------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0025978/ses-1/sub-0025978_ses-1_run-1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 33s Internal resampling (1.33x1.00x1.00mm > 1.00x1.00x1.00mm): 1s APP: Rough bias correction: Initialize 6s Estimate background 5s Initial correction 5s Refine background 3s Final correction 4s Final scaling 4s 34s Correct center-of-mass 4s Affine registration 8s SPM preprocessing 1 (estimate 1 - TPM registration): 71s SPM preprocessing 1 (estimate 2): 57s SPM preprocessing 2 (write): Write Segmentation 15s Update Segmentation 16s Update Skull-Stripping 38s Update probability maps 8s 78s Global intensity correction: 15s SANLM denoising after intensity normalization (medium): 23s Fast Optimized Shooting registration 32s Local adaptive segmentation (LASstr=0.50): Prepare maps 3s Prepare partitions 2s Prepare segments (LASmod = 1.00) 12s Estimate local tissue thresholds (WM) 17s Estimate local tissue thresholds (GM) 25s Intensity transformation 0s SANLM denoising after LAS (medium) 38s 101s ROI segmentation (partitioning): Atlas -> subject space 7s Major structures 3s Ventricle detection 14s Blood vessel detection 8s WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 21s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 3s Final corrections 4s 62s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 30s AMAP peaks: [CSF,GM,WM] = [0.360.05,0.670.08,0.980.05] 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 | 0.0814 0.0000 0.0814 | 32.0000 2 | 2.50 | 0.0791 0.0011 0.0802 | 29.4886 3 | 2.50 | 0.0784 0.0017 0.0801 | 26.9772 4 | 2.50 | 0.0780 0.0019 0.0799 | 24.6107 5 | 2.50 | 0.0778 0.0020 0.0798 | 22.6548 6 | 2.50 | 0.0775 0.0021 0.0796 | 20.6989 7 | 2.50 | 0.0772 0.0022 0.0795 | 18.9688 8 | 2.50 | 0.0770 0.0023 0.0793 | 17.4455 9 | 2.50 | 0.0767 0.0024 0.0791 | 15.9223 10 | 2.50 | 0.0764 0.0025 0.0789 | 14.6627 11 | 2.50 | 0.0761 0.0026 0.0787 | 13.4764 12 | 2.50 | 0.0758 0.0026 0.0785 | 12.3015 13 | 2.50 | 0.0755 0.0027 0.0782 | 11.3776 14 | 2.50 | 0.0752 0.0028 0.0780 | 10.4537 15 | 2.25 | 0.0732 0.0029 0.0761 | 9.5920 16 | 2.25 | 0.0706 0.0042 0.0748 | 8.8725 29 | 2.00 | 0.0709 0.0019 0.0728 | 3.3283 30 | 2.00 | 0.0653 0.0041 0.0694 | 3.1221 31 | 2.00 | 0.0634 0.0050 0.0684 | 2.9160 43 | 1.75 | 0.0621 0.0029 0.0650 | 1.5785 44 | 1.75 | 0.0584 0.0049 0.0632 | 1.5194 45 | 1.75 | 0.0571 0.0055 0.0627 | 1.4626 57 | 1.50 | 0.0556 0.0040 0.0596 | 1.0900 58 | 1.50 | 0.0529 0.0058 0.0586 | 1.0730 Shooting registration with 2.50:-0.25:1.50 mm takes: 147s Prepare output 10s 157s Jacobian determinant (RMS): 0.011 0.041 0.060 0.083 0.103 | 0.107282 Template Matching: 0.081 0.212 0.190 0.171 0.159 | 0.158621 Write result maps: 55s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 25s CSF distance: 14s PBT2x thickness: 42s 88s Create initial surface 83s Topology correction: 94s Surface refinement: 79s Reduction of surface collisions with optimization: 66s Spherical mapping with areal smoothing 87s Spherical registration 299s rh: Thickness estimation (0.50 mm): WM distance: 24s CSF distance: 13s PBT2x thickness: 41s 85s Create initial surface 81s Topology correction: 88s Surface refinement: 94s Reduction of surface collisions with optimization: 65s Spherical mapping with areal smoothing 77s Spherical registration 299s Final surface processing results: Average thickness (FS): 2.5498  0.6277 mm Surface intensity / position RMSE: 0.0685 / 0.0703 Euler number / defect number / defect size: 16.0 / 11.5 / 0.64% Display thickness: /var/lib/condor/execute/dir_2997985/ds/BNU_2/sub-0025978/ses-1/surf/lh.thickness.sub-0025978_ses-1_run-1_T1w Display thickness: /var/lib/condor/execute/dir_2997985/ds/BNU_2/sub-0025978/ses-1/surf/rh.thickness.sub-0025978_ses-1_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_2997985/ds/BNU_2/sub-0025978/ses-1/sub-0025978_ses-1_run-1_T1w.nii Surface ROI estimation: 8s Surface and thickness estimation takes: 1678s ROI estimation in native space: ROI estimation of 'cobra' atlas 8s ROI estimation of 'neuromorphometrics' atlas 29s 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 12s ROI estimation of 'mori' atlas 17s ROI estimation of 'anatomy3' atlas 25s ROI estimation of 'julichbrain' atlas 33s 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 52s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 78s ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s Write results 8s 335s Quality check: 10s Print 'Graphics' figure to: /var/lib/condor/execute/dir_2997985/ds/BNU_2/sub-0025978/ses-1/report/catreport_sub-0025978_ses-1_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 47 minute(s) and 46 second(s). Image Quality Rating (IQR): 80.99% (B-) GM volume (GMV): 50.74% (673.05 / 1326.42 ml) GM thickness (GMT): 2.55  0.63 mm Segmentations are saved in /var/lib/condor/execute/dir_2997985/ds/BNU_2/sub-0025978/ses-1/mri Reports are saved in /var/lib/condor/execute/dir_2997985/ds/BNU_2/sub-0025978/ses-1/report Labels are saved in /var/lib/condor/execute/dir_2997985/ds/BNU_2/sub-0025978/ses-1/label ------------------------------------------------------------------------