------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./condor/execute/dir_23851/ds/sub-50/sub-50_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 27s APP: Rough bias correction: Initialize 3s Estimate background 5s Initial correction 4s Refine background 2s Final correction 3s Final scaling 3s 24s Correct center-of-mass 3s Affine registration 6s SPM preprocessing 1 (estimate 1 - TPM registration): 8s Use initial fine affine registration. 53s SPM preprocessing 1 (estimate 2): 52s SPM preprocessing 2 (write): Write Segmentation 11s Update Segmentation 16s Update Skull-Stripping 25s Update probability maps 4s 56s Global intensity correction: 8s SANLM denoising after intensity normalization (medium): 8s Fast Optimized Shooting registration 34s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 1s Prepare segments (LASmod = 1.00) 14s Estimate local tissue thresholds (WM) 12s Estimate local tissue thresholds (GM) 18s Intensity transformation 0s SANLM denoising after LAS (medium) 12s 63s ROI segmentation (partitioning): Atlas -> subject space 6s Major structures 4s Ventricle detection 14s Blood vessel detection 9s WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 24s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 4s Final corrections 2s 65s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 39s AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.09,0.980.04] 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) 2s 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 | 0.0843 0.0000 0.0843 | 32.0000 2 | 2.50 | 0.0814 0.0013 0.0826 | 29.4886 3 | 2.50 | 0.0805 0.0019 0.0824 | 26.9772 4 | 2.50 | 0.0800 0.0022 0.0822 | 24.6107 5 | 2.50 | 0.0797 0.0023 0.0820 | 22.6548 6 | 2.50 | 0.0794 0.0024 0.0818 | 20.6989 7 | 2.50 | 0.0791 0.0025 0.0816 | 18.9688 8 | 2.50 | 0.0788 0.0026 0.0814 | 17.4455 9 | 2.50 | 0.0785 0.0027 0.0812 | 15.9223 10 | 2.50 | 0.0781 0.0028 0.0810 | 14.6627 11 | 2.50 | 0.0778 0.0029 0.0807 | 13.4764 12 | 2.50 | 0.0775 0.0030 0.0805 | 12.3015 13 | 2.50 | 0.0771 0.0031 0.0802 | 11.3776 14 | 2.50 | 0.0768 0.0032 0.0800 | 10.4537 15 | 2.25 | 0.0769 0.0032 0.0802 | 9.5920 16 | 2.25 | 0.0737 0.0050 0.0786 | 8.8725 29 | 2.00 | 0.0745 0.0022 0.0767 | 3.3283 30 | 2.00 | 0.0678 0.0049 0.0727 | 3.1221 31 | 2.00 | 0.0655 0.0060 0.0715 | 2.9160 43 | 1.75 | 0.0642 0.0035 0.0677 | 1.5785 44 | 1.75 | 0.0599 0.0058 0.0656 | 1.5194 45 | 1.75 | 0.0584 0.0066 0.0650 | 1.4626 57 | 1.50 | 0.0569 0.0048 0.0618 | 1.0900 58 | 1.50 | 0.0539 0.0068 0.0607 | 1.0730 59 | 1.50 | 0.0529 0.0074 0.0603 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 226s Prepare output 8s 234s Jacobian determinant (RMS): 0.011 0.042 0.066 0.094 0.121 | 0.130451 Template Matching: 0.084 0.221 0.197 0.175 0.159 | 0.158827 Write result maps: 19s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 37s CSF distance: 17s PBT2x thickness: 55s 116s Create initial surface 95s Topology correction: 90s Surface refinement: 91s Reduction of surface collisions with optimization: 77s Spherical mapping with areal smoothing 94s Spherical registration 274s rh: Thickness estimation (0.50 mm): WM distance: 40s CSF distance: 17s PBT2x thickness: 52s 116s Create initial surface 94s Topology correction: 90s Surface refinement: 119s Reduction of surface collisions with optimization: 77s Spherical mapping with areal smoothing 94s Spherical registration 277s Final surface processing results: Average thickness (FS): 2.4476  0.6059 mm Surface intensity / position RMSE: 0.0649 / 0.0672 Euler number / defect number / defect size: 22.0 / 15.0 / 0.68% Display thickness: /var/lib/condor/execute/dir_23851/ds/sub-50/surf/lh.thickness.sub-50_T1w Display thickness: /var/lib/condor/execute/dir_23851/ds/sub-50/surf/rh.thickness.sub-50_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_23851/ds/sub-50/sub-50_T1w.nii Surface ROI estimation: 9s Surface and thickness estimation takes: 1795s ROI estimation in native space: ROI estimation of 'cobra' atlas 7s ROI estimation of 'neuromorphometrics' atlas 24s ROI estimation of 'lpba40' atlas 7s ROI estimation of 'hammers' atlas 17s ROI estimation of 'thalamus' atlas 1s ROI estimation of 'ibsr' atlas 6s ROI estimation of 'aal3' atlas 10s ROI estimation of 'mori' atlas 15s ROI estimation of 'anatomy3' atlas 21s ROI estimation of 'julichbrain' atlas 28s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 9s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 13s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 45s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 64s Write results 66s 268s Quality check: 6s Print 'Graphics' figure to: /var/lib/condor/execute/dir_23851/ds/sub-50/report/catreport_sub-50_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 47 minute(s) and 55 second(s). Image Quality Rating (IQR): 82.45% (B-) GM volume (GMV): 46.89% (612.28 / 1305.84 ml) GM thickness (GMT): 2.45  0.61 mm Segmentations are saved in /var/lib/condor/execute/dir_23851/ds/sub-50/mri Reports are saved in /var/lib/condor/execute/dir_23851/ds/sub-50/report Labels are saved in /var/lib/condor/execute/dir_23851/ds/sub-50/label ------------------------------------------------------------------------