------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./execute/dir_2912350/ds/sub-22/sub-22_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 253s APP: Rough bias correction: Initialize 14s Estimate background 13s Initial correction 15s Refine background 6s Final correction 13s Final scaling 14s 90s Correct center-of-mass 4s Affine registration 17s SPM preprocessing 1 (estimate 1 - TPM registration): 164s SPM preprocessing 1 (estimate 2): 88s SPM preprocessing 2 (write): Write Segmentation 37s Update Segmentation 40s Update Skull-Stripping 89s Update probability maps 17s 183s Global intensity correction: 34s SANLM denoising after intensity normalization (medium): 51s Fast Optimized Shooting registration 55s Local adaptive segmentation (LASstr=0.50): Prepare maps 9s Prepare partitions 4s Prepare segments (LASmod = 1.00) 32s Estimate local tissue thresholds (WM) 42s Estimate local tissue thresholds (GM) 64s Intensity transformation 0s SANLM denoising after LAS (medium) 75s 235s ROI segmentation (partitioning): Atlas -> subject space 16s Major structures 8s Ventricle detection 34s Blood vessel detection 25s WMH detection (WMHCstr=0.50 > WMHCstr'=0.01) 62s Manual stroke lesion detection 0s Closing of deep structures 4s Side alignment 8s Final corrections 9s 165s Blood vessel correction (BVCstr=0.50): 3s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 61s AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 9s Level 1 cleanup (brain masking) 5s Level 2 cleanup (CSF correction) 3s Level 3 cleanup (CSF/WM PVE) 6s 23s 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 | 0.0849 0.0000 0.0849 | 32.0000 2 | 2.50 | 0.0812 0.0015 0.0827 | 29.4886 3 | 2.50 | 0.0801 0.0023 0.0824 | 26.9772 4 | 2.50 | 0.0796 0.0026 0.0822 | 24.6107 5 | 2.50 | 0.0791 0.0028 0.0820 | 22.6548 6 | 2.50 | 0.0788 0.0029 0.0817 | 20.6989 7 | 2.50 | 0.0784 0.0031 0.0815 | 18.9688 8 | 2.50 | 0.0780 0.0032 0.0812 | 17.4455 9 | 2.50 | 0.0776 0.0033 0.0809 | 15.9223 10 | 2.50 | 0.0771 0.0035 0.0806 | 14.6627 11 | 2.50 | 0.0767 0.0036 0.0803 | 13.4764 12 | 2.50 | 0.0762 0.0037 0.0799 | 12.3015 13 | 2.50 | 0.0758 0.0039 0.0796 | 11.3776 14 | 2.50 | 0.0753 0.0039 0.0793 | 10.4537 15 | 2.25 | 0.0752 0.0041 0.0792 | 9.5920 16 | 2.25 | 0.0714 0.0059 0.0773 | 8.8725 29 | 2.00 | 0.0719 0.0027 0.0746 | 3.3283 30 | 2.00 | 0.0651 0.0054 0.0705 | 3.1221 31 | 2.00 | 0.0628 0.0065 0.0693 | 2.9160 43 | 1.75 | 0.0616 0.0038 0.0654 | 1.5785 44 | 1.75 | 0.0575 0.0059 0.0634 | 1.5194 45 | 1.75 | 0.0560 0.0067 0.0627 | 1.4626 57 | 1.50 | 0.0545 0.0050 0.0594 | 1.0900 58 | 1.50 | 0.0515 0.0069 0.0584 | 1.0730 59 | 1.50 | 0.0505 0.0075 0.0580 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 198s Prepare output 22s 220s Jacobian determinant (RMS): 0.014 0.052 0.076 0.101 0.122 | 0.128122 Template Matching: 0.085 0.214 0.188 0.168 0.151 | 0.151499 Write result maps: 49s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 49s CSF distance: 19s PBT2x thickness: 56s 131s Create initial surface 87s Topology correction: 115s Surface refinement: 76s Reduction of surface collisions with optimization: 78s Spherical mapping with areal smoothing 100s Spherical registration 329s rh: Thickness estimation (0.50 mm): WM distance: 38s CSF distance: 18s PBT2x thickness: 55s 118s Create initial surface 86s Topology correction: 116s Surface refinement: 118s Reduction of surface collisions with optimization: 83s Spherical mapping with areal smoothing 108s Spherical registration 368s Final surface processing results: Average thickness (FS): 2.4885  0.6185 mm Surface intensity / position RMSE: 0.0730 / 0.0704 Euler number / defect number / defect size: 16.0 / 17.0 / 0.37% Display thickness: /var/lib/condor/execute/dir_2912350/ds/sub-22/surf/lh.thickness.sub-22_T1w Display thickness: /var/lib/condor/execute/dir_2912350/ds/sub-22/surf/rh.thickness.sub-22_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_2912350/ds/sub-22/sub-22_T1w.nii Surface ROI estimation: 10s Surface and thickness estimation takes: 2053s ROI estimation in native space: ROI estimation of 'cobra' atlas 17s ROI estimation of 'neuromorphometrics' atlas 61s ROI estimation of 'lpba40' atlas 17s ROI estimation of 'hammers' atlas 43s ROI estimation of 'thalamus' atlas 3s ROI estimation of 'ibsr' atlas 15s ROI estimation of 'aal3' atlas 24s ROI estimation of 'mori' atlas 36s ROI estimation of 'anatomy3' atlas 52s ROI estimation of 'julichbrain' atlas 71s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 28s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 48s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 113s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 169s Write results 170s 699s Quality check: 10s Print 'Graphics' figure to: /var/lib/condor/execute/dir_2912350/ds/sub-22/report/catreport_sub-22_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 77 minute(s) and 3 second(s). Image Quality Rating (IQR): 86.03% (B) GM volume (GMV): 49.25% (677.29 / 1375.32 ml) GM thickness (GMT): 2.49  0.62 mm Segmentations are saved in /var/lib/condor/execute/dir_2912350/ds/sub-22/mri Reports are saved in /var/lib/condor/execute/dir_2912350/ds/sub-22/report Labels are saved in /var/lib/condor/execute/dir_2912350/ds/sub-22/label ------------------------------------------------------------------------