------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0026004/ses-2/sub-0026004_ses-2_run-1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 47s APP: Rough bias correction: Initialize 6s Estimate background 5s Initial correction 5s Refine background 3s Final correction 5s Final scaling 4s 33s Correct center-of-mass 3s Affine registration 10s SPM preprocessing 1 (estimate 1 - TPM registration): 62s SPM preprocessing 1 (estimate 2): 53s SPM preprocessing 2 (write): Write Segmentation 14s Update Segmentation 17s Update Skull-Stripping 35s Update probability maps 7s 74s Global intensity correction: 14s SANLM denoising after intensity normalization (medium): 24s Fast Optimized Shooting registration 27s Local adaptive segmentation (LASstr=0.50): Prepare maps 3s Prepare partitions 2s Prepare segments (LASmod = 1.05) 13s Estimate local tissue thresholds (WM) 16s Estimate local tissue thresholds (GM) 23s Intensity transformation 0s SANLM denoising after LAS (medium) 42s 103s ROI segmentation (partitioning): Atlas -> subject space 6s Major structures 3s Ventricle detection 16s Blood vessel detection 9s WMH detection (WMHCstr=0.50 > WMHCstr'=0.05) 21s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 3s Final corrections 4s 63s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 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) 2s Level 2 cleanup (CSF correction) 1s Level 3 cleanup (CSF/WM PVE) 2s 10s 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 | 0.0871 0.0000 0.0871 | 32.0000 2 | 2.50 | 0.0838 0.0014 0.0851 | 29.4886 3 | 2.50 | 0.0828 0.0021 0.0849 | 26.9772 4 | 2.50 | 0.0823 0.0024 0.0847 | 24.6107 5 | 2.50 | 0.0819 0.0026 0.0845 | 22.6548 6 | 2.50 | 0.0815 0.0027 0.0842 | 20.6989 7 | 2.50 | 0.0812 0.0028 0.0840 | 18.9688 8 | 2.50 | 0.0808 0.0029 0.0837 | 17.4455 9 | 2.50 | 0.0804 0.0030 0.0835 | 15.9223 10 | 2.50 | 0.0800 0.0031 0.0832 | 14.6627 11 | 2.50 | 0.0797 0.0032 0.0829 | 13.4764 12 | 2.50 | 0.0793 0.0033 0.0826 | 12.3015 13 | 2.50 | 0.0788 0.0034 0.0823 | 11.3776 14 | 2.50 | 0.0785 0.0035 0.0820 | 10.4537 15 | 2.25 | 0.0795 0.0036 0.0831 | 9.5920 16 | 2.25 | 0.0761 0.0053 0.0814 | 8.8725 17 | 2.25 | 0.0747 0.0059 0.0807 | 8.1530 29 | 2.00 | 0.0772 0.0027 0.0799 | 3.3283 30 | 2.00 | 0.0709 0.0054 0.0763 | 3.1221 31 | 2.00 | 0.0686 0.0065 0.0751 | 2.9160 43 | 1.75 | 0.0677 0.0037 0.0714 | 1.5785 44 | 1.75 | 0.0629 0.0063 0.0692 | 1.5194 45 | 1.75 | 0.0612 0.0072 0.0684 | 1.4626 57 | 1.50 | 0.0599 0.0053 0.0652 | 1.0900 58 | 1.50 | 0.0563 0.0077 0.0640 | 1.0730 59 | 1.50 | 0.0551 0.0084 0.0635 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 137s Prepare output 9s 146s Jacobian determinant (RMS): 0.011 0.040 0.061 0.087 0.131 | 0.122403 Template Matching: 0.087 0.224 0.206 0.184 0.165 | 0.165292 Write result maps: 29s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 38s CSF distance: 13s PBT2x thickness: 41s 98s Create initial surface 76s Topology correction: 88s Surface refinement: 82s Reduction of surface collisions with optimization: 70s Spherical mapping with areal smoothing 74s Spherical registration 252s rh: Thickness estimation (0.50 mm): WM distance: 54s CSF distance: 14s PBT2x thickness: 41s 114s Create initial surface 76s Topology correction: 90s Surface refinement: 93s Reduction of surface collisions with optimization: 71s Spherical mapping with areal smoothing 90s Spherical registration 256s Final surface processing results: Average thickness (FS): 2.4381  0.6339 mm Surface intensity / position RMSE: 0.0677 / 0.0781 Euler number / defect number / defect size: 22.0 / 15.0 / 0.99% Display thickness: /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-2/surf/lh.thickness.sub-0026004_ses-2_run-1_T1w Display thickness: /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-2/surf/rh.thickness.sub-0026004_ses-2_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-2/sub-0026004_ses-2_run-1_T1w.nii Surface ROI estimation: 7s Surface and thickness estimation takes: 1616s ROI estimation in native space: ROI estimation of 'cobra' atlas 7s ROI estimation of 'neuromorphometrics' atlas 24s ROI estimation of 'lpba40' atlas 7s ROI estimation of 'hammers' atlas 17s 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 294s Quality check: 10s Print 'Graphics' figure to: /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-2/report/catreport_sub-0026004_ses-2_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 45 minute(s) and 33 second(s). Image Quality Rating (IQR): 82.71% (B-) GM volume (GMV): 44.93% (753.99 / 1678.13 ml) GM thickness (GMT): 2.44  0.63 mm Segmentations are saved in /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-2/mri Reports are saved in /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-2/report Labels are saved in /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-2/label ------------------------------------------------------------------------