------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./dir_11826/ds/sub-028/sub-028_ses-t0_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 27s APP: Rough bias correction: Initialize 6s Estimate background 6s Initial correction 6s Refine background 3s Final correction 5s Final scaling 6s 37s Correct center-of-mass 7s Affine registration 10s SPM preprocessing 1 (estimate 1 - TPM registration): 75s SPM preprocessing 1 (estimate 2): 57s SPM preprocessing 2 (write): Write Segmentation 15s Update Segmentation 17s Update Skull-Stripping 38s Update probability maps 8s 77s Global intensity correction: 14s SANLM denoising after intensity normalization (medium): 18s Fast Optimized Shooting registration 32s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 2s Prepare segments (LASmod = 1.11) 13s Estimate local tissue thresholds (WM) 16s Estimate local tissue thresholds (GM) 20s Intensity transformation 0s SANLM denoising after LAS (medium) 25s 83s ROI segmentation (partitioning): Atlas -> subject space 7s Major structures 3s Ventricle detection 12s Blood vessel detection 8s WMH detection (WMHCstr=0.50 > WMHCstr'=0.12) 24s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 3s Final corrections 4s 62s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 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) 3s Level 2 cleanup (CSF correction) 1s Level 3 cleanup (CSF/WM PVE) 3s 11s 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 | 0.0870 0.0000 0.0870 | 32.0000 2 | 2.50 | 0.0834 0.0015 0.0849 | 29.4886 3 | 2.50 | 0.0823 0.0023 0.0846 | 26.9772 4 | 2.50 | 0.0818 0.0026 0.0843 | 24.6107 5 | 2.50 | 0.0813 0.0028 0.0841 | 22.6548 6 | 2.50 | 0.0809 0.0029 0.0839 | 20.6989 7 | 2.50 | 0.0806 0.0030 0.0836 | 18.9688 8 | 2.50 | 0.0801 0.0032 0.0833 | 17.4455 9 | 2.50 | 0.0797 0.0033 0.0830 | 15.9223 10 | 2.50 | 0.0793 0.0034 0.0827 | 14.6627 11 | 2.50 | 0.0789 0.0036 0.0824 | 13.4764 12 | 2.50 | 0.0784 0.0036 0.0821 | 12.3015 13 | 2.50 | 0.0779 0.0038 0.0817 | 11.3776 14 | 2.50 | 0.0775 0.0039 0.0814 | 10.4537 15 | 2.25 | 0.0773 0.0040 0.0813 | 9.5920 16 | 2.25 | 0.0737 0.0058 0.0795 | 8.8725 29 | 2.00 | 0.0745 0.0026 0.0771 | 3.3283 30 | 2.00 | 0.0674 0.0055 0.0729 | 3.1221 31 | 2.00 | 0.0650 0.0066 0.0716 | 2.9160 43 | 1.75 | 0.0636 0.0039 0.0674 | 1.5785 44 | 1.75 | 0.0593 0.0061 0.0654 | 1.5194 45 | 1.75 | 0.0578 0.0069 0.0647 | 1.4626 57 | 1.50 | 0.0562 0.0051 0.0613 | 1.0900 58 | 1.50 | 0.0532 0.0071 0.0602 | 1.0730 59 | 1.50 | 0.0522 0.0077 0.0598 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 167s Prepare output 10s 176s Jacobian determinant (RMS): 0.013 0.051 0.077 0.105 0.128 | 0.135518 Template Matching: 0.087 0.221 0.195 0.173 0.156 | 0.156454 Write result maps: 23s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 30s CSF distance: 14s PBT2x thickness: 39s 89s Create initial surface 74s Topology correction: 71s Surface refinement: 66s Reduction of surface collisions with optimization: 55s Spherical mapping with areal smoothing 69s Spherical registration 295s rh: Thickness estimation (0.50 mm): WM distance: 40s CSF distance: 13s PBT2x thickness: 36s 94s Create initial surface 70s Topology correction: 70s Surface refinement: 65s Reduction of surface collisions with optimization: 58s Spherical mapping with areal smoothing 108s Spherical registration 296s Final surface processing results: Average thickness (FS): 2.4526  0.6210 mm Surface intensity / position RMSE: 0.0639 / 0.0662 Euler number / defect number / defect size: 18.0 / 15.0 / 0.97% Display thickness: /var/lib/condor/execute/dir_11826/ds/sub-028/surf/lh.thickness.sub-028_ses-t0_T1w Display thickness: /var/lib/condor/execute/dir_11826/ds/sub-028/surf/rh.thickness.sub-028_ses-t0_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_11826/ds/sub-028/sub-028_ses-t0_T1w.nii Surface ROI estimation: 8s Surface and thickness estimation takes: 1564s ROI estimation in native space: ROI estimation of 'cobra' atlas 7s ROI estimation of 'neuromorphometrics' atlas 27s ROI estimation of 'lpba40' atlas 8s ROI estimation of 'hammers' atlas 19s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 7s ROI estimation of 'aal3' atlas 11s ROI estimation of 'mori' atlas 17s ROI estimation of 'anatomy3' atlas 24s ROI estimation of 'julichbrain' atlas 34s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 13s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 23s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 62s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 131s Write results 132s 385s Quality check: 6s Print 'Graphics' figure to: /var/lib/condor/execute/dir_11826/ds/sub-028/report/catreport_sub-028_ses-t0_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 46 minute(s) and 55 second(s). Image Quality Rating (IQR): 83.99% (B) GM volume (GMV): 44.99% (588.83 / 1308.70 ml) GM thickness (GMT): 2.45  0.62 mm Segmentations are saved in /var/lib/condor/execute/dir_11826/ds/sub-028/mri Reports are saved in /var/lib/condor/execute/dir_11826/ds/sub-028/report Labels are saved in /var/lib/condor/execute/dir_11826/ds/sub-028/label ------------------------------------------------------------------------