------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0025966/ses-2/sub-0025966_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 38s Correct center-of-mass 4s Affine registration 10s SPM preprocessing 1 (estimate 1 - TPM registration): 95s SPM preprocessing 1 (estimate 2): 57s SPM preprocessing 2 (write): Write Segmentation 18s Update Segmentation 21s Update Skull-Stripping 44s Update probability maps 9s 91s Global intensity correction: 16s SANLM denoising after intensity normalization (medium): 34s Fast Optimized Shooting registration 33s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 2s Prepare segments (LASmod = 1.09) 16s Estimate local tissue thresholds (WM) 19s Estimate local tissue thresholds (GM) 27s Intensity transformation 0s SANLM denoising after LAS (medium) 42s 114s ROI segmentation (partitioning): Atlas -> subject space 8s Major structures 4s Ventricle detection 16s Blood vessel detection 10s WMH detection (WMHCstr=0.50 > WMHCstr'=0.12) 27s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 4s Final corrections 4s 76s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 38s AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.04] 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 13s 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 | 0.0852 0.0000 0.0852 | 32.0000 2 | 2.50 | 0.0826 0.0012 0.0838 | 29.4886 3 | 2.50 | 0.0819 0.0017 0.0836 | 26.9772 4 | 2.50 | 0.0815 0.0020 0.0835 | 24.6107 5 | 2.50 | 0.0812 0.0021 0.0833 | 22.6548 6 | 2.50 | 0.0810 0.0022 0.0832 | 20.6989 7 | 2.50 | 0.0807 0.0023 0.0830 | 18.9688 8 | 2.50 | 0.0804 0.0024 0.0828 | 17.4455 9 | 2.50 | 0.0801 0.0025 0.0826 | 15.9223 10 | 2.50 | 0.0798 0.0026 0.0824 | 14.6627 11 | 2.50 | 0.0795 0.0027 0.0822 | 13.4764 12 | 2.50 | 0.0792 0.0028 0.0819 | 12.3015 13 | 2.50 | 0.0788 0.0029 0.0817 | 11.3776 14 | 2.50 | 0.0785 0.0029 0.0815 | 10.4537 15 | 2.25 | 0.0779 0.0030 0.0809 | 9.5920 16 | 2.25 | 0.0749 0.0045 0.0794 | 8.8725 29 | 2.00 | 0.0762 0.0020 0.0782 | 3.3283 30 | 2.00 | 0.0697 0.0046 0.0743 | 3.1221 31 | 2.00 | 0.0675 0.0057 0.0732 | 2.9160 43 | 1.75 | 0.0664 0.0033 0.0697 | 1.5785 44 | 1.75 | 0.0618 0.0057 0.0675 | 1.5194 45 | 1.75 | 0.0603 0.0065 0.0668 | 1.4626 57 | 1.50 | 0.0587 0.0047 0.0634 | 1.0900 58 | 1.50 | 0.0554 0.0069 0.0622 | 1.0730 59 | 1.50 | 0.0543 0.0075 0.0618 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 181s Prepare output 11s 192s Jacobian determinant (RMS): 0.011 0.039 0.060 0.086 0.110 | 0.117239 Template Matching: 0.085 0.225 0.202 0.181 0.163 | 0.162924 Write result maps: 35s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 44s CSF distance: 17s PBT2x thickness: 50s 118s Create initial surface 101s Topology correction: 108s Surface refinement: 119s Reduction of surface collisions with optimization: 84s Spherical mapping with areal smoothing 89s Spherical registration 320s rh: Thickness estimation (0.50 mm): WM distance: 32s CSF distance: 17s PBT2x thickness: 49s 106s Create initial surface 100s Topology correction: 107s Surface refinement: 96s Reduction of surface collisions with optimization: 86s Spherical mapping with areal smoothing 103s Spherical registration 338s Final surface processing results: Average thickness (FS): 2.5293  0.6602 mm Surface intensity / position RMSE: 0.0676 / 0.0904 Euler number / defect number / defect size: 26.0 / 10.5 / 1.53% Display thickness: /var/lib/condor/execute/dir_2997796/ds/BNU_2/sub-0025966/ses-2/surf/lh.thickness.sub-0025966_ses-2_run-1_T1w Display thickness: /var/lib/condor/execute/dir_2997796/ds/BNU_2/sub-0025966/ses-2/surf/rh.thickness.sub-0025966_ses-2_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_2997796/ds/BNU_2/sub-0025966/ses-2/sub-0025966_ses-2_run-1_T1w.nii Surface ROI estimation: 13s Surface and thickness estimation takes: 1987s ROI estimation in native space: ROI estimation of 'cobra' atlas 15s ROI estimation of 'neuromorphometrics' atlas 50s ROI estimation of 'lpba40' atlas 14s ROI estimation of 'hammers' atlas 34s ROI estimation of 'thalamus' atlas 3s ROI estimation of 'ibsr' atlas 12s ROI estimation of 'aal3' atlas 21s ROI estimation of 'mori' atlas 29s ROI estimation of 'anatomy3' atlas 41s ROI estimation of 'julichbrain' atlas 48s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 19s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 35s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 67s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 90s ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s Write results 9s 487s Quality check: 13s Print 'Graphics' figure to: /var/lib/condor/execute/dir_2997796/ds/BNU_2/sub-0025966/ses-2/report/catreport_sub-0025966_ses-2_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 57 minute(s) and 48 second(s). Image Quality Rating (IQR): 83.94% (B) GM volume (GMV): 45.66% (786.51 / 1722.43 ml) GM thickness (GMT): 2.53  0.66 mm Segmentations are saved in /var/lib/condor/execute/dir_2997796/ds/BNU_2/sub-0025966/ses-2/mri Reports are saved in /var/lib/condor/execute/dir_2997796/ds/BNU_2/sub-0025966/ses-2/report Labels are saved in /var/lib/condor/execute/dir_2997796/ds/BNU_2/sub-0025966/ses-2/label ------------------------------------------------------------------------