------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./sub-season133_ses-1_acq-MPrageHiRes_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 67s APP: Rough bias correction: Initialize 11s Estimate background 11s Initial correction 22s Refine background 6s Final correction 16s Final scaling 13s 90s Correct center-of-mass 4s Affine registration 16s SPM preprocessing 1 (estimate 1 - TPM registration): 123s SPM preprocessing 1 (estimate 2): 111s SPM preprocessing 2 (write): Write Segmentation 27s Update Segmentation 32s Update Skull-Stripping 72s Update probability maps 14s 146s Global intensity correction: 28s SANLM denoising after intensity normalization (medium): 12s Fast Optimized Shooting registration 49s Local adaptive segmentation (LASstr=0.50): Prepare maps 8s Prepare partitions 4s Prepare segments (LASmod = 1.00) 26s Estimate local tissue thresholds (WM) 30s Estimate local tissue thresholds (GM) 39s Intensity transformation 0s SANLM denoising after LAS (medium) 34s 147s ROI segmentation (partitioning): Atlas -> subject space 15s Major structures 6s Ventricle detection 22s Blood vessel detection 16s WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 45s Manual stroke lesion detection 0s Closing of deep structures 3s Side alignment 6s Final corrections 8s 121s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 63s AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 7s Level 1 cleanup (brain masking) 5s Level 2 cleanup (CSF correction) 3s Level 3 cleanup (CSF/WM PVE) 5s 20s 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 | 0.0806 0.0000 0.0806 | 32.0000 2 | 2.50 | 0.0781 0.0011 0.0793 | 29.4886 3 | 2.50 | 0.0774 0.0017 0.0791 | 26.9772 4 | 2.50 | 0.0770 0.0019 0.0790 | 24.6107 5 | 2.50 | 0.0767 0.0021 0.0788 | 22.6548 6 | 2.50 | 0.0765 0.0022 0.0787 | 20.6989 7 | 2.50 | 0.0762 0.0023 0.0785 | 18.9688 8 | 2.50 | 0.0759 0.0024 0.0783 | 17.4455 9 | 2.50 | 0.0757 0.0024 0.0781 | 15.9223 10 | 2.50 | 0.0754 0.0025 0.0779 | 14.6627 11 | 2.50 | 0.0751 0.0026 0.0777 | 13.4764 12 | 2.50 | 0.0748 0.0027 0.0774 | 12.3015 13 | 2.50 | 0.0745 0.0028 0.0772 | 11.3776 14 | 2.50 | 0.0742 0.0028 0.0770 | 10.4537 15 | 2.25 | 0.0728 0.0029 0.0756 | 9.5920 16 | 2.25 | 0.0698 0.0043 0.0741 | 8.8725 29 | 2.00 | 0.0704 0.0020 0.0724 | 3.3283 30 | 2.00 | 0.0644 0.0043 0.0687 | 3.1221 31 | 2.00 | 0.0623 0.0053 0.0676 | 2.9160 43 | 1.75 | 0.0610 0.0031 0.0641 | 1.5785 44 | 1.75 | 0.0569 0.0052 0.0621 | 1.5194 45 | 1.75 | 0.0555 0.0059 0.0614 | 1.4626 57 | 1.50 | 0.0537 0.0043 0.0580 | 1.0900 58 | 1.50 | 0.0509 0.0062 0.0570 | 1.0730 59 | 1.50 | 0.0499 0.0067 0.0567 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 230s Prepare output 14s 244s Jacobian determinant (RMS): 0.011 0.041 0.060 0.084 0.108 | 0.115521 Template Matching: 0.081 0.209 0.187 0.166 0.150 | 0.149764 Write result maps: 46s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 42s CSF distance: 18s PBT2x thickness: 56s 123s Create initial surface 96s Topology correction: 109s Surface refinement: 88s Reduction of surface collisions with optimization: 84s Spherical mapping with areal smoothing 97s Spherical registration 272s rh: Thickness estimation (0.50 mm): WM distance: 52s CSF distance: 19s PBT2x thickness: 56s 135s Create initial surface 96s Topology correction: 116s Surface refinement: 88s Reduction of surface collisions with optimization: 90s Spherical mapping with areal smoothing 100s Spherical registration 269s Final surface processing results: Average thickness (FS): 2.6714  0.5931 mm Surface intensity / position RMSE: 0.0670 / 0.0663 Euler number / defect number / defect size: 12.0 / 13.0 / 0.35% Display thickness: /var/lib/condor/execute/dir_2524/ds/sub-season133/surf/lh.thickness.sub-season133_ses-1_acq-MPrageHiRes_T1w Display thickness: /var/lib/condor/execute/dir_2524/ds/sub-season133/surf/rh.thickness.sub-season133_ses-1_acq-MPrageHiRes_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_2524/ds/sub-season133/sub-season133_ses-1_acq-MPrageHiRes_T1w.nii Surface ROI estimation: 8s Surface and thickness estimation takes: 1880s ROI estimation in native space: ROI estimation of 'cobra' atlas 19s ROI estimation of 'neuromorphometrics' atlas 66s ROI estimation of 'lpba40' atlas 19s ROI estimation of 'hammers' atlas 46s ROI estimation of 'thalamus' atlas 3s ROI estimation of 'ibsr' atlas 16s ROI estimation of 'aal3' atlas 27s ROI estimation of 'mori' atlas 40s ROI estimation of 'anatomy3' atlas 57s ROI estimation of 'julichbrain' atlas 76s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 28s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 36s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 123s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 180s Write results 181s 739s Quality check: 8s Print 'Graphics' figure to: /var/lib/condor/execute/dir_2524/ds/sub-season133/report/catreport_sub-season133_ses-1_acq-MPrageHiRes_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 68 minute(s) and 7 second(s). Image Quality Rating (IQR): 87.06% (B+) GM volume (GMV): 49.51% (702.34 / 1418.51 ml) GM thickness (GMT): 2.67  0.59 mm Segmentations are saved in /var/lib/condor/execute/dir_2524/ds/sub-season133/mri Reports are saved in /var/lib/condor/execute/dir_2524/ds/sub-season133/report Labels are saved in /var/lib/condor/execute/dir_2524/ds/sub-season133/label ------------------------------------------------------------------------