------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./execute/dir_24738/ds/sub-23/sub-23_ses-01_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 43s APP: Rough bias correction: Initialize 5s Estimate background 7s Initial correction 6s Refine background 3s Final correction 5s Final scaling 6s 38s Correct center-of-mass 4s Affine registration 14s SPM preprocessing 1 (estimate 1 - TPM registration): 65s SPM preprocessing 1 (estimate 2): 65s SPM preprocessing 2 (write): Write Segmentation 17s Update Segmentation 19s Update Skull-Stripping 38s Update probability maps 8s 82s Global intensity correction: 15s SANLM denoising after intensity normalization (medium): 12s Fast Optimized Shooting registration 30s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 2s Prepare segments (LASmod = 1.08) 15s Estimate local tissue thresholds (WM) 18s Estimate local tissue thresholds (GM) 26s Intensity transformation 0s SANLM denoising after LAS (medium) 34s 101s ROI segmentation (partitioning): Atlas -> subject space 7s Major structures 4s Ventricle detection 16s Blood vessel detection 11s WMH detection (WMHCstr=0.50 > WMHCstr'=0.08) 32s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 4s Final corrections 4s 79s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 36s AMAP peaks: [CSF,GM,WM] = [0.360.05,0.670.08,0.980.04] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 4s Level 1 cleanup (brain masking) 3s Level 2 cleanup (CSF correction) 2s 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 | 0.0829 0.0000 0.0829 | 32.0000 2 | 2.50 | 0.0807 0.0011 0.0817 | 29.4886 3 | 2.50 | 0.0801 0.0016 0.0816 | 26.9772 4 | 2.50 | 0.0797 0.0018 0.0815 | 24.6107 5 | 2.50 | 0.0795 0.0019 0.0814 | 22.6548 6 | 2.50 | 0.0792 0.0020 0.0812 | 20.6989 7 | 2.50 | 0.0790 0.0021 0.0811 | 18.9688 8 | 2.50 | 0.0788 0.0021 0.0809 | 17.4455 9 | 2.50 | 0.0785 0.0022 0.0807 | 15.9223 10 | 2.50 | 0.0782 0.0023 0.0805 | 14.6627 11 | 2.50 | 0.0780 0.0024 0.0803 | 13.4764 12 | 2.50 | 0.0777 0.0024 0.0801 | 12.3015 13 | 2.50 | 0.0774 0.0025 0.0799 | 11.3776 14 | 2.50 | 0.0771 0.0025 0.0797 | 10.4537 15 | 2.25 | 0.0763 0.0026 0.0789 | 9.5920 16 | 2.25 | 0.0737 0.0039 0.0775 | 8.8725 29 | 2.00 | 0.0754 0.0017 0.0771 | 3.3283 30 | 2.00 | 0.0696 0.0041 0.0737 | 3.1221 31 | 2.00 | 0.0676 0.0051 0.0727 | 2.9160 43 | 1.75 | 0.0667 0.0029 0.0696 | 1.5785 44 | 1.75 | 0.0624 0.0052 0.0676 | 1.5194 45 | 1.75 | 0.0609 0.0061 0.0670 | 1.4626 57 | 1.50 | 0.0594 0.0044 0.0638 | 1.0900 58 | 1.50 | 0.0561 0.0065 0.0627 | 1.0730 59 | 1.50 | 0.0551 0.0072 0.0623 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 165s Prepare output 11s 176s Jacobian determinant (RMS): 0.010 0.037 0.055 0.080 0.103 | 0.110129 Template Matching: 0.083 0.221 0.203 0.183 0.165 | 0.165178 Write result maps: 24s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 41s CSF distance: 18s PBT2x thickness: 48s 113s Create initial surface 86s Topology correction: 112s Surface refinement: 115s Reduction of surface collisions with optimization: 93s Spherical mapping with areal smoothing 119s Spherical registration 306s rh: Thickness estimation (0.50 mm): WM distance: 44s CSF distance: 19s PBT2x thickness: 50s 119s Create initial surface 86s Topology correction: 108s Surface refinement: 81s Reduction of surface collisions with optimization: 89s Spherical mapping with areal smoothing 101s Spherical registration 311s Final surface processing results: Average thickness (FS): 2.4785  0.5645 mm Surface intensity / position RMSE: 0.0657 / 0.0675 Euler number / defect number / defect size: 20.0 / 14.5 / 0.77% Display thickness: /var/lib/condor/execute/dir_24738/ds/sub-23/surf/lh.thickness.sub-23_ses-01_T1w Display thickness: /var/lib/condor/execute/dir_24738/ds/sub-23/surf/rh.thickness.sub-23_ses-01_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_24738/ds/sub-23/sub-23_ses-01_T1w.nii Surface ROI estimation: 8s Surface and thickness estimation takes: 1942s 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 19s ROI estimation of 'thalamus' atlas 1s 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 71s Write results 71s 302s Quality check: 5s Print 'Graphics' figure to: /var/lib/condor/execute/dir_24738/ds/sub-23/report/catreport_sub-23_ses-01_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 52 minute(s) and 13 second(s). Image Quality Rating (IQR): 83.46% (B) GM volume (GMV): 45.08% (776.31 / 1722.19 ml) GM thickness (GMT): 2.48  0.56 mm Segmentations are saved in /var/lib/condor/execute/dir_24738/ds/sub-23/mri Reports are saved in /var/lib/condor/execute/dir_24738/ds/sub-23/report Labels are saved in /var/lib/condor/execute/dir_24738/ds/sub-23/label ------------------------------------------------------------------------