------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./condor/execute/dir_16954/ds/sub-22/sub-22_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 29s APP: Rough bias correction: Initialize 6s Estimate background 6s Initial correction 5s Refine background 3s Final correction 4s Final scaling 5s 36s Correct center-of-mass 5s Affine registration 9s SPM preprocessing 1 (estimate 1 - TPM registration): 66s SPM preprocessing 1 (estimate 2): 56s SPM preprocessing 2 (write): Write Segmentation 15s Update Segmentation 17s Update Skull-Stripping 40s Update probability maps 8s 80s Global intensity correction: 15s SANLM denoising after intensity normalization (medium): 8s Fast Optimized Shooting registration 30s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 2s Prepare segments (LASmod = 1.09) 13s Estimate local tissue thresholds (WM) 16s Estimate local tissue thresholds (GM) 22s Intensity transformation 0s SANLM denoising after LAS (medium) 26s 86s ROI segmentation (partitioning): Atlas -> subject space 7s Major structures 3s Ventricle detection 12s Blood vessel detection 8s WMH detection (WMHCstr=0.50 > WMHCstr'=0.03) 23s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 3s Final corrections 4s 62s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 30s AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.04] 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 10s 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 | 0.0832 0.0000 0.0832 | 32.0000 2 | 2.50 | 0.0807 0.0011 0.0818 | 29.4886 3 | 2.50 | 0.0800 0.0017 0.0817 | 26.9772 4 | 2.50 | 0.0796 0.0019 0.0815 | 24.6107 5 | 2.50 | 0.0793 0.0020 0.0814 | 22.6548 6 | 2.50 | 0.0791 0.0021 0.0812 | 20.6989 7 | 2.50 | 0.0788 0.0022 0.0810 | 18.9688 8 | 2.50 | 0.0785 0.0023 0.0808 | 17.4455 9 | 2.50 | 0.0783 0.0024 0.0806 | 15.9223 10 | 2.50 | 0.0780 0.0025 0.0804 | 14.6627 11 | 2.50 | 0.0777 0.0025 0.0802 | 13.4764 12 | 2.50 | 0.0774 0.0026 0.0800 | 12.3015 13 | 2.50 | 0.0771 0.0027 0.0797 | 11.3776 14 | 2.50 | 0.0768 0.0027 0.0795 | 10.4537 15 | 2.25 | 0.0760 0.0028 0.0788 | 9.5920 16 | 2.25 | 0.0732 0.0041 0.0773 | 8.8725 29 | 2.00 | 0.0748 0.0019 0.0766 | 3.3283 30 | 2.00 | 0.0688 0.0043 0.0731 | 3.1221 31 | 2.00 | 0.0667 0.0052 0.0720 | 2.9160 43 | 1.75 | 0.0657 0.0030 0.0687 | 1.5785 44 | 1.75 | 0.0613 0.0053 0.0666 | 1.5194 45 | 1.75 | 0.0599 0.0061 0.0660 | 1.4626 57 | 1.50 | 0.0585 0.0044 0.0629 | 1.0900 58 | 1.50 | 0.0554 0.0064 0.0618 | 1.0730 59 | 1.50 | 0.0544 0.0070 0.0615 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 144s Prepare output 9s 153s Jacobian determinant (RMS): 0.011 0.038 0.055 0.076 0.096 | 0.102235 Template Matching: 0.083 0.220 0.200 0.180 0.163 | 0.163289 Write result maps: 22s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 32s CSF distance: 15s PBT2x thickness: 42s 95s Create initial surface 82s Topology correction: 95s Surface refinement: 81s Reduction of surface collisions with optimization: 70s Spherical mapping with areal smoothing 80s Spherical registration 301s rh: Thickness estimation (0.50 mm): WM distance: 43s CSF distance: 15s PBT2x thickness: 42s 106s Create initial surface 81s Topology correction: 91s Surface refinement: 68s Reduction of surface collisions with optimization: 64s Spherical mapping with areal smoothing 76s Spherical registration 263s Final surface processing results: Average thickness (FS): 2.5196  0.5829 mm Surface intensity / position RMSE: 0.0650 / 0.0653 Euler number / defect number / defect size: 12.0 / 10.0 / 0.61% Display thickness: /var/lib/condor/execute/dir_16954/ds/sub-22/surf/lh.thickness.sub-22_T1w Display thickness: /var/lib/condor/execute/dir_16954/ds/sub-22/surf/rh.thickness.sub-22_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_16954/ds/sub-22/sub-22_T1w.nii Surface ROI estimation: 7s Surface and thickness estimation takes: 1639s ROI estimation in native space: ROI estimation of 'cobra' atlas 7s ROI estimation of 'neuromorphometrics' atlas 25s ROI estimation of 'lpba40' atlas 7s ROI estimation of 'hammers' atlas 18s 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 22s ROI estimation of 'julichbrain' atlas 29s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 20s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 46s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 70s Write results 70s 290s Quality check: 4s Print 'Graphics' figure to: /var/lib/condor/execute/dir_16954/ds/sub-22/report/catreport_sub-22_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 45 minute(s) and 1 second(s). Image Quality Rating (IQR): 83.37% (B) GM volume (GMV): 47.26% (670.14 / 1417.89 ml) GM thickness (GMT): 2.52  0.58 mm Segmentations are saved in /var/lib/condor/execute/dir_16954/ds/sub-22/mri Reports are saved in /var/lib/condor/execute/dir_16954/ds/sub-22/report Labels are saved in /var/lib/condor/execute/dir_16954/ds/sub-22/label ------------------------------------------------------------------------