------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./sub-season121_ses-1_acq-MPrageHiRes_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 51s APP: Rough bias correction: Initialize 9s Estimate background 9s Initial correction 16s Refine background 5s Final correction 13s Final scaling 13s 73s Correct center-of-mass 3s Affine registration 15s SPM preprocessing 1 (estimate 1 - TPM registration): 129s SPM preprocessing 1 (estimate 2): 151s SPM preprocessing 2 (write): Write Segmentation 24s Update Segmentation 30s Update Skull-Stripping 59s Update probability maps 12s 125s Global intensity correction: 22s SANLM denoising after intensity normalization (medium): 15s Fast Optimized Shooting registration 45s Local adaptive segmentation (LASstr=0.50): Prepare maps 8s Prepare partitions 4s Prepare segments (LASmod = 1.08) 24s Estimate local tissue thresholds (WM) 28s Estimate local tissue thresholds (GM) 38s Intensity transformation 0s SANLM denoising after LAS (medium) 30s 135s ROI segmentation (partitioning): Atlas -> subject space 13s Major structures 7s Ventricle detection 20s Blood vessel detection 16s WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 50s Manual stroke lesion detection 0s Closing of deep structures 3s Side alignment 7s Final corrections 6s 122s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 46s AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.04] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 7s Level 1 cleanup (brain masking) 4s Level 2 cleanup (CSF correction) 2s Level 3 cleanup (CSF/WM PVE) 4s 18s 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 | 0.0825 0.0000 0.0825 | 32.0000 2 | 2.50 | 0.0795 0.0013 0.0808 | 29.4886 3 | 2.50 | 0.0787 0.0019 0.0806 | 26.9772 4 | 2.50 | 0.0782 0.0022 0.0804 | 24.6107 5 | 2.50 | 0.0779 0.0023 0.0802 | 22.6548 6 | 2.50 | 0.0776 0.0024 0.0800 | 20.6989 7 | 2.50 | 0.0773 0.0025 0.0798 | 18.9688 8 | 2.50 | 0.0770 0.0026 0.0796 | 17.4455 9 | 2.50 | 0.0767 0.0027 0.0794 | 15.9223 10 | 2.50 | 0.0763 0.0028 0.0791 | 14.6627 11 | 2.50 | 0.0760 0.0029 0.0789 | 13.4764 12 | 2.50 | 0.0756 0.0029 0.0786 | 12.3015 13 | 2.50 | 0.0753 0.0031 0.0783 | 11.3776 14 | 2.50 | 0.0750 0.0031 0.0781 | 10.4537 15 | 2.25 | 0.0749 0.0032 0.0781 | 9.5920 16 | 2.25 | 0.0717 0.0047 0.0765 | 8.8725 29 | 2.00 | 0.0736 0.0021 0.0758 | 3.3283 30 | 2.00 | 0.0675 0.0046 0.0721 | 3.1221 31 | 2.00 | 0.0654 0.0056 0.0710 | 2.9160 43 | 1.75 | 0.0647 0.0032 0.0680 | 1.5785 44 | 1.75 | 0.0603 0.0056 0.0659 | 1.5194 45 | 1.75 | 0.0587 0.0064 0.0652 | 1.4626 57 | 1.50 | 0.0575 0.0047 0.0622 | 1.0900 58 | 1.50 | 0.0542 0.0068 0.0611 | 1.0730 59 | 1.50 | 0.0531 0.0076 0.0607 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 212s Prepare output 13s 225s Jacobian determinant (RMS): 0.011 0.042 0.062 0.089 0.115 | 0.122553 Template Matching: 0.083 0.215 0.196 0.176 0.159 | 0.159348 Write result maps: 37s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 44s CSF distance: 20s PBT2x thickness: 58s 130s Create initial surface 99s Topology correction: 120s Surface refinement: 103s Reduction of surface collisions with optimization: 86s Spherical mapping with areal smoothing 110s Spherical registration 266s rh: Thickness estimation (0.50 mm): WM distance: 44s CSF distance: 20s PBT2x thickness: 59s 130s Create initial surface 101s Topology correction: 119s Surface refinement: 131s Reduction of surface collisions with optimization: 87s Spherical mapping with areal smoothing 110s Spherical registration 263s Final surface processing results: Average thickness (FS): 2.5236  0.6085 mm Surface intensity / position RMSE: 0.0753 / 0.0854 Euler number / defect number / defect size: 98.0 / 31.5 / 2.31% Display thickness: /var/lib/condor/execute/dir_10496/ds/sub-season121/surf/lh.thickness.sub-season121_ses-1_acq-MPrageHiRes_T1w Display thickness: /var/lib/condor/execute/dir_10496/ds/sub-season121/surf/rh.thickness.sub-season121_ses-1_acq-MPrageHiRes_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_10496/ds/sub-season121/sub-season121_ses-1_acq-MPrageHiRes_T1w.nii Surface ROI estimation: 9s Surface and thickness estimation takes: 1975s ROI estimation in native space: ROI estimation of 'cobra' atlas 18s ROI estimation of 'neuromorphometrics' atlas 65s ROI estimation of 'lpba40' atlas 19s ROI estimation of 'hammers' atlas 45s ROI estimation of 'thalamus' atlas 3s ROI estimation of 'ibsr' atlas 16s ROI estimation of 'aal3' atlas 26s ROI estimation of 'mori' atlas 38s ROI estimation of 'anatomy3' atlas 55s ROI estimation of 'julichbrain' atlas 73s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 27s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 34s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 116s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 174s Write results 174s 709s Quality check: 7s Print 'Graphics' figure to: /var/lib/condor/execute/dir_10496/ds/sub-season121/report/catreport_sub-season121_ses-1_acq-MPrageHiRes_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 67 minute(s) and 37 second(s). Image Quality Rating (IQR): 86.88% (B+) GM volume (GMV): 51.06% (836.00 / 1637.33 ml) GM thickness (GMT): 2.52  0.61 mm Segmentations are saved in /var/lib/condor/execute/dir_10496/ds/sub-season121/mri Reports are saved in /var/lib/condor/execute/dir_10496/ds/sub-season121/report Labels are saved in /var/lib/condor/execute/dir_10496/ds/sub-season121/label ------------------------------------------------------------------------