------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./condor/execute/dir_9269/ds/sub-46/sub-46_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 71s APP: Rough bias correction: Initialize 8s Estimate background 14s Initial correction 9s Refine background 6s Final correction 7s Final scaling 13s 64s Correct center-of-mass 3s Affine registration 10s SPM preprocessing 1 (estimate 1 - TPM registration): 74s SPM preprocessing 1 (estimate 2): 72s SPM preprocessing 2 (write): Write Segmentation 19s Update Segmentation 22s Update Skull-Stripping 47s Update probability maps 11s 99s Global intensity correction: 20s SANLM denoising after intensity normalization (medium): 11s Fast Optimized Shooting registration 43s Local adaptive segmentation (LASstr=0.50): Prepare maps 5s Prepare partitions 3s Prepare segments (LASmod = 1.10) 17s Estimate local tissue thresholds (WM) 22s Estimate local tissue thresholds (GM) 29s Intensity transformation 0s SANLM denoising after LAS (medium) 31s 109s ROI segmentation (partitioning): Atlas -> subject space 9s Major structures 4s Ventricle detection 15s Blood vessel detection 10s WMH detection (WMHCstr=0.48 > WMHCstr'=0.06) 26s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 4s Final corrections 5s 75s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 43s AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.04] 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 12s 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 | 0.0863 0.0000 0.0863 | 32.0000 2 | 2.50 | 0.0833 0.0013 0.0846 | 29.4886 3 | 2.50 | 0.0824 0.0019 0.0843 | 26.9772 4 | 2.50 | 0.0820 0.0022 0.0841 | 24.6107 5 | 2.50 | 0.0816 0.0023 0.0839 | 22.6548 6 | 2.50 | 0.0813 0.0024 0.0837 | 20.6989 7 | 2.50 | 0.0810 0.0025 0.0835 | 18.9688 8 | 2.50 | 0.0807 0.0026 0.0833 | 17.4455 9 | 2.50 | 0.0804 0.0027 0.0830 | 15.9223 10 | 2.50 | 0.0800 0.0028 0.0828 | 14.6627 11 | 2.50 | 0.0797 0.0029 0.0826 | 13.4764 12 | 2.50 | 0.0793 0.0029 0.0823 | 12.3015 13 | 2.50 | 0.0790 0.0030 0.0820 | 11.3776 14 | 2.50 | 0.0786 0.0031 0.0817 | 10.4537 15 | 2.25 | 0.0781 0.0032 0.0813 | 9.5920 16 | 2.25 | 0.0749 0.0047 0.0796 | 8.8725 29 | 2.00 | 0.0760 0.0021 0.0782 | 3.3283 30 | 2.00 | 0.0699 0.0045 0.0744 | 3.1221 31 | 2.00 | 0.0678 0.0055 0.0733 | 2.9160 43 | 1.75 | 0.0666 0.0032 0.0699 | 1.5785 44 | 1.75 | 0.0625 0.0053 0.0679 | 1.5194 45 | 1.75 | 0.0611 0.0061 0.0672 | 1.4626 57 | 1.50 | 0.0596 0.0045 0.0641 | 1.0900 58 | 1.50 | 0.0566 0.0064 0.0630 | 1.0730 Shooting registration with 2.50:-0.25:1.50 mm takes: 193s Prepare output 11s 203s Jacobian determinant (RMS): 0.011 0.041 0.060 0.082 0.103 | 0.108048 Template Matching: 0.086 0.225 0.203 0.183 0.170 | 0.169821 Write result maps: 29s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 44s CSF distance: 19s PBT2x thickness: 57s 128s Create initial surface 99s Topology correction: 114s Surface refinement: 137s Reduction of surface collisions with optimization: 91s Spherical mapping with areal smoothing 102s Spherical registration 269s rh: Thickness estimation (0.50 mm): WM distance: 54s CSF distance: 19s PBT2x thickness: 57s 138s Create initial surface 100s Topology correction: 114s Surface refinement: 102s Reduction of surface collisions with optimization: 88s Spherical mapping with areal smoothing 97s Spherical registration 265s Final surface processing results: Average thickness (FS): 2.4898  0.5790 mm Surface intensity / position RMSE: 0.0625 / 0.0617 Euler number / defect number / defect size: 16.0 / 18.0 / 0.45% Display thickness: /var/lib/condor/execute/dir_9269/ds/sub-46/surf/lh.thickness.sub-46_T1w Display thickness: /var/lib/condor/execute/dir_9269/ds/sub-46/surf/rh.thickness.sub-46_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_9269/ds/sub-46/sub-46_T1w.nii Surface ROI estimation: 8s Surface and thickness estimation takes: 1947s ROI estimation in native space: ROI estimation of 'cobra' atlas 13s ROI estimation of 'neuromorphometrics' atlas 50s ROI estimation of 'lpba40' atlas 14s ROI estimation of 'hammers' atlas 35s ROI estimation of 'thalamus' atlas 3s ROI estimation of 'ibsr' atlas 12s ROI estimation of 'aal3' atlas 20s ROI estimation of 'mori' atlas 30s ROI estimation of 'anatomy3' atlas 43s ROI estimation of 'julichbrain' atlas 57s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 21s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 27s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 92s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 138s Write results 139s 558s Quality check: 5s Print 'Graphics' figure to: /var/lib/condor/execute/dir_9269/ds/sub-46/report/catreport_sub-46_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 59 minute(s) and 8 second(s). Image Quality Rating (IQR): 84.22% (B) GM volume (GMV): 46.54% (697.71 / 1499.07 ml) GM thickness (GMT): 2.49  0.58 mm Segmentations are saved in /var/lib/condor/execute/dir_9269/ds/sub-46/mri Reports are saved in /var/lib/condor/execute/dir_9269/ds/sub-46/report Labels are saved in /var/lib/condor/execute/dir_9269/ds/sub-46/label ------------------------------------------------------------------------