------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./ds/sub-f3300jh/sub-f3300jh_ses-wave1bas_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 183s APP: Rough bias correction: Initialize 16s Estimate background 16s Initial correction 15s Refine background 8s Final correction 13s Final scaling 15s 98s Correct center-of-mass 5s Affine registration 19s SPM preprocessing 1 (estimate 1 - TPM registration): 175s SPM preprocessing 1 (estimate 2): 88s SPM preprocessing 2 (write): Write Segmentation 40s Update Segmentation 47s Update Skull-Stripping 101s Update probability maps 20s 208s Global intensity correction: 40s SANLM denoising after intensity normalization (medium): 37s Fast Optimized Shooting registration 62s Local adaptive segmentation (LASstr=0.50): Prepare maps 12s Prepare partitions 6s Prepare segments (LASmod = 1.00) 38s Estimate local tissue thresholds (WM) 40s Estimate local tissue thresholds (GM) 57s Intensity transformation 0s SANLM denoising after LAS (medium) 62s 222s ROI segmentation (partitioning): Atlas -> subject space 21s Major structures 9s Ventricle detection 37s Blood vessel detection 25s WMH detection (WMHCstr=0.50 > WMHCstr'=0.08) 65s Manual stroke lesion detection 0s Closing of deep structures 5s Side alignment 11s Final corrections 11s 183s Blood vessel correction (BVCstr=0.50): 4s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 88s AMAP peaks: [CSF,GM,WM] = [0.360.07,0.680.07,0.980.05] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 11s Level 1 cleanup (brain masking) 6s Level 2 cleanup (CSF correction) 4s Level 3 cleanup (CSF/WM PVE) 7s 29s 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 | 0.0911 0.0000 0.0911 | 32.0000 2 | 2.50 | 0.0860 0.0018 0.0878 | 29.4886 3 | 2.50 | 0.0844 0.0029 0.0873 | 26.9772 4 | 2.50 | 0.0837 0.0033 0.0869 | 24.6107 5 | 2.50 | 0.0831 0.0035 0.0866 | 22.6548 6 | 2.50 | 0.0826 0.0037 0.0863 | 20.6989 7 | 2.50 | 0.0821 0.0038 0.0859 | 18.9688 8 | 2.50 | 0.0815 0.0040 0.0855 | 17.4455 9 | 2.50 | 0.0810 0.0041 0.0851 | 15.9223 10 | 2.50 | 0.0805 0.0043 0.0848 | 14.6627 11 | 2.50 | 0.0800 0.0044 0.0844 | 13.4764 12 | 2.50 | 0.0794 0.0045 0.0839 | 12.3015 13 | 2.50 | 0.0789 0.0046 0.0835 | 11.3776 14 | 2.50 | 0.0784 0.0047 0.0831 | 10.4537 15 | 2.25 | 0.0787 0.0049 0.0835 | 9.5920 16 | 2.25 | 0.0746 0.0069 0.0815 | 8.8725 17 | 2.25 | 0.0730 0.0076 0.0805 | 8.1530 29 | 2.00 | 0.0742 0.0035 0.0776 | 3.3283 30 | 2.00 | 0.0679 0.0061 0.0740 | 3.1221 31 | 2.00 | 0.0657 0.0071 0.0728 | 2.9160 43 | 1.75 | 0.0648 0.0041 0.0689 | 1.5785 44 | 1.75 | 0.0603 0.0064 0.0667 | 1.5194 45 | 1.75 | 0.0587 0.0072 0.0660 | 1.4626 57 | 1.50 | 0.0571 0.0054 0.0625 | 1.0900 58 | 1.50 | 0.0539 0.0074 0.0613 | 1.0730 59 | 1.50 | 0.0528 0.0081 0.0609 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 267s Prepare output 19s 286s Jacobian determinant (RMS): 0.015 0.056 0.082 0.108 0.131 | 0.137608 Template Matching: 0.091 0.219 0.197 0.176 0.158 | 0.158321 Write result maps: 59s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 56s CSF distance: 24s PBT2x thickness: 66s 155s Create initial surface 116s Topology correction: 133s Surface refinement: 112s Reduction of surface collisions with optimization: 110s Spherical mapping with areal smoothing 120s Spherical registration 302s rh: Thickness estimation (0.50 mm): WM distance: 103s CSF distance: 23s PBT2x thickness: 64s 199s Create initial surface 111s Topology correction: 131s Surface refinement: 138s Reduction of surface collisions with optimization: 101s Spherical mapping with areal smoothing 116s Spherical registration 289s Final surface processing results: Average thickness (FS): 2.5040  0.5645 mm Surface intensity / position RMSE: 0.0644 / 0.0583 Euler number / defect number / defect size: 8.0 / 6.0 / 0.22% Display thickness: /var/lib/condor/execute/dir_17538/ds/sub-f3300jh/surf/lh.thickness.sub-f3300jh_ses-wave1bas_T1w Display thickness: /var/lib/condor/execute/dir_17538/ds/sub-f3300jh/surf/rh.thickness.sub-f3300jh_ses-wave1bas_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_17538/ds/sub-f3300jh/sub-f3300jh_ses-wave1bas_T1w.nii Surface ROI estimation: 10s Surface and thickness estimation takes: 2286s ROI estimation in native space: ROI estimation of 'cobra' atlas 27s ROI estimation of 'neuromorphometrics' atlas 101s ROI estimation of 'lpba40' atlas 29s ROI estimation of 'hammers' atlas 72s ROI estimation of 'thalamus' atlas 5s ROI estimation of 'ibsr' atlas 26s ROI estimation of 'aal3' atlas 43s ROI estimation of 'mori' atlas 62s ROI estimation of 'anatomy3' atlas 91s ROI estimation of 'julichbrain' atlas 120s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 45s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 59s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 201s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 284s Write results 286s 1168s Quality check: 11s Print 'Graphics' figure to: /var/lib/condor/execute/dir_17538/ds/sub-f3300jh/report/catreport_sub-f3300jh_ses-wave1bas_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 90 minute(s) and 51 second(s). Image Quality Rating (IQR): 86.74% (B+) GM volume (GMV): 48.04% (699.10 / 1455.32 ml) GM thickness (GMT): 2.50  0.56 mm Segmentations are saved in /var/lib/condor/execute/dir_17538/ds/sub-f3300jh/mri Reports are saved in /var/lib/condor/execute/dir_17538/ds/sub-f3300jh/report Labels are saved in /var/lib/condor/execute/dir_17538/ds/sub-f3300jh/label ------------------------------------------------------------------------