------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./condor/execute/dir_4348/ds/sub-40/sub-40_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 23s APP: Rough bias correction: Initialize 5s Estimate background 6s Initial correction 6s Refine background 3s Final correction 5s Final scaling 5s 36s Correct center-of-mass 6s Affine registration 9s SPM preprocessing 1 (estimate 1 - TPM registration): 70s SPM preprocessing 1 (estimate 2): 56s SPM preprocessing 2 (write): Write Segmentation 14s Update Segmentation 16s Update Skull-Stripping 36s Update probability maps 7s 73s Global intensity correction: 13s SANLM denoising after intensity normalization (medium): 7s Fast Optimized Shooting registration 29s Local adaptive segmentation (LASstr=0.50): Prepare maps 3s Prepare partitions 2s Prepare segments (LASmod = 1.00) 12s Estimate local tissue thresholds (WM) 15s Estimate local tissue thresholds (GM) 21s Intensity transformation 0s SANLM denoising after LAS (medium) 24s 81s ROI segmentation (partitioning): Atlas -> subject space 7s Major structures 3s Ventricle detection 15s Blood vessel detection 8s WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 24s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 3s Final corrections 4s 66s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 34s AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05] 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 | 0.0817 0.0000 0.0817 | 32.0000 2 | 2.50 | 0.0793 0.0011 0.0804 | 29.4886 3 | 2.50 | 0.0786 0.0017 0.0803 | 26.9772 4 | 2.50 | 0.0782 0.0019 0.0801 | 24.6107 5 | 2.50 | 0.0779 0.0021 0.0800 | 22.6548 6 | 2.50 | 0.0777 0.0022 0.0798 | 20.6989 7 | 2.50 | 0.0774 0.0023 0.0797 | 18.9688 8 | 2.50 | 0.0771 0.0024 0.0795 | 17.4455 9 | 2.50 | 0.0768 0.0024 0.0793 | 15.9223 10 | 2.50 | 0.0765 0.0026 0.0791 | 14.6627 11 | 2.50 | 0.0762 0.0026 0.0789 | 13.4764 12 | 2.50 | 0.0759 0.0027 0.0786 | 12.3015 13 | 2.50 | 0.0756 0.0028 0.0784 | 11.3776 14 | 2.50 | 0.0753 0.0029 0.0782 | 10.4537 15 | 2.25 | 0.0752 0.0030 0.0781 | 9.5920 16 | 2.25 | 0.0722 0.0045 0.0766 | 8.8725 29 | 2.00 | 0.0737 0.0020 0.0758 | 3.3283 30 | 2.00 | 0.0677 0.0044 0.0721 | 3.1221 31 | 2.00 | 0.0655 0.0054 0.0709 | 2.9160 43 | 1.75 | 0.0645 0.0032 0.0677 | 1.5785 44 | 1.75 | 0.0604 0.0053 0.0657 | 1.5194 45 | 1.75 | 0.0589 0.0061 0.0650 | 1.4626 57 | 1.50 | 0.0576 0.0045 0.0620 | 1.0900 58 | 1.50 | 0.0545 0.0064 0.0609 | 1.0730 59 | 1.50 | 0.0534 0.0070 0.0605 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 162s Prepare output 9s 172s Jacobian determinant (RMS): 0.012 0.042 0.063 0.086 0.107 | 0.113944 Template Matching: 0.082 0.217 0.196 0.177 0.160 | 0.160265 Write result maps: 21s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 25s CSF distance: 14s PBT2x thickness: 42s 87s Create initial surface 82s Topology correction: 90s Surface refinement: 69s Reduction of surface collisions with optimization: 65s Spherical mapping with areal smoothing 80s Spherical registration 294s rh: Thickness estimation (0.50 mm): WM distance: 28s CSF distance: 14s PBT2x thickness: 41s 88s Create initial surface 79s Topology correction: 93s Surface refinement: 87s Reduction of surface collisions with optimization: 67s Spherical mapping with areal smoothing 79s Spherical registration 304s Final surface processing results: Average thickness (FS): 2.4651  0.6043 mm Surface intensity / position RMSE: 0.0696 / 0.0712 Euler number / defect number / defect size: 30.0 / 18.0 / 0.81% Display thickness: /var/lib/condor/execute/dir_4348/ds/sub-40/surf/lh.thickness.sub-40_T1w Display thickness: /var/lib/condor/execute/dir_4348/ds/sub-40/surf/rh.thickness.sub-40_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_4348/ds/sub-40/sub-40_T1w.nii Surface ROI estimation: 8s Surface and thickness estimation takes: 1652s ROI estimation in native space: ROI estimation of 'cobra' atlas 7s ROI estimation of 'neuromorphometrics' atlas 26s ROI estimation of 'lpba40' atlas 7s ROI estimation of 'hammers' atlas 18s ROI estimation of 'thalamus' atlas 1s ROI estimation of 'ibsr' atlas 6s ROI estimation of 'aal3' atlas 10s ROI estimation of 'mori' atlas 15s ROI estimation of 'anatomy3' atlas 22s ROI estimation of 'julichbrain' atlas 28s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 20s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 47s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 77s Write results 79s 299s Quality check: 5s Print 'Graphics' figure to: /var/lib/condor/execute/dir_4348/ds/sub-40/report/catreport_sub-40_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 46 minute(s) and 36 second(s). Image Quality Rating (IQR): 82.68% (B-) GM volume (GMV): 49.46% (671.33 / 1357.45 ml) GM thickness (GMT): 2.47  0.60 mm Segmentations are saved in /var/lib/condor/execute/dir_4348/ds/sub-40/mri Reports are saved in /var/lib/condor/execute/dir_4348/ds/sub-40/report Labels are saved in /var/lib/condor/execute/dir_4348/ds/sub-40/label ------------------------------------------------------------------------