-140_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_19497/ds/sub-140/sub-140_T1w.nii Surface ROI estimation: 9s Surface and thickness estimation takes: 1977s ROI estimation in native space: ROI estimation of 'cobra' atlas 9s ROI estimation of 'neuromorphometrics' atlas 30s ROI estimation of 'lpba40' atlas 9s ROI estimation of 'hammers' atlas 21s 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 30s ROI estimation of 'julichbrain' atlas 38s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 26s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 61s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 90s Write results 91s 372s Quality check: 6s Print 'Graphics' figure to: /var/lib/condor/execute/dir_19497/ds/sub-140/report/catreport_sub-140_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 56 minute(s) and 30 second(s). Image Quality Rating (IQR): 80.92% (B-) GM volume (GMV): 48.25% (668.27 / 1385.12 ml) GM thickness (GMT): 2.57  0.60 mm Segmentations are saved in /var/lib/condor/execute/dir_19497/ds/sub-140/mri Reports are saved in /var/lib/condor/execute/dir_19497/ds/sub-140/report Labels are saved in /var/lib/condor/execute/dir_19497/ds/sub-140/label ------------------------------------------------------------------------