------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./dir_14707/ds/sub-022/sub-022_ses-t0_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 10s APP: Rough bias correction: Initialize 5s Estimate background 5s Initial correction 5s Refine background 2s Final correction 4s Final scaling 5s 31s Correct center-of-mass 2s Affine registration 8s SPM preprocessing 1 (estimate 1 - TPM registration): 57s SPM preprocessing 1 (estimate 2): 44s SPM preprocessing 2 (write): Write Segmentation 12s Update Segmentation 16s Update Skull-Stripping 33s Update probability maps 6s 68s Global intensity correction: 12s SANLM denoising after intensity normalization (medium): 6s Fast Optimized Shooting registration 25s Local adaptive segmentation (LASstr=0.50): Prepare maps 3s Prepare partitions 1s Prepare segments (LASmod = 1.10) 13s Estimate local tissue thresholds (WM) 14s Estimate local tissue thresholds (GM) 18s Intensity transformation 0s SANLM denoising after LAS (medium) 13s 66s ROI segmentation (partitioning): Atlas -> subject space 6s Major structures 3s Ventricle detection 12s Blood vessel detection 8s WMH detection (WMHCstr=0.50 > WMHCstr'=0.06) 24s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 3s Final corrections 3s 61s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 31s AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05] 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 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 | 0.0830 0.0000 0.0830 | 32.0000 2 | 2.50 | 0.0805 0.0011 0.0816 | 29.4886 3 | 2.50 | 0.0797 0.0017 0.0815 | 26.9772 4 | 2.50 | 0.0794 0.0020 0.0813 | 24.6107 5 | 2.50 | 0.0791 0.0021 0.0812 | 22.6548 6 | 2.50 | 0.0788 0.0022 0.0810 | 20.6989 7 | 2.50 | 0.0786 0.0023 0.0808 | 18.9688 8 | 2.50 | 0.0783 0.0024 0.0807 | 17.4455 9 | 2.50 | 0.0780 0.0024 0.0804 | 15.9223 10 | 2.50 | 0.0777 0.0025 0.0802 | 14.6627 11 | 2.50 | 0.0774 0.0026 0.0800 | 13.4764 12 | 2.50 | 0.0771 0.0027 0.0798 | 12.3015 13 | 2.50 | 0.0768 0.0028 0.0795 | 11.3776 14 | 2.50 | 0.0765 0.0028 0.0793 | 10.4537 15 | 2.25 | 0.0753 0.0029 0.0782 | 9.5920 16 | 2.25 | 0.0724 0.0043 0.0767 | 8.8725 29 | 2.00 | 0.0737 0.0019 0.0756 | 3.3283 30 | 2.00 | 0.0678 0.0043 0.0721 | 3.1221 31 | 2.00 | 0.0659 0.0053 0.0711 | 2.9160 43 | 1.75 | 0.0651 0.0030 0.0681 | 1.5785 44 | 1.75 | 0.0609 0.0052 0.0661 | 1.5194 45 | 1.75 | 0.0594 0.0060 0.0655 | 1.4626 57 | 1.50 | 0.0581 0.0044 0.0625 | 1.0900 58 | 1.50 | 0.0549 0.0064 0.0614 | 1.0730 59 | 1.50 | 0.0539 0.0071 0.0610 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 131s Prepare output 8s 139s Jacobian determinant (RMS): 0.011 0.039 0.057 0.081 0.105 | 0.111812 Template Matching: 0.083 0.217 0.198 0.178 0.162 | 0.161594 Write result maps: 18s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 34s CSF distance: 14s PBT2x thickness: 40s 94s Create initial surface 79s Topology correction: 91s Surface refinement: 79s Reduction of surface collisions with optimization: 67s Spherical mapping with areal smoothing 72s Spherical registration 246s rh: Thickness estimation (0.50 mm): WM distance: 38s CSF distance: 14s PBT2x thickness: 40s 97s Create initial surface 79s Topology correction: 91s Surface refinement: 104s Reduction of surface collisions with optimization: 70s Spherical mapping with areal smoothing 73s Spherical registration 243s Final surface processing results: Average thickness (FS): 2.4362  0.6731 mm Surface intensity / position RMSE: 0.0765 / 0.0844 Euler number / defect number / defect size: 86.0 / 48.0 / 2.45% Display thickness: /var/lib/condor/execute/dir_14707/ds/sub-022/surf/lh.thickness.sub-022_ses-t0_T1w Display thickness: /var/lib/condor/execute/dir_14707/ds/sub-022/surf/rh.thickness.sub-022_ses-t0_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_14707/ds/sub-022/sub-022_ses-t0_T1w.nii Surface ROI estimation: 7s Surface and thickness estimation takes: 1561s ROI estimation in native space: ROI estimation of 'cobra' atlas 6s ROI estimation of 'neuromorphometrics' atlas 21s 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 9s ROI estimation of 'mori' atlas 13s ROI estimation of 'anatomy3' atlas 19s ROI estimation of 'julichbrain' atlas 25s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 10s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 18s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 40s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 60s Write results 61s 250s Quality check: 4s Print 'Graphics' figure to: /var/lib/condor/execute/dir_14707/ds/sub-022/report/catreport_sub-022_ses-t0_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 41 minute(s) and 18 second(s). Image Quality Rating (IQR): 81.01% (B-) GM volume (GMV): 45.36% (738.95 / 1629.18 ml) GM thickness (GMT): 2.44  0.67 mm Segmentations are saved in /var/lib/condor/execute/dir_14707/ds/sub-022/mri Reports are saved in /var/lib/condor/execute/dir_14707/ds/sub-022/report Labels are saved in /var/lib/condor/execute/dir_14707/ds/sub-022/label ------------------------------------------------------------------------