------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./dir_16358/ds/sub-203/sub-203_ses-20110727_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 26s Internal resampling (3.90x0.56x0.56mm > 1.00x1.00x1.00mm): 1s APP: Rough bias correction: Initialize 4s Estimate background 6s Initial correction 5s Refine background 2s Final correction 5s Final scaling 4s 31s Correct center-of-mass 4s Affine registration 8s SPM preprocessing 1 (estimate 1 - TPM registration): 66s SPM preprocessing 1 (estimate 2): 67s SPM preprocessing 2 (write): Write Segmentation 12s Update Segmentation 16s Update Skull-Stripping 30s Update probability maps 11s 70s Global intensity correction: 11s SANLM denoising after intensity normalization (medium): 12s Fast Optimized Shooting registration 27s Local adaptive segmentation (LASstr=0.50): Prepare maps 3s Prepare partitions 1s Prepare segments (LASmod = 1.63) 12s Estimate local tissue thresholds (WM) 11s Estimate local tissue thresholds (GM) 13s Intensity transformation 0s SANLM denoising after LAS (medium) 21s 64s ROI segmentation (partitioning): Atlas -> subject space 6s Major structures 3s Ventricle detection 10s Blood vessel detection 8s WMH detection (WMHCstr=0.50 > WMHCstr'=0.23) 20s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 3s Final corrections 3s 54s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 28s AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.970.05] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 4s Level 1 cleanup (brain masking) 2s Level 2 cleanup (CSF correction) 1s Level 3 cleanup (CSF/WM PVE) 2s 9s 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 | 0.0921 0.0000 0.0921 | 32.0000 2 | 2.50 | 0.0883 0.0015 0.0898 | 29.4886 3 | 2.50 | 0.0871 0.0024 0.0895 | 26.9772 4 | 2.50 | 0.0865 0.0027 0.0892 | 24.6107 5 | 2.50 | 0.0860 0.0029 0.0890 | 22.6548 6 | 2.50 | 0.0856 0.0031 0.0887 | 20.6989 7 | 2.50 | 0.0852 0.0032 0.0884 | 18.9688 8 | 2.50 | 0.0848 0.0034 0.0881 | 17.4455 9 | 2.50 | 0.0843 0.0035 0.0878 | 15.9223 10 | 2.50 | 0.0838 0.0036 0.0875 | 14.6627 11 | 2.50 | 0.0834 0.0038 0.0871 | 13.4764 12 | 2.50 | 0.0829 0.0039 0.0868 | 12.3015 13 | 2.50 | 0.0824 0.0040 0.0864 | 11.3776 14 | 2.50 | 0.0819 0.0041 0.0860 | 10.4537 15 | 2.25 | 0.0832 0.0043 0.0875 | 9.5920 16 | 2.25 | 0.0794 0.0062 0.0856 | 8.8725 17 | 2.25 | 0.0778 0.0069 0.0847 | 8.1530 18 | 2.25 | 0.0768 0.0072 0.0840 | 7.5234 19 | 2.25 | 0.0760 0.0074 0.0834 | 6.9630 20 | 2.25 | 0.0753 0.0074 0.0827 | 6.4027 21 | 2.25 | 0.0747 0.0074 0.0821 | 5.9447 29 | 2.00 | 0.0765 0.0044 0.0809 | 3.3283 30 | 2.00 | 0.0715 0.0067 0.0783 | 3.1221 31 | 2.00 | 0.0697 0.0076 0.0773 | 2.9160 43 | 1.75 | 0.0687 0.0043 0.0730 | 1.5785 44 | 1.75 | 0.0639 0.0069 0.0708 | 1.5194 45 | 1.75 | 0.0624 0.0078 0.0702 | 1.4626 57 | 1.50 | 0.0615 0.0057 0.0672 | 1.0900 58 | 1.50 | 0.0581 0.0080 0.0661 | 1.0730 59 | 1.50 | 0.0570 0.0087 0.0657 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 171s Prepare output 9s 180s Jacobian determinant (RMS): 0.013 0.052 0.084 0.111 0.139 | 0.147830 Template Matching: 0.092 0.224 0.209 0.187 0.171 | 0.170990 Write result maps: 52s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 27s CSF distance: 14s PBT2x thickness: 40s 87s Create initial surface 89s Topology correction: 98s Surface refinement: 97s Reduction of surface collisions with optimization: 62s Spherical mapping with areal smoothing 77s Spherical registration 300s rh: Thickness estimation (0.50 mm): WM distance: 30s CSF distance: 13s PBT2x thickness: 38s 87s Create initial surface 84s Topology correction: 95s Surface refinement: 83s Reduction of surface collisions with optimization: 61s Spherical mapping with areal smoothing 75s Spherical registration 309s Final surface processing results: Average thickness (FS): 2.0914  0.5996 mm Surface intensity / position RMSE: 0.0795 / 0.0929 Euler number / defect number / defect size: 106.0 / 71.0 / 3.61% Display thickness: /var/lib/condor/execute/dir_16358/ds/sub-203/surf/lh.thickness.sub-203_ses-20110727_T1w Display thickness: /var/lib/condor/execute/dir_16358/ds/sub-203/surf/rh.thickness.sub-203_ses-20110727_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_16358/ds/sub-203/sub-203_ses-20110727_T1w.nii Surface ROI estimation: 9s Surface and thickness estimation takes: 1690s ROI estimation in native space: ROI estimation of 'cobra' atlas 6s ROI estimation of 'neuromorphometrics' atlas 23s ROI estimation of 'lpba40' atlas 6s ROI estimation of 'hammers' atlas 15s ROI estimation of 'thalamus' atlas 1s ROI estimation of 'ibsr' atlas 5s ROI estimation of 'aal3' atlas 10s ROI estimation of 'mori' atlas 13s ROI estimation of 'anatomy3' atlas 18s ROI estimation of 'julichbrain' atlas 23s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 9s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 17s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 36s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 53s Write results 54s 238s Quality check: 8s Print 'Graphics' figure to: /var/lib/condor/execute/dir_16358/ds/sub-203/report/catreport_sub-203_ses-20110727_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 45 minute(s) and 19 second(s). Image Quality Rating (IQR): 60.51% (D-) GM volume (GMV): 41.02% (589.68 / 1437.56 ml) GM thickness (GMT): 2.09  0.60 mm Segmentations are saved in /var/lib/condor/execute/dir_16358/ds/sub-203/mri Reports are saved in /var/lib/condor/execute/dir_16358/ds/sub-203/report Labels are saved in /var/lib/condor/execute/dir_16358/ds/sub-203/label ------------------------------------------------------------------------