------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./condor/execute/dir_29671/ds/sub-07/sub-07_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 37s APP: Rough bias correction: Initialize 6s Estimate background 6s Initial correction 6s Refine background 3s Final correction 5s Final scaling 6s 38s Correct center-of-mass 5s Affine registration 10s SPM preprocessing 1 (estimate 1 - TPM registration): 12s Use initial fine affine registration. 77s SPM preprocessing 1 (estimate 2): 70s SPM preprocessing 2 (write): Write Segmentation 17s Update Segmentation 21s Update Skull-Stripping 43s Update probability maps 9s 89s Global intensity correction: 16s SANLM denoising after intensity normalization (medium): 16s Fast Optimized Shooting registration 32s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 5s Prepare segments (LASmod = 1.00) 15s Estimate local tissue thresholds (WM) 19s Estimate local tissue thresholds (GM) 27s Intensity transformation 0s SANLM denoising after LAS (medium) 27s 101s ROI segmentation (partitioning): Atlas -> subject space 8s Major structures 4s Ventricle detection 18s Blood vessel detection 11s WMH detection (WMHCstr=0.50 > WMHCstr'=0.02) 31s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 4s Final corrections 4s 81s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 37s 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) 3s Level 2 cleanup (CSF correction) 2s Level 3 cleanup (CSF/WM PVE) 3s 12s 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 | 0.0873 0.0000 0.0873 | 32.0000 2 | 2.50 | 0.0837 0.0015 0.0851 | 29.4886 3 | 2.50 | 0.0826 0.0023 0.0848 | 26.9772 4 | 2.50 | 0.0820 0.0026 0.0846 | 24.6107 5 | 2.50 | 0.0816 0.0028 0.0844 | 22.6548 6 | 2.50 | 0.0812 0.0029 0.0841 | 20.6989 7 | 2.50 | 0.0808 0.0031 0.0839 | 18.9688 8 | 2.50 | 0.0804 0.0032 0.0836 | 17.4455 9 | 2.50 | 0.0800 0.0033 0.0833 | 15.9223 10 | 2.50 | 0.0796 0.0034 0.0830 | 14.6627 11 | 2.50 | 0.0792 0.0035 0.0827 | 13.4764 12 | 2.50 | 0.0787 0.0036 0.0824 | 12.3015 13 | 2.50 | 0.0783 0.0038 0.0821 | 11.3776 14 | 2.50 | 0.0779 0.0038 0.0817 | 10.4537 15 | 2.25 | 0.0777 0.0040 0.0816 | 9.5920 16 | 2.25 | 0.0743 0.0056 0.0799 | 8.8725 29 | 2.00 | 0.0755 0.0025 0.0780 | 3.3283 30 | 2.00 | 0.0691 0.0051 0.0742 | 3.1221 31 | 2.00 | 0.0670 0.0061 0.0730 | 2.9160 43 | 1.75 | 0.0660 0.0035 0.0695 | 1.5785 44 | 1.75 | 0.0618 0.0057 0.0675 | 1.5194 45 | 1.75 | 0.0604 0.0065 0.0669 | 1.4626 57 | 1.50 | 0.0593 0.0048 0.0641 | 1.0900 58 | 1.50 | 0.0562 0.0067 0.0630 | 1.0730 59 | 1.50 | 0.0552 0.0074 0.0626 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 157s Prepare output 11s 168s Jacobian determinant (RMS): 0.014 0.049 0.072 0.097 0.121 | 0.128716 Template Matching: 0.087 0.223 0.201 0.181 0.166 | 0.165607 Write result maps: 24s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 26s CSF distance: 13s PBT2x thickness: 39s 83s Create initial surface 64s Topology correction: 73s Surface refinement: 74s Reduction of surface collisions with optimization: 57s Spherical mapping with areal smoothing 70s Spherical registration 301s rh: Thickness estimation (0.50 mm): WM distance: 30s CSF distance: 13s PBT2x thickness: 39s 88s Create initial surface 64s Topology correction: 75s Surface refinement: 83s Reduction of surface collisions with optimization: 56s Spherical mapping with areal smoothing 69s Spherical registration 292s Final surface processing results: Average thickness (FS): 2.4431  0.6362 mm Surface intensity / position RMSE: 0.0774 / 0.0849 Euler number / defect number / defect size: 42.0 / 20.0 / 1.58% Display thickness: /var/lib/condor/execute/dir_29671/ds/sub-07/surf/lh.thickness.sub-07_T1w Display thickness: /var/lib/condor/execute/dir_29671/ds/sub-07/surf/rh.thickness.sub-07_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_29671/ds/sub-07/sub-07_T1w.nii Surface ROI estimation: 7s Surface and thickness estimation takes: 1534s ROI estimation in native space: ROI estimation of 'cobra' atlas 8s ROI estimation of 'neuromorphometrics' atlas 29s ROI estimation of 'lpba40' atlas 8s ROI estimation of 'hammers' atlas 20s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 7s ROI estimation of 'aal3' atlas 12s ROI estimation of 'mori' atlas 17s ROI estimation of 'anatomy3' atlas 25s ROI estimation of 'julichbrain' atlas 34s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 14s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 24s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 54s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 81s Write results 82s 335s Quality check: 6s Print 'Graphics' figure to: /var/lib/condor/execute/dir_29671/ds/sub-07/report/catreport_sub-07_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 46 minute(s) and 32 second(s). Image Quality Rating (IQR): 76.80% (C+) GM volume (GMV): 48.56% (624.73 / 1286.55 ml) GM thickness (GMT): 2.44  0.64 mm Segmentations are saved in /var/lib/condor/execute/dir_29671/ds/sub-07/mri Reports are saved in /var/lib/condor/execute/dir_29671/ds/sub-07/report Labels are saved in /var/lib/condor/execute/dir_29671/ds/sub-07/label ------------------------------------------------------------------------