------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./dir_12076/ds/sub-021/sub-021_ses-t0_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 11s APP: Rough bias correction: Initialize 5s Estimate background 7s Initial correction 6s Refine background 3s Final correction 5s Final scaling 6s 36s Correct center-of-mass 2s Affine registration 10s SPM preprocessing 1 (estimate 1 - TPM registration): 69s SPM preprocessing 1 (estimate 2): 60s SPM preprocessing 2 (write): Write Segmentation 15s Update Segmentation 18s Update Skull-Stripping 38s Update probability maps 8s 79s Global intensity correction: 14s SANLM denoising after intensity normalization (medium): 7s Fast Optimized Shooting registration 29s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 2s Prepare segments (LASmod = 1.10) 15s Estimate local tissue thresholds (WM) 16s Estimate local tissue thresholds (GM) 22s Intensity transformation 0s SANLM denoising after LAS (medium) 16s 78s ROI segmentation (partitioning): Atlas -> subject space 7s Major structures 4s Ventricle detection 16s Blood vessel detection 10s WMH detection (WMHCstr=0.50 > WMHCstr'=0.19) 30s 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] = [0.360.06,0.680.07,0.980.04] Final cleanup (gcutstr=0.25): 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 12s 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 | 0.0854 0.0000 0.0854 | 32.0000 2 | 2.50 | 0.0828 0.0012 0.0839 | 29.4886 3 | 2.50 | 0.0819 0.0018 0.0838 | 26.9772 4 | 2.50 | 0.0815 0.0021 0.0836 | 24.6107 5 | 2.50 | 0.0812 0.0022 0.0834 | 22.6548 6 | 2.50 | 0.0809 0.0023 0.0832 | 20.6989 7 | 2.50 | 0.0806 0.0025 0.0831 | 18.9688 8 | 2.50 | 0.0803 0.0026 0.0829 | 17.4455 9 | 2.50 | 0.0800 0.0027 0.0826 | 15.9223 10 | 2.50 | 0.0796 0.0028 0.0824 | 14.6627 11 | 2.50 | 0.0793 0.0029 0.0822 | 13.4764 12 | 2.50 | 0.0789 0.0030 0.0819 | 12.3015 13 | 2.50 | 0.0786 0.0031 0.0817 | 11.3776 14 | 2.50 | 0.0782 0.0032 0.0814 | 10.4537 15 | 2.25 | 0.0776 0.0033 0.0809 | 9.5920 16 | 2.25 | 0.0744 0.0049 0.0793 | 8.8725 29 | 2.00 | 0.0753 0.0022 0.0775 | 3.3283 30 | 2.00 | 0.0682 0.0051 0.0733 | 3.1221 31 | 2.00 | 0.0658 0.0062 0.0721 | 2.9160 43 | 1.75 | 0.0644 0.0036 0.0680 | 1.5785 44 | 1.75 | 0.0599 0.0060 0.0659 | 1.5194 45 | 1.75 | 0.0585 0.0068 0.0653 | 1.4626 57 | 1.50 | 0.0566 0.0050 0.0616 | 1.0900 58 | 1.50 | 0.0536 0.0070 0.0606 | 1.0730 59 | 1.50 | 0.0526 0.0076 0.0602 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 148s Prepare output 10s 158s Jacobian determinant (RMS): 0.011 0.042 0.067 0.096 0.121 | 0.128554 Template Matching: 0.085 0.223 0.197 0.175 0.158 | 0.157868 Write result maps: 20s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 48s CSF distance: 15s PBT2x thickness: 43s 112s Create initial surface 85s Topology correction: 89s Surface refinement: 76s Reduction of surface collisions with optimization: 67s Spherical mapping with areal smoothing 74s Spherical registration 255s rh: Thickness estimation (0.50 mm): WM distance: 53s CSF distance: 15s PBT2x thickness: 45s 119s Create initial surface 87s Topology correction: 95s Surface refinement: 97s Reduction of surface collisions with optimization: 71s Spherical mapping with areal smoothing 77s Spherical registration 285s Final surface processing results: Average thickness (FS): 2.5564  0.6435 mm Surface intensity / position RMSE: 0.0600 / 0.0628 Euler number / defect number / defect size: 18.0 / 12.5 / 0.59% Display thickness: /var/lib/condor/execute/dir_12076/ds/sub-021/surf/lh.thickness.sub-021_ses-t0_T1w Display thickness: /var/lib/condor/execute/dir_12076/ds/sub-021/surf/rh.thickness.sub-021_ses-t0_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_12076/ds/sub-021/sub-021_ses-t0_T1w.nii Surface ROI estimation: 9s Surface and thickness estimation takes: 1676s ROI estimation in native space: ROI estimation of 'cobra' atlas 10s ROI estimation of 'neuromorphometrics' atlas 32s ROI estimation of 'lpba40' atlas 9s ROI estimation of 'hammers' atlas 20s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 7s ROI estimation of 'aal3' atlas 14s ROI estimation of 'mori' atlas 21s ROI estimation of 'anatomy3' atlas 25s ROI estimation of 'julichbrain' atlas 32s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 13s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 22s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 46s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 64s Write results 64s 316s Quality check: 5s Print 'Graphics' figure to: /var/lib/condor/execute/dir_12076/ds/sub-021/report/catreport_sub-021_ses-t0_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 46 minute(s) and 12 second(s). Image Quality Rating (IQR): 84.61% (B) GM volume (GMV): 41.62% (728.65 / 1750.87 ml) GM thickness (GMT): 2.56  0.64 mm Segmentations are saved in /var/lib/condor/execute/dir_12076/ds/sub-021/mri Reports are saved in /var/lib/condor/execute/dir_12076/ds/sub-021/report Labels are saved in /var/lib/condor/execute/dir_12076/ds/sub-021/label ------------------------------------------------------------------------