------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0025953/ses-1/sub-0025953_ses-1_run-1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 24s Internal resampling (1.33x1.00x1.00mm > 1.00x1.00x1.00mm): 1s APP: Rough bias correction: Initialize 4s Estimate background 4s Initial correction 4s Refine background 2s Final correction 3s Final scaling 3s 23s Correct center-of-mass 2s Affine registration 6s SPM preprocessing 1 (estimate 1 - TPM registration): 51s SPM preprocessing 1 (estimate 2): 49s SPM preprocessing 2 (write): Write Segmentation 12s Update Segmentation 13s Update Skull-Stripping 27s Update probability maps 6s 58s Global intensity correction: 10s SANLM denoising after intensity normalization (medium): 20s Fast Optimized Shooting registration 22s Local adaptive segmentation (LASstr=0.50): Prepare maps 2s Prepare partitions 1s Prepare segments (LASmod = 1.08) 10s Estimate local tissue thresholds (WM) 12s Estimate local tissue thresholds (GM) 18s Intensity transformation 0s SANLM denoising after LAS (medium) 27s 72s ROI segmentation (partitioning): Atlas -> subject space 5s Major structures 2s Ventricle detection 8s Blood vessel detection 6s WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 14s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 2s Final corrections 3s 42s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 23s AMAP peaks: [CSF,GM,WM] = [0.370.05,0.680.08,0.980.04] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 3s Level 1 cleanup (brain masking) 2s Level 2 cleanup (CSF correction) 1s Level 3 cleanup (CSF/WM PVE) 2s 7s 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 | 0.0824 0.0000 0.0824 | 32.0000 2 | 2.50 | 0.0797 0.0012 0.0809 | 29.4886 3 | 2.50 | 0.0790 0.0018 0.0808 | 26.9772 4 | 2.50 | 0.0786 0.0020 0.0806 | 24.6107 5 | 2.50 | 0.0783 0.0022 0.0805 | 22.6548 6 | 2.50 | 0.0781 0.0022 0.0803 | 20.6989 7 | 2.50 | 0.0778 0.0023 0.0801 | 18.9688 8 | 2.50 | 0.0775 0.0024 0.0799 | 17.4455 9 | 2.50 | 0.0772 0.0025 0.0797 | 15.9223 10 | 2.50 | 0.0769 0.0026 0.0795 | 14.6627 11 | 2.50 | 0.0766 0.0027 0.0793 | 13.4764 12 | 2.50 | 0.0763 0.0027 0.0790 | 12.3015 13 | 2.50 | 0.0760 0.0028 0.0788 | 11.3776 14 | 2.50 | 0.0757 0.0029 0.0786 | 10.4537 15 | 2.25 | 0.0748 0.0029 0.0777 | 9.5920 16 | 2.25 | 0.0718 0.0044 0.0762 | 8.8725 29 | 2.00 | 0.0729 0.0020 0.0749 | 3.3283 30 | 2.00 | 0.0668 0.0044 0.0713 | 3.1221 31 | 2.00 | 0.0648 0.0054 0.0702 | 2.9160 43 | 1.75 | 0.0638 0.0031 0.0669 | 1.5785 44 | 1.75 | 0.0596 0.0053 0.0649 | 1.5194 45 | 1.75 | 0.0582 0.0061 0.0643 | 1.4626 57 | 1.50 | 0.0567 0.0044 0.0612 | 1.0900 58 | 1.50 | 0.0537 0.0064 0.0601 | 1.0730 59 | 1.50 | 0.0527 0.0071 0.0598 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 110s Prepare output 7s 117s Jacobian determinant (RMS): 0.010 0.038 0.058 0.082 0.105 | 0.111279 Template Matching: 0.082 0.215 0.194 0.175 0.158 | 0.158119 Write result maps: 37s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 20s CSF distance: 10s PBT2x thickness: 31s 66s Create initial surface 60s Topology correction: 70s Surface refinement: 62s Reduction of surface collisions with optimization: 51s Spherical mapping with areal smoothing 60s Spherical registration 182s rh: Thickness estimation (0.50 mm): WM distance: 18s CSF distance: 10s PBT2x thickness: 31s 65s Create initial surface 60s Topology correction: 72s Surface refinement: 55s Reduction of surface collisions with optimization: 52s Spherical mapping with areal smoothing 63s Spherical registration 197s Final surface processing results: Average thickness (FS): 2.4992  0.6272 mm Surface intensity / position RMSE: 0.0658 / 0.0629 Euler number / defect number / defect size: 14.0 / 14.0 / 0.19% Display thickness: /var/lib/condor/execute/dir_1954942/ds/BNU_2/sub-0025953/ses-1/surf/lh.thickness.sub-0025953_ses-1_run-1_T1w Display thickness: /var/lib/condor/execute/dir_1954942/ds/BNU_2/sub-0025953/ses-1/surf/rh.thickness.sub-0025953_ses-1_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_1954942/ds/BNU_2/sub-0025953/ses-1/sub-0025953_ses-1_run-1_T1w.nii Surface ROI estimation: 7s Surface and thickness estimation takes: 1187s ROI estimation in native space: ROI estimation of 'cobra' atlas 6s ROI estimation of 'neuromorphometrics' atlas 22s ROI estimation of 'lpba40' atlas 6s ROI estimation of 'hammers' atlas 16s ROI estimation of 'thalamus' atlas 1s ROI estimation of 'ibsr' atlas 6s ROI estimation of 'aal3' atlas 9s ROI estimation of 'mori' atlas 13s ROI estimation of 'anatomy3' atlas 19s ROI estimation of 'julichbrain' atlas 24s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 10s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 18s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 40s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 58s ROI estimation of 'Tian_Subcortex_S2_7T' atlas 5s Write results 6s 254s Quality check: 8s Print 'Graphics' figure to: /var/lib/condor/execute/dir_1954942/ds/BNU_2/sub-0025953/ses-1/report/catreport_sub-0025953_ses-1_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 34 minute(s) and 28 second(s). Image Quality Rating (IQR): 82.08% (B-) GM volume (GMV): 48.27% (742.16 / 1537.53 ml) GM thickness (GMT): 2.50  0.63 mm Segmentations are saved in /var/lib/condor/execute/dir_1954942/ds/BNU_2/sub-0025953/ses-1/mri Reports are saved in /var/lib/condor/execute/dir_1954942/ds/BNU_2/sub-0025953/ses-1/report Labels are saved in /var/lib/condor/execute/dir_1954942/ds/BNU_2/sub-0025953/ses-1/label ------------------------------------------------------------------------