------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0025945/ses-2/sub-0025945_ses-2_run-1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 54s 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 4s Affine registration 9s SPM preprocessing 1 (estimate 1 - TPM registration): 79s SPM preprocessing 1 (estimate 2): 68s SPM preprocessing 2 (write): Write Segmentation 17s Update Segmentation 19s Update Skull-Stripping 42s Update probability maps 9s 87s Global intensity correction: 17s SANLM denoising after intensity normalization (medium): 30s Fast Optimized Shooting registration 32s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 2s Prepare segments (LASmod = 1.00) 15s Estimate local tissue thresholds (WM) 19s Estimate local tissue thresholds (GM) 27s Intensity transformation 0s SANLM denoising after LAS (medium) 40s 111s ROI segmentation (partitioning): Atlas -> subject space 8s Major structures 4s Ventricle detection 19s Blood vessel detection 9s WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 25s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 4s Final corrections 4s 74s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 35s AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.07,0.990.04] 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 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 | 0.0792 0.0000 0.0792 | 32.0000 2 | 2.50 | 0.0772 0.0010 0.0782 | 29.4886 3 | 2.50 | 0.0766 0.0014 0.0781 | 26.9772 4 | 2.50 | 0.0764 0.0016 0.0780 | 24.6107 5 | 2.50 | 0.0762 0.0017 0.0779 | 22.6548 6 | 2.50 | 0.0760 0.0018 0.0777 | 20.6989 7 | 2.50 | 0.0758 0.0018 0.0776 | 18.9688 8 | 2.50 | 0.0756 0.0019 0.0775 | 17.4455 9 | 2.50 | 0.0754 0.0020 0.0773 | 15.9223 10 | 2.50 | 0.0751 0.0020 0.0772 | 14.6627 11 | 2.50 | 0.0749 0.0021 0.0770 | 13.4764 12 | 2.50 | 0.0747 0.0021 0.0768 | 12.3015 13 | 2.50 | 0.0745 0.0022 0.0767 | 11.3776 14 | 2.50 | 0.0742 0.0023 0.0765 | 10.4537 15 | 2.25 | 0.0723 0.0023 0.0746 | 9.5920 16 | 2.25 | 0.0699 0.0035 0.0734 | 8.8725 29 | 2.00 | 0.0716 0.0016 0.0732 | 3.3283 30 | 2.00 | 0.0664 0.0037 0.0700 | 3.1221 31 | 2.00 | 0.0646 0.0045 0.0691 | 2.9160 43 | 1.75 | 0.0640 0.0026 0.0665 | 1.5785 44 | 1.75 | 0.0598 0.0047 0.0646 | 1.5194 45 | 1.75 | 0.0585 0.0055 0.0640 | 1.4626 57 | 1.50 | 0.0570 0.0039 0.0610 | 1.0900 58 | 1.50 | 0.0540 0.0059 0.0599 | 1.0730 59 | 1.50 | 0.0529 0.0066 0.0595 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 168s Prepare output 11s 179s Jacobian determinant (RMS): 0.010 0.034 0.050 0.071 0.093 | 0.099121 Template Matching: 0.079 0.210 0.194 0.175 0.159 | 0.158829 Write result maps: 34s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 29s CSF distance: 17s PBT2x thickness: 48s 101s Create initial surface 95s Topology correction: 105s Surface refinement: 96s Reduction of surface collisions with optimization: 88s Spherical mapping with areal smoothing 92s Spherical registration 296s rh: Thickness estimation (0.50 mm): WM distance: 28s CSF distance: 16s PBT2x thickness: 48s 98s Create initial surface 93s Topology correction: 106s Surface refinement: 92s Reduction of surface collisions with optimization: 89s Spherical mapping with areal smoothing 100s Spherical registration 315s Final surface processing results: Average thickness (FS): 2.6215  0.5879 mm Surface intensity / position RMSE: 0.0656 / 0.0638 Euler number / defect number / defect size: 14.0 / 13.5 / 0.48% Display thickness: /var/lib/condor/execute/dir_2999354/ds/BNU_2/sub-0025945/ses-2/surf/lh.thickness.sub-0025945_ses-2_run-1_T1w Display thickness: /var/lib/condor/execute/dir_2999354/ds/BNU_2/sub-0025945/ses-2/surf/rh.thickness.sub-0025945_ses-2_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_2999354/ds/BNU_2/sub-0025945/ses-2/sub-0025945_ses-2_run-1_T1w.nii Surface ROI estimation: 11s Surface and thickness estimation takes: 1874s ROI estimation in native space: ROI estimation of 'cobra' atlas 11s ROI estimation of 'neuromorphometrics' atlas 41s ROI estimation of 'lpba40' atlas 11s ROI estimation of 'hammers' atlas 29s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 10s ROI estimation of 'aal3' atlas 14s ROI estimation of 'mori' atlas 20s ROI estimation of 'anatomy3' atlas 32s ROI estimation of 'julichbrain' atlas 40s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 33s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 67s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 101s ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s Write results 9s 439s Quality check: 12s Print 'Graphics' figure to: /var/lib/condor/execute/dir_2999354/ds/BNU_2/sub-0025945/ses-2/report/catreport_sub-0025945_ses-2_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 54 minute(s) and 37 second(s). Image Quality Rating (IQR): 82.52% (B-) GM volume (GMV): 50.51% (777.86 / 1540.08 ml) GM thickness (GMT): 2.62  0.59 mm Segmentations are saved in /var/lib/condor/execute/dir_2999354/ds/BNU_2/sub-0025945/ses-2/mri Reports are saved in /var/lib/condor/execute/dir_2999354/ds/BNU_2/sub-0025945/ses-2/report Labels are saved in /var/lib/condor/execute/dir_2999354/ds/BNU_2/sub-0025945/ses-2/label ------------------------------------------------------------------------