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- CAT12.8.1 r1980: 1/1: ./execute/dir_29172/ds/sub-1016/sub-1016_T1w.n
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- SANLM denoising (medium): 42s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 8s
- Initial correction 7s
- Refine background 4s
- Final correction 5s
- Final scaling 5s
- 44s
- Correct center-of-mass 7s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 90s
- SPM preprocessing 1 (estimate 2): 79s
- SPM preprocessing 2 (write):
- Write Segmentation 23s
- Update Segmentation 25s
- Update Skull-Stripping 51s
- Update probability maps 11s
- 110s
- Global intensity correction: 20s
- SANLM denoising after intensity normalization (medium): 33s
- Fast Optimized Shooting registration 49s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 6s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.00) 19s
- Estimate local tissue thresholds (WM) 21s
- Estimate local tissue thresholds (GM) 29s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 24s
- 106s
- ROI segmentation (partitioning):
- Atlas -> subject space 11s
- Major structures 5s
- Ventricle detection 18s
- Blood vessel detection 12s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.01) 30s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 5s
- Final corrections 6s
- 89s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 50s
- AMAP peaks: [CSF,GM,WM] = [0.360.07,0.680.07,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 6s
- Level 1 cleanup (brain masking) 4s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 3s
- 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 | 0.0796 0.0000 0.0796 | 32.0000
- 2 | 2.50 | 0.0780 0.0009 0.0789 | 29.4886
- 3 | 2.50 | 0.0776 0.0013 0.0789 | 26.9772
- 4 | 2.50 | 0.0774 0.0014 0.0788 | 24.6107
- 5 | 2.50 | 0.0772 0.0015 0.0787 | 22.6548
- 6 | 2.50 | 0.0770 0.0016 0.0786 | 20.6989
- 7 | 2.50 | 0.0768 0.0016 0.0785 | 18.9688
- 8 | 2.50 | 0.0767 0.0017 0.0784 | 17.4455
- 9 | 2.50 | 0.0765 0.0018 0.0782 | 15.9223
- 10 | 2.50 | 0.0763 0.0018 0.0781 | 14.6627
- 11 | 2.50 | 0.0761 0.0019 0.0780 | 13.4764
- 12 | 2.50 | 0.0759 0.0019 0.0778 | 12.3015
- 13 | 2.50 | 0.0757 0.0020 0.0777 | 11.3776
- 14 | 2.50 | 0.0755 0.0021 0.0775 | 10.4537
- 15 | 2.25 | 0.0728 0.0021 0.0749 | 9.5920
- 16 | 2.25 | 0.0707 0.0032 0.0739 | 8.8725
- 29 | 2.00 | 0.0714 0.0014 0.0728 | 3.3283
- 30 | 2.00 | 0.0660 0.0036 0.0696 | 3.1221
- 31 | 2.00 | 0.0642 0.0045 0.0687 | 2.9160
- 43 | 1.75 | 0.0630 0.0026 0.0655 | 1.5785
- 44 | 1.75 | 0.0589 0.0047 0.0636 | 1.5194
- 45 | 1.75 | 0.0577 0.0054 0.0631 | 1.4626
- 57 | 1.50 | 0.0559 0.0039 0.0598 | 1.0900
- 58 | 1.50 | 0.0530 0.0057 0.0588 | 1.0730
- Shooting registration with 2.50:-0.25:1.50 mm takes: 216s
- Prepare output 12s
- 228s
- Jacobian determinant (RMS): 0.010 0.033 0.049 0.073 0.096 | 0.101060
- Template Matching: 0.080 0.212 0.193 0.173 0.159 | 0.159056
- Write result maps: 38s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 48s
- CSF distance: 20s
- PBT2x thickness: 62s
- 138s
- Create initial surface 109s
- Topology correction: 120s
- Surface refinement: 138s
- Reduction of surface collisions with optimization: 92s
- Spherical mapping with areal smoothing 107s
- Spherical registration 303s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 40s
- CSF distance: 21s
- PBT2x thickness: 62s
- 131s
- Create initial surface 109s
- Topology correction: 120s
- Surface refinement: 141s
- Reduction of surface collisions with optimization: 93s
- Spherical mapping with areal smoothing 115s
- Spherical registration 318s
- Final surface processing results:
- Average thickness (FS): 2.6114 0.6137 mm
- Surface intensity / position RMSE: 0.0607 / 0.0601
- Euler number / defect number / defect size: 12.0 / 12.0 / 0.32%
- Display thickness: /var/lib/condor/execute/dir_29172/ds/sub-1016/surf/lh.thickness.sub-1016_T1w
- Display thickness: /var/lib/condor/execute/dir_29172/ds/sub-1016/surf/rh.thickness.sub-1016_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_29172/ds/sub-1016/sub-1016_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 2150s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 14s
- ROI estimation of 'neuromorphometrics' atlas 53s
- ROI estimation of 'lpba40' atlas 15s
- ROI estimation of 'hammers' atlas 37s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 13s
- ROI estimation of 'aal3' atlas 22s
- ROI estimation of 'mori' atlas 33s
- ROI estimation of 'anatomy3' atlas 47s
- ROI estimation of 'julichbrain' atlas 62s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 23s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 30s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 100s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 149s
- Write results 150s
- 603s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_29172/ds/sub-1016/report/catreport_sub-1016_T1w.pdf
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- CAT preprocessing takes 65 minute(s) and 3 second(s).
- Image Quality Rating (IQR): 83.13% (B-)
- GM volume (GMV): 46.74% (683.11 / 1461.46 ml)
- GM thickness (GMT): 2.61 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_29172/ds/sub-1016/mri
- Reports are saved in /var/lib/condor/execute/dir_29172/ds/sub-1016/report
- Labels are saved in /var/lib/condor/execute/dir_29172/ds/sub-1016/label
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