------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./execute/dir_2739317/ds/sub-86/sub-86_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 93s APP: Rough bias correction: Initialize 7s Estimate background 14s Initial correction 13s Refine background 6s Final correction 7s Final scaling 10s 65s Correct center-of-mass 17s Affine registration 10s ------------------------------------------------------------------------------ WARNING 01: cat_run_job1639:StrokeLesionButNoCorrection There are 1.23 cm of zeros within the brain but Stroke Lesion Correction (SLC) inactive (available in the expert mode). ------------------------------------------------------------------------------ SPM preprocessing 1 (estimate 1 - TPM registration): 17s Use initial fine affine registration. 13s Use previous fine affine registration. 69s SPM preprocessing 1 (estimate 2): 59s SPM preprocessing 2 (write): Write Segmentation 21s Update Segmentation 22s Update Skull-Stripping 49s Update probability maps 12s 104s Global intensity correction: 19s SANLM denoising after intensity normalization (medium): 15s Fast Optimized Shooting registration 41s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 2s Prepare segments (LASmod = 1.00) 17s Estimate local tissue thresholds (WM) 25s Estimate local tissue thresholds (GM) 33s Intensity transformation 0s SANLM denoising after LAS (medium) 35s 120s ROI segmentation (partitioning): Atlas -> subject space 8s Major structures 4s Ventricle detection 19s Blood vessel detection 11s WMH detection (WMHCstr=0.48 > WMHCstr'=0.07) 36s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 4s Final corrections 5s 89s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 34s AMAP peaks: [CSF,GM,WM] = [0.350.04,0.670.08,0.980.05] Final cleanup (gcutstr=0.24): Level 1 cleanup (ROI estimation) 5s Level 1 cleanup (brain masking) 3s Level 2 cleanup (CSF correction) 2s Level 3 cleanup (CSF/WM PVE) 3s 13s 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 | 0.1108 0.0000 0.1108 | 32.0000 2 | 2.50 | 0.1057 0.0019 0.1076 | 29.4886 3 | 2.50 | 0.1040 0.0031 0.1071 | 26.9772 4 | 2.50 | 0.1031 0.0036 0.1067 | 24.6107 5 | 2.50 | 0.1024 0.0040 0.1064 | 22.6548 6 | 2.50 | 0.1017 0.0042 0.1060 | 20.6989 7 | 2.50 | 0.1010 0.0045 0.1055 | 18.9688 8 | 2.50 | 0.1003 0.0048 0.1051 | 17.4455 9 | 2.50 | 0.0996 0.0050 0.1046 | 15.9223 10 | 2.50 | 0.0989 0.0053 0.1042 | 14.6627 11 | 2.50 | 0.0981 0.0056 0.1037 | 13.4764 12 | 2.50 | 0.0973 0.0058 0.1031 | 12.3015 13 | 2.50 | 0.0965 0.0061 0.1026 | 11.3776 14 | 2.50 | 0.0957 0.0064 0.1020 | 10.4537 15 | 2.25 | 0.1045 0.0067 0.1111 | 9.5920 16 | 2.25 | 0.0985 0.0099 0.1085 | 8.8725 17 | 2.25 | 0.0959 0.0112 0.1071 | 8.1530 18 | 2.25 | 0.0941 0.0118 0.1059 | 7.5234 19 | 2.25 | 0.0926 0.0123 0.1048 | 6.9630 20 | 2.25 | 0.0911 0.0125 0.1036 | 6.4027 21 | 2.25 | 0.0897 0.0129 0.1026 | 5.9447 22 | 2.25 | 0.0883 0.0131 0.1015 | 5.5083 23 | 2.25 | 0.0870 0.0133 0.1003 | 5.0803 24 | 2.25 | 0.0855 0.0136 0.0991 | 4.7404 25 | 2.25 | 0.0843 0.0137 0.0979 | 4.4005 26 | 2.25 | 0.0830 0.0138 0.0968 | 4.0868 27 | 2.25 | 0.0818 0.0139 0.0957 | 3.8221 28 | 2.25 | 0.0807 0.0140 0.0946 | 3.5574 29 | 2.00 | 0.0813 0.0138 0.0951 | 3.3283 30 | 2.00 | 0.0785 0.0144 0.0929 | 3.1221 31 | 2.00 | 0.0772 0.0144 0.0916 | 2.9160 32 | 2.00 | 0.0760 0.0145 0.0906 | 2.7495 33 | 2.00 | 0.0751 0.0145 0.0896 | 2.5890 34 | 2.00 | 0.0741 0.0144 0.0886 | 2.4330 43 | 1.75 | 0.0734 0.0096 0.0830 | 1.5785 44 | 1.75 | 0.0682 0.0126 0.0808 | 1.5194 45 | 1.75 | 0.0660 0.0138 0.0798 | 1.4626 57 | 1.50 | 0.0651 0.0106 0.0757 | 1.0900 Problem with Shooting (dets: 0.00133101 .. 1.99458) 58 | 1.50 | 0.0603 0.0138 0.0741 | 1.0730 59 | 1.50 | 0.0584 0.0149 0.0733 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 259s Prepare output 14s 273s Jacobian determinant (RMS): 0.016 0.077 0.194 0.321 2.074 | 0.626112 Template Matching: 0.111 0.104 0.222 0.198 0.175 | 0.175236 Write result maps: 29s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 57s CSF distance: 23s PBT2x thickness: 64s 151s Create initial surface 110s Topology correction: 128s Surface refinement: 103s Reduction of surface collisions with optimization: 95s Spherical mapping with areal smoothing 115s Spherical registration 355s rh: Thickness estimation (0.50 mm): WM distance: 61s CSF distance: 23s PBT2x thickness: 64s 156s Create initial surface 111s Topology correction: 122s Surface refinement: 97s Reduction of surface collisions with optimization: 90s Spherical mapping with areal smoothing 109s Spherical registration 327s Final surface processing results: Average thickness (FS): 2.4555  0.6144 mm Surface intensity / position RMSE: 0.0715 / 0.0769 Euler number / defect number / defect size: 34.0 / 20.0 / 1.50% Display thickness: /var/lib/condor/execute/dir_2739317/ds/sub-86/surf/lh.thickness.sub-86_T1w Display thickness: /var/lib/condor/execute/dir_2739317/ds/sub-86/surf/rh.thickness.sub-86_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_2739317/ds/sub-86/sub-86_T1w.nii Surface ROI estimation: 10s Surface and thickness estimation takes: 2188s ROI estimation in native space: ROI estimation of 'cobra' atlas 9s ROI estimation of 'neuromorphometrics' atlas 31s ROI estimation of 'lpba40' atlas 9s ROI estimation of 'hammers' atlas 22s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 8s ROI estimation of 'aal3' atlas 12s ROI estimation of 'mori' atlas 18s ROI estimation of 'anatomy3' atlas 26s ROI estimation of 'julichbrain' atlas 35s 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 56s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 84s Write results 85s 350s Quality check: 5s Print 'Graphics' figure to: /var/lib/condor/execute/dir_2739317/ds/sub-86/report/catreport_sub-86_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 62 minute(s) and 6 second(s). Image Quality Rating (IQR): 80.56% (B-) GM volume (GMV): 42.61% (676.81 / 1588.23 ml) GM thickness (GMT): 2.46  0.61 mm Segmentations are saved in /var/lib/condor/execute/dir_2739317/ds/sub-86/mri Reports are saved in /var/lib/condor/execute/dir_2739317/ds/sub-86/report Labels are saved in /var/lib/condor/execute/dir_2739317/ds/sub-86/label ------------------------------------------------------------------------