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- CAT12.8.1 r1980: 1/1: ./condor/execute/dir_4546/ds/sub-09/sub-09_T1w.n
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- SANLM denoising (medium): 72s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 6s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 38s
- Correct center-of-mass 2s
- Affine registration 9s
- SPM preprocessing 1 (estimate 1 - TPM registration): 67s
- SPM preprocessing 1 (estimate 2): 77s
- SPM preprocessing 2 (write):
- Write Segmentation 16s
- Update Segmentation 18s
- Update Skull-Stripping 40s
- Update probability maps 9s
- 83s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 10s
- Fast Optimized Shooting registration 33s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.19) 14s
- Estimate local tissue thresholds (WM) 19s
- Estimate local tissue thresholds (GM) 26s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 39s
- 109s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 3s
- Ventricle detection 14s
- Blood vessel detection 9s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.03) 22s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 3s
- Final corrections 5s
- 66s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 34s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- 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 | 0.0861 0.0000 0.0861 | 32.0000
- 2 | 2.50 | 0.0831 0.0013 0.0844 | 29.4886
- 3 | 2.50 | 0.0823 0.0019 0.0842 | 26.9772
- 4 | 2.50 | 0.0818 0.0022 0.0840 | 24.6107
- 5 | 2.50 | 0.0815 0.0023 0.0838 | 22.6548
- 6 | 2.50 | 0.0812 0.0024 0.0836 | 20.6989
- 7 | 2.50 | 0.0809 0.0025 0.0834 | 18.9688
- 8 | 2.50 | 0.0806 0.0026 0.0832 | 17.4455
- 9 | 2.50 | 0.0803 0.0027 0.0829 | 15.9223
- 10 | 2.50 | 0.0799 0.0028 0.0827 | 14.6627
- 11 | 2.50 | 0.0796 0.0028 0.0824 | 13.4764
- 12 | 2.50 | 0.0793 0.0029 0.0822 | 12.3015
- 13 | 2.50 | 0.0789 0.0030 0.0819 | 11.3776
- 14 | 2.50 | 0.0786 0.0030 0.0816 | 10.4537
- 15 | 2.25 | 0.0778 0.0031 0.0809 | 9.5920
- 16 | 2.25 | 0.0751 0.0045 0.0796 | 8.8725
- 17 | 2.25 | 0.0740 0.0050 0.0789 | 8.1530
- 29 | 2.00 | 0.0755 0.0023 0.0778 | 3.3283
- 30 | 2.00 | 0.0703 0.0045 0.0748 | 3.1221
- 31 | 2.00 | 0.0685 0.0053 0.0739 | 2.9160
- 43 | 1.75 | 0.0677 0.0030 0.0708 | 1.5785
- 44 | 1.75 | 0.0636 0.0053 0.0688 | 1.5194
- 45 | 1.75 | 0.0622 0.0060 0.0682 | 1.4626
- 57 | 1.50 | 0.0611 0.0044 0.0655 | 1.0900
- 58 | 1.50 | 0.0580 0.0064 0.0644 | 1.0730
- Shooting registration with 2.50:-0.25:1.50 mm takes: 140s
- Prepare output 10s
- 151s
- Jacobian determinant (RMS): 0.011 0.039 0.056 0.077 0.098 | 0.102558
- Template Matching: 0.086 0.222 0.206 0.187 0.174 | 0.174034
- Write result maps: 25s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 30s
- CSF distance: 15s
- PBT2x thickness: 44s
- 95s
- Create initial surface 85s
- Topology correction: 98s
- Surface refinement: 86s
- Reduction of surface collisions with optimization: 75s
- Spherical mapping with areal smoothing 85s
- Spherical registration 301s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 27s
- CSF distance: 15s
- PBT2x thickness: 45s
- 94s
- Create initial surface 90s
- Topology correction: 103s
- Surface refinement: 73s
- Reduction of surface collisions with optimization: 73s
- Spherical mapping with areal smoothing 87s
- Spherical registration 289s
- Final surface processing results:
- Average thickness (FS): 2.4023 0.6141 mm
- Surface intensity / position RMSE: 0.0827 / 0.1053
- Euler number / defect number / defect size: 102.0 / 44.0 / 3.07%
- Display thickness: /var/lib/condor/execute/dir_4546/ds/sub-09/surf/lh.thickness.sub-09_T1w
- Display thickness: /var/lib/condor/execute/dir_4546/ds/sub-09/surf/rh.thickness.sub-09_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_4546/ds/sub-09/sub-09_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1732s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 33s
- ROI estimation of 'lpba40' atlas 9s
- ROI estimation of 'hammers' atlas 23s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 9s
- ROI estimation of 'aal3' atlas 14s
- ROI estimation of 'mori' atlas 19s
- ROI estimation of 'anatomy3' atlas 28s
- ROI estimation of 'julichbrain' atlas 39s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 29s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 63s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 90s
- Write results 90s
- 383s
- Quality check: 5s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_4546/ds/sub-09/report/catreport_sub-09_T1w.pdf
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- CAT preprocessing takes 50 minute(s) and 51 second(s).
- Image Quality Rating (IQR): 73.38% (C)
- GM volume (GMV): 46.66% (702.75 / 1506.04 ml)
- GM thickness (GMT): 2.40 0.62 mm
- Segmentations are saved in /var/lib/condor/execute/dir_4546/ds/sub-09/mri
- Reports are saved in /var/lib/condor/execute/dir_4546/ds/sub-09/report
- Labels are saved in /var/lib/condor/execute/dir_4546/ds/sub-09/label
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