------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0025970/ses-1/sub-0025970_ses-1_run-1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 22s Internal resampling (1.33x1.00x1.00mm > 1.00x1.00x1.00mm): 1s APP: Rough bias correction: Initialize 4s Estimate background 3s Initial correction 3s Refine background 2s Final correction 3s Final scaling 3s 22s Correct center-of-mass 2s Affine registration 5s SPM preprocessing 1 (estimate 1 - TPM registration): 42s SPM preprocessing 1 (estimate 2): 38s SPM preprocessing 2 (write): Write Segmentation 11s Update Segmentation 13s Update Skull-Stripping 28s Update probability maps 6s 58s Global intensity correction: 10s SANLM denoising after intensity normalization (medium): 17s Fast Optimized Shooting registration 22s Local adaptive segmentation (LASstr=0.50): Prepare maps 2s Prepare partitions 1s Prepare segments (LASmod = 1.13) 9s Estimate local tissue thresholds (WM) 12s Estimate local tissue thresholds (GM) 17s Intensity transformation 0s SANLM denoising after LAS (medium) 25s 70s ROI segmentation (partitioning): Atlas -> subject space 5s Major structures 2s Ventricle detection 7s Blood vessel detection 6s WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 12s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 2s Final corrections 3s 38s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 23s AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.990.04] 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 | 0.0799 0.0000 0.0799 | 32.0000 2 | 2.50 | 0.0777 0.0010 0.0787 | 29.4886 3 | 2.50 | 0.0770 0.0015 0.0786 | 26.9772 4 | 2.50 | 0.0767 0.0017 0.0785 | 24.6107 5 | 2.50 | 0.0765 0.0019 0.0783 | 22.6548 6 | 2.50 | 0.0762 0.0020 0.0782 | 20.6989 7 | 2.50 | 0.0760 0.0020 0.0780 | 18.9688 8 | 2.50 | 0.0758 0.0021 0.0779 | 17.4455 9 | 2.50 | 0.0755 0.0022 0.0777 | 15.9223 10 | 2.50 | 0.0753 0.0023 0.0776 | 14.6627 11 | 2.50 | 0.0750 0.0024 0.0774 | 13.4764 12 | 2.50 | 0.0747 0.0024 0.0772 | 12.3015 13 | 2.50 | 0.0745 0.0025 0.0770 | 11.3776 14 | 2.50 | 0.0742 0.0026 0.0768 | 10.4537 15 | 2.25 | 0.0723 0.0026 0.0749 | 9.5920 16 | 2.25 | 0.0698 0.0039 0.0737 | 8.8725 29 | 2.00 | 0.0707 0.0018 0.0724 | 3.3283 30 | 2.00 | 0.0653 0.0039 0.0692 | 3.1221 31 | 2.00 | 0.0635 0.0048 0.0683 | 2.9160 43 | 1.75 | 0.0625 0.0027 0.0652 | 1.5785 44 | 1.75 | 0.0587 0.0047 0.0634 | 1.5194 45 | 1.75 | 0.0574 0.0054 0.0628 | 1.4626 57 | 1.50 | 0.0558 0.0039 0.0598 | 1.0900 58 | 1.50 | 0.0530 0.0057 0.0588 | 1.0730 Shooting registration with 2.50:-0.25:1.50 mm takes: 95s Prepare output 7s 102s Jacobian determinant (RMS): 0.011 0.039 0.056 0.078 0.100 | 0.105152 Template Matching: 0.080 0.209 0.190 0.172 0.159 | 0.159101 Write result maps: 36s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 21s CSF distance: 9s PBT2x thickness: 29s 64s Create initial surface 54s Topology correction: 64s Surface refinement: 52s Reduction of surface collisions with optimization: 46s Spherical mapping with areal smoothing 56s Spherical registration 181s rh: Thickness estimation (0.50 mm): WM distance: 16s CSF distance: 9s PBT2x thickness: 27s 56s Create initial surface 51s Topology correction: 62s Surface refinement: 52s Reduction of surface collisions with optimization: 43s Spherical mapping with areal smoothing 55s Spherical registration 187s Final surface processing results: Average thickness (FS): 2.5347  0.6208 mm Surface intensity / position RMSE: 0.0643 / 0.0631 Euler number / defect number / defect size: 10.0 / 8.0 / 0.20% Display thickness: /var/lib/condor/execute/dir_1955758/ds/BNU_2/sub-0025970/ses-1/surf/lh.thickness.sub-0025970_ses-1_run-1_T1w Display thickness: /var/lib/condor/execute/dir_1955758/ds/BNU_2/sub-0025970/ses-1/surf/rh.thickness.sub-0025970_ses-1_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_1955758/ds/BNU_2/sub-0025970/ses-1/sub-0025970_ses-1_run-1_T1w.nii Surface ROI estimation: 6s Surface and thickness estimation takes: 1089s ROI estimation in native space: ROI estimation of 'cobra' atlas 6s ROI estimation of 'neuromorphometrics' atlas 20s ROI estimation of 'lpba40' atlas 6s ROI estimation of 'hammers' atlas 14s ROI estimation of 'thalamus' atlas 1s ROI estimation of 'ibsr' atlas 5s ROI estimation of 'aal3' atlas 8s ROI estimation of 'mori' atlas 13s ROI estimation of 'anatomy3' atlas 20s ROI estimation of 'julichbrain' atlas 26s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 47s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 71s ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s Write results 7s 277s Quality check: 8s Print 'Graphics' figure to: /var/lib/condor/execute/dir_1955758/ds/BNU_2/sub-0025970/ses-1/report/catreport_sub-0025970_ses-1_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 32 minute(s) and 40 second(s). Image Quality Rating (IQR): 82.30% (B-) GM volume (GMV): 48.31% (695.05 / 1438.79 ml) GM thickness (GMT): 2.53  0.62 mm Segmentations are saved in /var/lib/condor/execute/dir_1955758/ds/BNU_2/sub-0025970/ses-1/mri Reports are saved in /var/lib/condor/execute/dir_1955758/ds/BNU_2/sub-0025970/ses-1/report Labels are saved in /var/lib/condor/execute/dir_1955758/ds/BNU_2/sub-0025970/ses-1/label ------------------------------------------------------------------------