------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./dir_13776/ds/sub-001/sub-001_ses-t1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 13s APP: Rough bias correction: Initialize 7s Estimate background 8s Initial correction 7s Refine background 4s Final correction 6s Final scaling 7s 45s Correct center-of-mass 5s Affine registration 10s SPM preprocessing 1 (estimate 1 - TPM registration): 84s SPM preprocessing 1 (estimate 2): 93s SPM preprocessing 2 (write): Write Segmentation 18s Update Segmentation 21s Update Skull-Stripping 45s Update probability maps 9s 93s Global intensity correction: 17s SANLM denoising after intensity normalization (medium): 7s Fast Optimized Shooting registration 39s Local adaptive segmentation (LASstr=0.50): Prepare maps 5s Prepare partitions 2s Prepare segments (LASmod = 1.02) 17s Estimate local tissue thresholds (WM) 18s Estimate local tissue thresholds (GM) 23s Intensity transformation 0s SANLM denoising after LAS (medium) 13s 84s ROI segmentation (partitioning): Atlas -> subject space 10s Major structures 4s Ventricle detection 13s Blood vessel detection 10s WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 29s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 4s Final corrections 5s 77s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.05): 45s AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 5s Level 1 cleanup (brain masking) 4s 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 | 0.0831 0.0000 0.0831 | 32.0000 2 | 2.50 | 0.0801 0.0013 0.0814 | 29.4886 3 | 2.50 | 0.0792 0.0020 0.0812 | 26.9772 4 | 2.50 | 0.0787 0.0022 0.0810 | 24.6107 5 | 2.50 | 0.0784 0.0024 0.0808 | 22.6548 6 | 2.50 | 0.0781 0.0025 0.0806 | 20.6989 7 | 2.50 | 0.0777 0.0026 0.0804 | 18.9688 8 | 2.50 | 0.0774 0.0028 0.0801 | 17.4455 9 | 2.50 | 0.0770 0.0028 0.0799 | 15.9223 10 | 2.50 | 0.0766 0.0030 0.0796 | 14.6627 11 | 2.50 | 0.0763 0.0031 0.0794 | 13.4764 12 | 2.50 | 0.0759 0.0032 0.0791 | 12.3015 13 | 2.50 | 0.0755 0.0033 0.0788 | 11.3776 14 | 2.50 | 0.0751 0.0034 0.0785 | 10.4537 15 | 2.25 | 0.0750 0.0035 0.0785 | 9.5920 16 | 2.25 | 0.0719 0.0051 0.0769 | 8.8725 29 | 2.00 | 0.0731 0.0023 0.0754 | 3.3283 30 | 2.00 | 0.0666 0.0049 0.0715 | 3.1221 31 | 2.00 | 0.0643 0.0060 0.0703 | 2.9160 43 | 1.75 | 0.0633 0.0035 0.0668 | 1.5785 44 | 1.75 | 0.0591 0.0057 0.0648 | 1.5194 45 | 1.75 | 0.0576 0.0065 0.0641 | 1.4626 57 | 1.50 | 0.0563 0.0048 0.0611 | 1.0900 58 | 1.50 | 0.0532 0.0068 0.0600 | 1.0730 59 | 1.50 | 0.0521 0.0075 0.0596 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 208s Prepare output 11s 218s Jacobian determinant (RMS): 0.012 0.046 0.069 0.096 0.120 | 0.127617 Template Matching: 0.083 0.216 0.193 0.173 0.156 | 0.156303 Write result maps: 29s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 36s CSF distance: 18s PBT2x thickness: 54s 114s Create initial surface 91s Topology correction: 107s Surface refinement: 127s Reduction of surface collisions with optimization: 92s Spherical mapping with areal smoothing 94s Spherical registration 249s rh: Thickness estimation (0.50 mm): WM distance: 36s CSF distance: 17s PBT2x thickness: 54s 114s Create initial surface 93s Topology correction: 108s Surface refinement: 97s Reduction of surface collisions with optimization: 90s Spherical mapping with areal smoothing 93s Spherical registration 243s Final surface processing results: Average thickness (FS): 2.5738  0.6695 mm Surface intensity / position RMSE: 0.0750 / 0.0860 Euler number / defect number / defect size: 22.0 / 16.5 / 1.01% Display thickness: /var/lib/condor/execute/dir_13776/ds/sub-001/surf/lh.thickness.sub-001_ses-t1_T1w Display thickness: /var/lib/condor/execute/dir_13776/ds/sub-001/surf/rh.thickness.sub-001_ses-t1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_13776/ds/sub-001/sub-001_ses-t1_T1w.nii Surface ROI estimation: 7s Surface and thickness estimation takes: 1811s ROI estimation in native space: ROI estimation of 'cobra' atlas 13s ROI estimation of 'neuromorphometrics' atlas 47s ROI estimation of 'lpba40' atlas 14s ROI estimation of 'hammers' atlas 33s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 12s ROI estimation of 'aal3' atlas 19s ROI estimation of 'mori' atlas 29s ROI estimation of 'anatomy3' atlas 41s ROI estimation of 'julichbrain' atlas 55s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 20s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 27s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 88s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 132s Write results 133s 533s Quality check: 5s Print 'Graphics' figure to: /var/lib/condor/execute/dir_13776/ds/sub-001/report/catreport_sub-001_ses-t1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 55 minute(s) and 37 second(s). Image Quality Rating (IQR): 84.40% (B) GM volume (GMV): 49.95% (735.58 / 1472.76 ml) GM thickness (GMT): 2.57  0.67 mm Segmentations are saved in /var/lib/condor/execute/dir_13776/ds/sub-001/mri Reports are saved in /var/lib/condor/execute/dir_13776/ds/sub-001/report Labels are saved in /var/lib/condor/execute/dir_13776/ds/sub-001/label ------------------------------------------------------------------------