------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0025989/ses-5/sub-0025989_ses-5_run-1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 44s APP: Rough bias correction: Initialize 5s Estimate background 5s Initial correction 5s Refine background 2s Final correction 4s Final scaling 4s 30s Correct center-of-mass 3s Affine registration 7s SPM preprocessing 1 (estimate 1 - TPM registration): 54s SPM preprocessing 1 (estimate 2): 46s SPM preprocessing 2 (write): Write Segmentation 14s Update Segmentation 15s Update Skull-Stripping 34s Update probability maps 7s 70s Global intensity correction: 14s SANLM denoising after intensity normalization (medium): 20s Fast Optimized Shooting registration 27s Local adaptive segmentation (LASstr=0.50): Prepare maps 3s Prepare partitions 2s Prepare segments (LASmod = 1.18) 11s Estimate local tissue thresholds (WM) 15s Estimate local tissue thresholds (GM) 21s Intensity transformation 0s SANLM denoising after LAS (medium) 38s 94s ROI segmentation (partitioning): Atlas -> subject space 6s Major structures 3s Ventricle detection 9s Blood vessel detection 7s WMH detection (WMHCstr=0.50 > WMHCstr'=0.10) 19s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 3s Final corrections 4s 52s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 27s AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05] 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 9s 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 | 0.0849 0.0000 0.0849 | 32.0000 2 | 2.50 | 0.0818 0.0013 0.0831 | 29.4886 3 | 2.50 | 0.0809 0.0020 0.0829 | 26.9772 4 | 2.50 | 0.0805 0.0023 0.0827 | 24.6107 5 | 2.50 | 0.0801 0.0024 0.0825 | 22.6548 6 | 2.50 | 0.0798 0.0025 0.0823 | 20.6989 7 | 2.50 | 0.0795 0.0026 0.0821 | 18.9688 8 | 2.50 | 0.0792 0.0027 0.0819 | 17.4455 9 | 2.50 | 0.0788 0.0028 0.0816 | 15.9223 10 | 2.50 | 0.0785 0.0029 0.0814 | 14.6627 11 | 2.50 | 0.0782 0.0030 0.0811 | 13.4764 12 | 2.50 | 0.0778 0.0030 0.0808 | 12.3015 13 | 2.50 | 0.0774 0.0031 0.0806 | 11.3776 14 | 2.50 | 0.0771 0.0032 0.0803 | 10.4537 15 | 2.25 | 0.0763 0.0033 0.0796 | 9.5920 16 | 2.25 | 0.0730 0.0049 0.0779 | 8.8725 29 | 2.00 | 0.0742 0.0022 0.0764 | 3.3283 30 | 2.00 | 0.0675 0.0049 0.0724 | 3.1221 31 | 2.00 | 0.0652 0.0060 0.0712 | 2.9160 43 | 1.75 | 0.0638 0.0035 0.0672 | 1.5785 44 | 1.75 | 0.0593 0.0058 0.0651 | 1.5194 45 | 1.75 | 0.0578 0.0066 0.0644 | 1.4626 57 | 1.50 | 0.0560 0.0048 0.0608 | 1.0900 58 | 1.50 | 0.0530 0.0068 0.0598 | 1.0730 59 | 1.50 | 0.0520 0.0074 0.0594 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 134s Prepare output 8s 142s Jacobian determinant (RMS): 0.012 0.042 0.063 0.089 0.112 | 0.118890 Template Matching: 0.085 0.219 0.196 0.173 0.156 | 0.156049 Write result maps: 28s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 34s CSF distance: 12s PBT2x thickness: 35s 86s Create initial surface 70s Topology correction: 76s Surface refinement: 83s Reduction of surface collisions with optimization: 54s Spherical mapping with areal smoothing 63s Spherical registration 251s rh: Thickness estimation (0.50 mm): WM distance: 29s CSF distance: 12s PBT2x thickness: 35s 81s Create initial surface 69s Topology correction: 76s Surface refinement: 62s Reduction of surface collisions with optimization: 54s Spherical mapping with areal smoothing 63s Spherical registration 262s Final surface processing results: Average thickness (FS): 2.3896  0.6195 mm Surface intensity / position RMSE: 0.0609 / 0.0623 Euler number / defect number / defect size: 18.0 / 12.0 / 0.56% Display thickness: /var/lib/condor/execute/dir_912714/ds/XHCUMS/sub-0025989/ses-5/surf/lh.thickness.sub-0025989_ses-5_run-1_T1w Display thickness: /var/lib/condor/execute/dir_912714/ds/XHCUMS/sub-0025989/ses-5/surf/rh.thickness.sub-0025989_ses-5_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_912714/ds/XHCUMS/sub-0025989/ses-5/sub-0025989_ses-5_run-1_T1w.nii Surface ROI estimation: 7s Surface and thickness estimation takes: 1424s ROI estimation in native space: ROI estimation of 'cobra' atlas 7s ROI estimation of 'neuromorphometrics' atlas 25s ROI estimation of 'lpba40' atlas 7s ROI estimation of 'hammers' atlas 18s ROI estimation of 'thalamus' atlas 1s ROI estimation of 'ibsr' atlas 6s ROI estimation of 'aal3' atlas 10s ROI estimation of 'mori' atlas 15s ROI estimation of 'anatomy3' atlas 22s ROI estimation of 'julichbrain' atlas 29s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 47s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 69s ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s Write results 7s 298s Quality check: 9s Print 'Graphics' figure to: /var/lib/condor/execute/dir_912714/ds/XHCUMS/sub-0025989/ses-5/report/catreport_sub-0025989_ses-5_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 41 minute(s) and 24 second(s). Image Quality Rating (IQR): 82.75% (B-) GM volume (GMV): 42.43% (611.33 / 1440.95 ml) GM thickness (GMT): 2.39  0.62 mm Segmentations are saved in /var/lib/condor/execute/dir_912714/ds/XHCUMS/sub-0025989/ses-5/mri Reports are saved in /var/lib/condor/execute/dir_912714/ds/XHCUMS/sub-0025989/ses-5/report Labels are saved in /var/lib/condor/execute/dir_912714/ds/XHCUMS/sub-0025989/ses-5/label ------------------------------------------------------------------------