------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0027229/ses-1/sub-0027229_ses-1_run-1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 44s APP: Rough bias correction: Initialize 7s Estimate background 7s Initial correction 7s Refine background 4s Final correction 5s Final scaling 5s 41s Correct center-of-mass 4s Affine registration 10s SPM preprocessing 1 (estimate 1 - TPM registration): 86s SPM preprocessing 1 (estimate 2): 81s SPM preprocessing 2 (write): Write Segmentation 20s Update Segmentation 21s Update Skull-Stripping 51s Update probability maps 10s 103s Global intensity correction: 20s SANLM denoising after intensity normalization (medium): 30s Fast Optimized Shooting registration 43s Local adaptive segmentation (LASstr=0.50): Prepare maps 4s Prepare partitions 2s Prepare segments (LASmod = 1.00) 17s Estimate local tissue thresholds (WM) 22s Estimate local tissue thresholds (GM) 33s Intensity transformation 0s SANLM denoising after LAS (medium) 51s 133s ROI segmentation (partitioning): Atlas -> subject space 8s Major structures 4s Ventricle detection 15s Blood vessel detection 13s WMH detection (WMHCstr=0.50 > WMHCstr'=0.28) 24s 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 0.06): 40s AMAP peaks: [CSF,GM,WM] = [0.360.05,0.670.08,0.990.05] 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 | 0.0914 0.0000 0.0914 | 32.0000 2 | 2.50 | 0.0877 0.0015 0.0892 | 29.4886 3 | 2.50 | 0.0865 0.0023 0.0888 | 26.9772 4 | 2.50 | 0.0859 0.0027 0.0886 | 24.6107 5 | 2.50 | 0.0855 0.0029 0.0884 | 22.6548 6 | 2.50 | 0.0851 0.0030 0.0881 | 20.6989 7 | 2.50 | 0.0846 0.0032 0.0878 | 18.9688 8 | 2.50 | 0.0842 0.0034 0.0875 | 17.4455 9 | 2.50 | 0.0837 0.0035 0.0872 | 15.9223 10 | 2.50 | 0.0832 0.0037 0.0869 | 14.6627 11 | 2.50 | 0.0827 0.0038 0.0866 | 13.4764 12 | 2.50 | 0.0822 0.0039 0.0862 | 12.3015 13 | 2.50 | 0.0817 0.0041 0.0858 | 11.3776 14 | 2.50 | 0.0812 0.0043 0.0854 | 10.4537 15 | 2.25 | 0.0848 0.0044 0.0892 | 9.5920 16 | 2.25 | 0.0807 0.0065 0.0872 | 8.8725 17 | 2.25 | 0.0788 0.0074 0.0861 | 8.1530 18 | 2.25 | 0.0775 0.0078 0.0853 | 7.5234 19 | 2.25 | 0.0765 0.0081 0.0845 | 6.9630 20 | 2.25 | 0.0756 0.0081 0.0837 | 6.4027 21 | 2.25 | 0.0747 0.0083 0.0830 | 5.9447 29 | 2.00 | 0.0767 0.0050 0.0817 | 3.3283 30 | 2.00 | 0.0712 0.0075 0.0787 | 3.1221 31 | 2.00 | 0.0689 0.0085 0.0774 | 2.9160 43 | 1.75 | 0.0675 0.0049 0.0724 | 1.5785 44 | 1.75 | 0.0625 0.0076 0.0701 | 1.5194 45 | 1.75 | 0.0607 0.0085 0.0692 | 1.4626 57 | 1.50 | 0.0595 0.0063 0.0658 | 1.0900 58 | 1.50 | 0.0560 0.0086 0.0646 | 1.0730 59 | 1.50 | 0.0548 0.0093 0.0641 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 224s Prepare output 14s 238s Jacobian determinant (RMS): 0.014 0.054 0.091 0.119 0.146 | 0.154569 Template Matching: 0.091 0.224 0.207 0.182 0.165 | 0.164536 Write result maps: 46s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 55s CSF distance: 19s PBT2x thickness: 52s 132s Create initial surface 89s Topology correction: 80s Surface refinement: 89s Reduction of surface collisions with optimization: 57s Spherical mapping with areal smoothing 86s Spherical registration 322s rh: Thickness estimation (0.50 mm): WM distance: 42s CSF distance: 17s PBT2x thickness: 51s 116s Create initial surface 85s Topology correction: 80s Surface refinement: 95s Reduction of surface collisions with optimization: 56s Spherical mapping with areal smoothing 83s Spherical registration 340s Final surface processing results: Average thickness (FS): 2.3394  0.5957 mm Surface intensity / position RMSE: 0.0625 / 0.0616 Euler number / defect number / defect size: 18.0 / 10.0 / 0.55% Display thickness: /var/lib/condor/execute/dir_3344642/ds/IBA_TRT/sub-0027229/ses-1/surf/lh.thickness.sub-0027229_ses-1_run-1_T1w Display thickness: /var/lib/condor/execute/dir_3344642/ds/IBA_TRT/sub-0027229/ses-1/surf/rh.thickness.sub-0027229_ses-1_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_3344642/ds/IBA_TRT/sub-0027229/ses-1/sub-0027229_ses-1_run-1_T1w.nii Surface ROI estimation: 9s Surface and thickness estimation takes: 1814s ROI estimation in native space: ROI estimation of 'cobra' atlas 9s ROI estimation of 'neuromorphometrics' atlas 34s ROI estimation of 'lpba40' atlas 10s ROI estimation of 'hammers' atlas 24s ROI estimation of 'thalamus' atlas 2s ROI estimation of 'ibsr' atlas 9s ROI estimation of 'aal3' atlas 14s ROI estimation of 'mori' atlas 20s ROI estimation of 'anatomy3' atlas 29s ROI estimation of 'julichbrain' atlas 40s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 16s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 28s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 66s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 119s ROI estimation of 'Tian_Subcortex_S2_7T' atlas 11s Write results 13s 433s Quality check: 16s Print 'Graphics' figure to: /var/lib/condor/execute/dir_3344642/ds/IBA_TRT/sub-0027229/ses-1/report/catreport_sub-0027229_ses-1_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 56 minute(s) and 25 second(s). Image Quality Rating (IQR): 84.68% (B) GM volume (GMV): 37.83% (553.03 / 1461.95 ml) GM thickness (GMT): 2.34  0.60 mm Segmentations are saved in /var/lib/condor/execute/dir_3344642/ds/IBA_TRT/sub-0027229/ses-1/mri Reports are saved in /var/lib/condor/execute/dir_3344642/ds/IBA_TRT/sub-0027229/ses-1/report Labels are saved in /var/lib/condor/execute/dir_3344642/ds/IBA_TRT/sub-0027229/ses-1/label ------------------------------------------------------------------------