------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./dir_32090/ds/sub-1000/sub-1000_ses-01_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 188s APP: Rough bias correction: Initialize 9s Estimate background 8s Initial correction 15s Refine background 4s Final correction 9s Final scaling 7s 60s Correct center-of-mass 4s Affine registration 21s SPM preprocessing 1 (estimate 1 - TPM registration): 85s SPM preprocessing 1 (estimate 2): 59s SPM preprocessing 2 (write): Write Segmentation 21s Update Segmentation 23s Update Skull-Stripping 53s Update probability maps 11s 109s Global intensity correction: 21s SANLM denoising after intensity normalization (medium): 17s Fast Optimized Shooting registration 34s Local adaptive segmentation (LASstr=0.50): Prepare maps 5s Prepare partitions 4s Prepare segments (LASmod = 1.27) 16s Estimate local tissue thresholds (WM) 23s Estimate local tissue thresholds (GM) 32s Intensity transformation 0s SANLM denoising after LAS (medium) 42s 127s ROI segmentation (partitioning): Atlas -> subject space 9s Major structures 4s Ventricle detection 17s Blood vessel detection 11s WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 34s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 4s Final corrections 6s 86s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 36s AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.04] Final cleanup (gcutstr=0.25): 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 | 0.0833 0.0000 0.0833 | 32.0000 2 | 2.50 | 0.0806 0.0011 0.0817 | 29.4886 3 | 2.50 | 0.0798 0.0017 0.0815 | 26.9772 4 | 2.50 | 0.0794 0.0019 0.0814 | 24.6107 5 | 2.50 | 0.0791 0.0021 0.0812 | 22.6548 6 | 2.50 | 0.0789 0.0021 0.0810 | 20.6989 7 | 2.50 | 0.0786 0.0022 0.0808 | 18.9688 8 | 2.50 | 0.0784 0.0023 0.0807 | 17.4455 9 | 2.50 | 0.0781 0.0023 0.0804 | 15.9223 10 | 2.50 | 0.0778 0.0024 0.0802 | 14.6627 11 | 2.50 | 0.0775 0.0025 0.0800 | 13.4764 12 | 2.50 | 0.0773 0.0025 0.0798 | 12.3015 13 | 2.50 | 0.0770 0.0026 0.0796 | 11.3776 14 | 2.50 | 0.0767 0.0026 0.0793 | 10.4537 15 | 2.25 | 0.0771 0.0027 0.0798 | 9.5920 16 | 2.25 | 0.0744 0.0040 0.0784 | 8.8725 29 | 2.00 | 0.0767 0.0018 0.0785 | 3.3283 30 | 2.00 | 0.0708 0.0042 0.0750 | 3.1221 31 | 2.00 | 0.0687 0.0052 0.0739 | 2.9160 43 | 1.75 | 0.0682 0.0030 0.0712 | 1.5785 44 | 1.75 | 0.0636 0.0054 0.0690 | 1.5194 45 | 1.75 | 0.0620 0.0063 0.0683 | 1.4626 57 | 1.50 | 0.0611 0.0046 0.0657 | 1.0900 58 | 1.50 | 0.0576 0.0068 0.0644 | 1.0730 59 | 1.50 | 0.0564 0.0076 0.0640 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 151s Prepare output 12s 163s Jacobian determinant (RMS): 0.010 0.035 0.055 0.084 0.113 | 0.120419 Template Matching: 0.083 0.223 0.206 0.186 0.169 | 0.169282 Write result maps: 31s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 28s CSF distance: 15s PBT2x thickness: 45s 94s Create initial surface 88s Topology correction: 106s Surface refinement: 89s Reduction of surface collisions with optimization: 74s Spherical mapping with areal smoothing 86s Spherical registration 291s rh: Thickness estimation (0.50 mm): WM distance: 29s CSF distance: 15s PBT2x thickness: 43s 92s Create initial surface 82s Topology correction: 107s Surface refinement: 113s Reduction of surface collisions with optimization: 72s Spherical mapping with areal smoothing 80s Spherical registration 275s Final surface processing results: Average thickness (FS): 2.4252  0.6462 mm Surface intensity / position RMSE: 0.0852 / 0.1090 Euler number / defect number / defect size: 104.0 / 47.0 / 3.45% Display thickness: /var/lib/condor/execute/dir_32090/ds/sub-1000/surf/lh.thickness.sub-1000_ses-01_T1w Display thickness: /var/lib/condor/execute/dir_32090/ds/sub-1000/surf/rh.thickness.sub-1000_ses-01_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_32090/ds/sub-1000/sub-1000_ses-01_T1w.nii Surface ROI estimation: 7s Surface and thickness estimation takes: 1751s ROI estimation in native space: ROI estimation of 'cobra' atlas 11s ROI estimation of 'neuromorphometrics' atlas 42s ROI estimation of 'lpba40' atlas 12s ROI estimation of 'hammers' atlas 31s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 11s ROI estimation of 'aal3' atlas 17s ROI estimation of 'mori' atlas 24s ROI estimation of 'anatomy3' atlas 34s ROI estimation of 'julichbrain' atlas 46s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 18s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 32s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 74s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 112s Write results 113s 469s Quality check: 6s Print 'Graphics' figure to: /var/lib/condor/execute/dir_32090/ds/sub-1000/report/catreport_sub-1000_ses-01_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 56 minute(s) and 23 second(s). Image Quality Rating (IQR): 80.37% (B-) GM volume (GMV): 50.53% (716.32 / 1417.54 ml) GM thickness (GMT): 2.43  0.65 mm Segmentations are saved in /var/lib/condor/execute/dir_32090/ds/sub-1000/mri Reports are saved in /var/lib/condor/execute/dir_32090/ds/sub-1000/report Labels are saved in /var/lib/condor/execute/dir_32090/ds/sub-1000/label ------------------------------------------------------------------------