------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0025997/ses-3/sub-0025997_ses-3_run-1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 43s APP: Rough bias correction: Initialize 5s Estimate background 5s Initial correction 5s Refine background 3s Final correction 4s Final scaling 4s 32s Correct center-of-mass 3s Affine registration 9s SPM preprocessing 1 (estimate 1 - TPM registration): 62s SPM preprocessing 1 (estimate 2): 50s SPM preprocessing 2 (write): Write Segmentation 14s Update Segmentation 17s Update Skull-Stripping 35s Update probability maps 7s 73s Global intensity correction: 14s SANLM denoising after intensity normalization (medium): 22s Fast Optimized Shooting registration 27s Local adaptive segmentation (LASstr=0.50): Prepare maps 3s Prepare partitions 2s Prepare segments (LASmod = 1.03) 12s Estimate local tissue thresholds (WM) 15s Estimate local tissue thresholds (GM) 21s Intensity transformation 0s SANLM denoising after LAS (medium) 37s 94s ROI segmentation (partitioning): Atlas -> subject space 6s Major structures 3s Ventricle detection 12s Blood vessel detection 8s WMH detection (WMHCstr=0.50 > WMHCstr'=0.20) 20s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 3s Final corrections 4s 57s Blood vessel correction (BVCstr=0.50): 1s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 29s 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 | 0.0874 0.0000 0.0874 | 32.0000 2 | 2.50 | 0.0849 0.0012 0.0861 | 29.4886 3 | 2.50 | 0.0841 0.0018 0.0859 | 26.9772 4 | 2.50 | 0.0837 0.0020 0.0857 | 24.6107 5 | 2.50 | 0.0834 0.0022 0.0855 | 22.6548 6 | 2.50 | 0.0831 0.0023 0.0853 | 20.6989 7 | 2.50 | 0.0828 0.0024 0.0852 | 18.9688 8 | 2.50 | 0.0825 0.0025 0.0850 | 17.4455 9 | 2.50 | 0.0822 0.0025 0.0847 | 15.9223 10 | 2.50 | 0.0819 0.0026 0.0845 | 14.6627 11 | 2.50 | 0.0815 0.0027 0.0843 | 13.4764 12 | 2.50 | 0.0812 0.0028 0.0840 | 12.3015 13 | 2.50 | 0.0809 0.0029 0.0838 | 11.3776 14 | 2.50 | 0.0806 0.0030 0.0835 | 10.4537 15 | 2.25 | 0.0805 0.0030 0.0835 | 9.5920 16 | 2.25 | 0.0774 0.0045 0.0819 | 8.8725 17 | 2.25 | 0.0762 0.0051 0.0813 | 8.1530 18 | 2.25 | 0.0755 0.0053 0.0807 | 7.5234 19 | 2.25 | 0.0748 0.0054 0.0802 | 6.9630 29 | 2.00 | 0.0766 0.0028 0.0794 | 3.3283 30 | 2.00 | 0.0713 0.0051 0.0764 | 3.1221 31 | 2.00 | 0.0695 0.0060 0.0755 | 2.9160 43 | 1.75 | 0.0686 0.0034 0.0719 | 1.5785 44 | 1.75 | 0.0640 0.0059 0.0699 | 1.5194 45 | 1.75 | 0.0625 0.0067 0.0692 | 1.4626 57 | 1.50 | 0.0609 0.0048 0.0658 | 1.0900 58 | 1.50 | 0.0576 0.0070 0.0647 | 1.0730 59 | 1.50 | 0.0566 0.0077 0.0643 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 141s Prepare output 9s 149s Jacobian determinant (RMS): 0.010 0.036 0.057 0.081 0.105 | 0.112387 Template Matching: 0.087 0.225 0.209 0.188 0.170 | 0.169734 Write result maps: 28s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 56s CSF distance: 13s PBT2x thickness: 38s 113s Create initial surface 73s Topology correction: 83s Surface refinement: 90s Reduction of surface collisions with optimization: 57s Spherical mapping with areal smoothing 65s Spherical registration 256s rh: Thickness estimation (0.50 mm): WM distance: 44s CSF distance: 13s PBT2x thickness: 39s 101s Create initial surface 75s Topology correction: 81s Surface refinement: 70s Reduction of surface collisions with optimization: 59s Spherical mapping with areal smoothing 67s Spherical registration 244s Final surface processing results: Average thickness (FS): 2.3640  0.5870 mm Surface intensity / position RMSE: 0.0576 / 0.0585 Euler number / defect number / defect size: 12.0 / 15.5 / 0.17% Display thickness: /var/lib/condor/execute/dir_912710/ds/XHCUMS/sub-0025997/ses-3/surf/lh.thickness.sub-0025997_ses-3_run-1_T1w Display thickness: /var/lib/condor/execute/dir_912710/ds/XHCUMS/sub-0025997/ses-3/surf/rh.thickness.sub-0025997_ses-3_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_912710/ds/XHCUMS/sub-0025997/ses-3/sub-0025997_ses-3_run-1_T1w.nii Surface ROI estimation: 7s Surface and thickness estimation takes: 1516s 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 21s ROI estimation of 'julichbrain' atlas 28s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 20s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 45s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 68s ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s Write results 7s 291s Quality check: 10s Print 'Graphics' figure to: /var/lib/condor/execute/dir_912710/ds/XHCUMS/sub-0025997/ses-3/report/catreport_sub-0025997_ses-3_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 43 minute(s) and 18 second(s). Image Quality Rating (IQR): 82.44% (B-) GM volume (GMV): 40.93% (672.39 / 1642.74 ml) GM thickness (GMT): 2.36  0.59 mm Segmentations are saved in /var/lib/condor/execute/dir_912710/ds/XHCUMS/sub-0025997/ses-3/mri Reports are saved in /var/lib/condor/execute/dir_912710/ds/XHCUMS/sub-0025997/ses-3/report Labels are saved in /var/lib/condor/execute/dir_912710/ds/XHCUMS/sub-0025997/ses-3/label ------------------------------------------------------------------------