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- CAT12.8.1 r1980: 1/1: ./dir_2536405/ds/sub-sc038/sub-sc038_T1w.n
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- SANLM denoising (medium): 25s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 8s
- Initial correction 8s
- Refine background 4s
- Final correction 7s
- Final scaling 6s
- 49s
- Correct center-of-mass 6s
- Affine registration 14s
- SPM preprocessing 1 (estimate 1 - TPM registration): 108s
- SPM preprocessing 1 (estimate 2): 76s
- SPM preprocessing 2 (write):
- Write Segmentation 20s
- Update Segmentation 23s
- Update Skull-Stripping 51s
- Update probability maps 10s
- 104s
- Global intensity correction: 19s
- SANLM denoising after intensity normalization (medium): 16s
- Fast Optimized Shooting registration 42s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.24) 18s
- Estimate local tissue thresholds (WM) 25s
- Estimate local tissue thresholds (GM) 34s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 28s
- 117s
- ROI segmentation (partitioning):
- Atlas -> subject space 10s
- Major structures 5s
- Ventricle detection 17s
- Blood vessel detection 13s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 31s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 7s
- 89s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 42s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- 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) 4s
- 15s
- 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 | 0.0800 0.0013 0.0813 | 29.4886
- 3 | 2.50 | 0.0791 0.0020 0.0811 | 26.9772
- 4 | 2.50 | 0.0787 0.0022 0.0809 | 24.6107
- 5 | 2.50 | 0.0783 0.0024 0.0807 | 22.6548
- 6 | 2.50 | 0.0780 0.0025 0.0805 | 20.6989
- 7 | 2.50 | 0.0777 0.0026 0.0803 | 18.9688
- 8 | 2.50 | 0.0774 0.0027 0.0801 | 17.4455
- 9 | 2.50 | 0.0770 0.0028 0.0798 | 15.9223
- 10 | 2.50 | 0.0767 0.0029 0.0796 | 14.6627
- 11 | 2.50 | 0.0763 0.0030 0.0793 | 13.4764
- 12 | 2.50 | 0.0760 0.0031 0.0790 | 12.3015
- 13 | 2.50 | 0.0756 0.0032 0.0788 | 11.3776
- 14 | 2.50 | 0.0752 0.0032 0.0785 | 10.4537
- 15 | 2.25 | 0.0747 0.0033 0.0780 | 9.5920
- 16 | 2.25 | 0.0714 0.0049 0.0763 | 8.8725
- 29 | 2.00 | 0.0726 0.0022 0.0748 | 3.3283
- 30 | 2.00 | 0.0665 0.0047 0.0711 | 3.1221
- 31 | 2.00 | 0.0644 0.0056 0.0700 | 2.9160
- 43 | 1.75 | 0.0634 0.0032 0.0666 | 1.5785
- 44 | 1.75 | 0.0592 0.0054 0.0646 | 1.5194
- 45 | 1.75 | 0.0578 0.0061 0.0640 | 1.4626
- 57 | 1.50 | 0.0565 0.0045 0.0610 | 1.0900
- 58 | 1.50 | 0.0535 0.0064 0.0599 | 1.0730
- 59 | 1.50 | 0.0524 0.0071 0.0595 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 211s
- Prepare output 15s
- 226s
- Jacobian determinant (RMS): 0.012 0.044 0.064 0.086 0.107 | 0.113552
- Template Matching: 0.083 0.214 0.193 0.173 0.157 | 0.157209
- Write result maps: 34s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 60s
- CSF distance: 20s
- PBT2x thickness: 57s
- 144s
- Create initial surface 99s
- Topology correction: 115s
- Surface refinement: 119s
- Reduction of surface collisions with optimization: 87s
- Spherical mapping with areal smoothing 115s
- Spherical registration 336s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 45s
- CSF distance: 19s
- PBT2x thickness: 57s
- 129s
- Create initial surface 98s
- Topology correction: 123s
- Surface refinement: 112s
- Reduction of surface collisions with optimization: 93s
- Spherical mapping with areal smoothing 119s
- Spherical registration 336s
- Final surface processing results:
- Average thickness (FS): 2.4973 0.6574 mm
- Surface intensity / position RMSE: 0.0744 / 0.0855
- Euler number / defect number / defect size: 26.0 / 18.0 / 1.02%
- Display thickness: /var/lib/condor/execute/dir_2536405/ds/sub-sc038/surf/lh.thickness.sub-sc038_T1w
- Display thickness: /var/lib/condor/execute/dir_2536405/ds/sub-sc038/surf/rh.thickness.sub-sc038_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2536405/ds/sub-sc038/sub-sc038_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 2144s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 10s
- ROI estimation of 'neuromorphometrics' atlas 39s
- ROI estimation of 'lpba40' atlas 12s
- ROI estimation of 'hammers' atlas 26s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 10s
- ROI estimation of 'aal3' atlas 16s
- ROI estimation of 'mori' atlas 24s
- ROI estimation of 'anatomy3' atlas 34s
- ROI estimation of 'julichbrain' atlas 45s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 18s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 33s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 66s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 89s
- Write results 90s
- 426s
- Quality check: 7s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2536405/ds/sub-sc038/report/catreport_sub-sc038_T1w.pdf
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- CAT preprocessing takes 62 minute(s) and 26 second(s).
- Image Quality Rating (IQR): 84.62% (B)
- GM volume (GMV): 49.09% (692.41 / 1410.39 ml)
- GM thickness (GMT): 2.50 0.66 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2536405/ds/sub-sc038/mri
- Reports are saved in /var/lib/condor/execute/dir_2536405/ds/sub-sc038/report
- Labels are saved in /var/lib/condor/execute/dir_2536405/ds/sub-sc038/label
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