------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./dir_4176/ds/sub-047/sub-047_ses-t14_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 10s APP: Rough bias correction: Initialize 4s Estimate background 4s Initial correction 5s Refine background 2s Final correction 4s Final scaling 5s 28s Correct center-of-mass 3s Affine registration 6s SPM preprocessing 1 (estimate 1 - TPM registration): 52s SPM preprocessing 1 (estimate 2): 50s SPM preprocessing 2 (write): Write Segmentation 11s Update Segmentation 13s Update Skull-Stripping 29s Update probability maps 6s 59s Global intensity correction: 10s SANLM denoising after intensity normalization (medium): 7s Fast Optimized Shooting registration 25s Local adaptive segmentation (LASstr=0.50): Prepare maps 3s Prepare partitions 2s Prepare segments (LASmod = 1.00) 10s Estimate local tissue thresholds (WM) 12s Estimate local tissue thresholds (GM) 15s Intensity transformation 0s SANLM denoising after LAS (medium) 12s 55s ROI segmentation (partitioning): Atlas -> subject space 6s Major structures 3s Ventricle detection 7s Blood vessel detection 6s WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 18s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 3s Final corrections 3s 47s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 20s AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 3s Level 1 cleanup (brain masking) 2s Level 2 cleanup (CSF correction) 1s Level 3 cleanup (CSF/WM PVE) 2s 8s 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 | 0.0799 0.0013 0.0812 | 29.4886 3 | 2.50 | 0.0789 0.0020 0.0810 | 26.9772 4 | 2.50 | 0.0785 0.0023 0.0808 | 24.6107 5 | 2.50 | 0.0781 0.0025 0.0806 | 22.6548 6 | 2.50 | 0.0777 0.0026 0.0803 | 20.6989 7 | 2.50 | 0.0774 0.0027 0.0801 | 18.9688 8 | 2.50 | 0.0770 0.0028 0.0799 | 17.4455 9 | 2.50 | 0.0767 0.0029 0.0796 | 15.9223 10 | 2.50 | 0.0763 0.0031 0.0794 | 14.6627 11 | 2.50 | 0.0759 0.0032 0.0791 | 13.4764 12 | 2.50 | 0.0755 0.0032 0.0788 | 12.3015 13 | 2.50 | 0.0751 0.0034 0.0785 | 11.3776 14 | 2.50 | 0.0747 0.0034 0.0782 | 10.4537 15 | 2.25 | 0.0741 0.0035 0.0777 | 9.5920 16 | 2.25 | 0.0708 0.0051 0.0760 | 8.8725 29 | 2.00 | 0.0715 0.0023 0.0739 | 3.3283 30 | 2.00 | 0.0652 0.0048 0.0701 | 3.1221 31 | 2.00 | 0.0630 0.0058 0.0689 | 2.9160 43 | 1.75 | 0.0616 0.0034 0.0651 | 1.5785 44 | 1.75 | 0.0576 0.0055 0.0631 | 1.5194 45 | 1.75 | 0.0562 0.0063 0.0624 | 1.4626 57 | 1.50 | 0.0546 0.0046 0.0592 | 1.0900 58 | 1.50 | 0.0517 0.0064 0.0581 | 1.0730 59 | 1.50 | 0.0508 0.0070 0.0578 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 127s Prepare output 7s 134s Jacobian determinant (RMS): 0.012 0.047 0.070 0.096 0.118 | 0.125314 Template Matching: 0.083 0.213 0.189 0.168 0.152 | 0.152268 Write result maps: 17s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 32s CSF distance: 11s PBT2x thickness: 33s 80s Create initial surface 54s Topology correction: 61s Surface refinement: 52s Reduction of surface collisions with optimization: 39s Spherical mapping with areal smoothing 52s Spherical registration 168s rh: Thickness estimation (0.50 mm): WM distance: 32s CSF distance: 11s PBT2x thickness: 33s 80s Create initial surface 54s Topology correction: 62s Surface refinement: 68s Reduction of surface collisions with optimization: 40s Spherical mapping with areal smoothing 55s Spherical registration 180s Final surface processing results: Average thickness (FS): 2.5079  0.6596 mm Surface intensity / position RMSE: 0.0674 / 0.0685 Euler number / defect number / defect size: 14.0 / 14.0 / 0.38% Display thickness: /var/lib/condor/execute/dir_4176/ds/sub-047/surf/lh.thickness.sub-047_ses-t14_T1w Display thickness: /var/lib/condor/execute/dir_4176/ds/sub-047/surf/rh.thickness.sub-047_ses-t14_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_4176/ds/sub-047/sub-047_ses-t14_T1w.nii Surface ROI estimation: 5s Surface and thickness estimation takes: 1106s ROI estimation in native space: ROI estimation of 'cobra' atlas 9s ROI estimation of 'neuromorphometrics' atlas 35s ROI estimation of 'lpba40' atlas 10s ROI estimation of 'hammers' atlas 25s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 9s ROI estimation of 'aal3' atlas 14s ROI estimation of 'mori' atlas 21s ROI estimation of 'anatomy3' atlas 30s ROI estimation of 'julichbrain' atlas 41s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 19s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 66s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 94s Write results 94s 390s Quality check: 4s Print 'Graphics' figure to: /var/lib/condor/execute/dir_4176/ds/sub-047/report/catreport_sub-047_ses-t14_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 34 minute(s) and 53 second(s). Image Quality Rating (IQR): 84.45% (B) GM volume (GMV): 45.72% (666.11 / 1457.00 ml) GM thickness (GMT): 2.51  0.66 mm Segmentations are saved in /var/lib/condor/execute/dir_4176/ds/sub-047/mri Reports are saved in /var/lib/condor/execute/dir_4176/ds/sub-047/report Labels are saved in /var/lib/condor/execute/dir_4176/ds/sub-047/label ------------------------------------------------------------------------