------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./execute/dir_3732/ds/sub-sc037/sub-sc037_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 26s APP: Rough bias correction: Initialize 6s Estimate background 6s Initial correction 6s Refine background 3s Final correction 5s Final scaling 5s 37s Correct center-of-mass 2s Affine registration 9s SPM preprocessing 1 (estimate 1 - TPM registration): 71s SPM preprocessing 1 (estimate 2): 50s SPM preprocessing 2 (write): Write Segmentation 16s Update Segmentation 18s Update Skull-Stripping 39s Update probability maps 8s 81s Global intensity correction: 14s SANLM denoising after intensity normalization (medium): 16s Fast Optimized Shooting registration 32s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 4s Prepare segments (LASmod = 1.08) 16s Estimate local tissue thresholds (WM) 17s Estimate local tissue thresholds (GM) 23s Intensity transformation 0s SANLM denoising after LAS (medium) 16s 84s ROI segmentation (partitioning): Atlas -> subject space 7s Major structures 4s Ventricle detection 14s Blood vessel detection 9s WMH detection (WMHCstr=0.50 > WMHCstr'=0.04) 27s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 4s Final corrections 4s 70s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 33s AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05] Final cleanup (gcutstr=0.25): 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 | 0.0848 0.0000 0.0848 | 32.0000 2 | 2.50 | 0.0819 0.0013 0.0832 | 29.4886 3 | 2.50 | 0.0811 0.0019 0.0830 | 26.9772 4 | 2.50 | 0.0807 0.0021 0.0828 | 24.6107 5 | 2.50 | 0.0804 0.0023 0.0827 | 22.6548 6 | 2.50 | 0.0801 0.0024 0.0825 | 20.6989 7 | 2.50 | 0.0798 0.0025 0.0823 | 18.9688 8 | 2.50 | 0.0795 0.0026 0.0821 | 17.4455 9 | 2.50 | 0.0792 0.0027 0.0818 | 15.9223 10 | 2.50 | 0.0789 0.0028 0.0816 | 14.6627 11 | 2.50 | 0.0785 0.0029 0.0814 | 13.4764 12 | 2.50 | 0.0782 0.0029 0.0811 | 12.3015 13 | 2.50 | 0.0779 0.0030 0.0809 | 11.3776 14 | 2.50 | 0.0776 0.0031 0.0806 | 10.4537 15 | 2.25 | 0.0767 0.0032 0.0799 | 9.5920 16 | 2.25 | 0.0739 0.0046 0.0784 | 8.8725 29 | 2.00 | 0.0753 0.0020 0.0774 | 3.3283 30 | 2.00 | 0.0694 0.0044 0.0738 | 3.1221 31 | 2.00 | 0.0674 0.0054 0.0728 | 2.9160 43 | 1.75 | 0.0666 0.0031 0.0696 | 1.5785 44 | 1.75 | 0.0622 0.0054 0.0676 | 1.5194 45 | 1.75 | 0.0608 0.0062 0.0670 | 1.4626 57 | 1.50 | 0.0594 0.0045 0.0639 | 1.0900 58 | 1.50 | 0.0562 0.0066 0.0628 | 1.0730 59 | 1.50 | 0.0551 0.0072 0.0624 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 160s Prepare output 10s 169s Jacobian determinant (RMS): 0.012 0.043 0.063 0.087 0.112 | 0.118169 Template Matching: 0.085 0.222 0.202 0.182 0.165 | 0.165435 Write result maps: 21s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 45s CSF distance: 16s PBT2x thickness: 48s 115s Create initial surface 96s Topology correction: 109s Surface refinement: 97s Reduction of surface collisions with optimization: 85s Spherical mapping with areal smoothing 101s Spherical registration 300s rh: Thickness estimation (0.50 mm): WM distance: 36s CSF distance: 18s PBT2x thickness: 48s 108s Create initial surface 92s Topology correction: 101s Surface refinement: 91s Reduction of surface collisions with optimization: 77s Spherical mapping with areal smoothing 88s Spherical registration 299s Final surface processing results: Average thickness (FS): 2.5246  0.6328 mm Surface intensity / position RMSE: 0.0708 / 0.0810 Euler number / defect number / defect size: 16.0 / 12.5 / 1.06% Display thickness: /var/lib/condor/execute/dir_3732/ds/sub-sc037/surf/lh.thickness.sub-sc037_T1w Display thickness: /var/lib/condor/execute/dir_3732/ds/sub-sc037/surf/rh.thickness.sub-sc037_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_3732/ds/sub-sc037/sub-sc037_T1w.nii Surface ROI estimation: 9s Surface and thickness estimation takes: 1861s 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 24s ROI estimation of 'julichbrain' atlas 32s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 13s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 23s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 50s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 77s Write results 78s 319s Quality check: 5s Print 'Graphics' figure to: /var/lib/condor/execute/dir_3732/ds/sub-sc037/report/catreport_sub-sc037_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 50 minute(s) and 2 second(s). Image Quality Rating (IQR): 85.63% (B) GM volume (GMV): 48.53% (749.08 / 1543.68 ml) GM thickness (GMT): 2.52  0.64 mm Segmentations are saved in /var/lib/condor/execute/dir_3732/ds/sub-sc037/mri Reports are saved in /var/lib/condor/execute/dir_3732/ds/sub-sc037/report Labels are saved in /var/lib/condor/execute/dir_3732/ds/sub-sc037/label ------------------------------------------------------------------------