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- CAT12.8.1 r1980: 1/1: ./execute/dir_7854/ds/sub-sc004/sub-sc004_T1w.n
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- SANLM denoising (medium): 23s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 6s
- Initial correction 5s
- Refine background 3s
- Final correction 4s
- Final scaling 4s
- 37s
- Correct center-of-mass 6s
- Affine registration 9s
- SPM preprocessing 1 (estimate 1 - TPM registration): 76s
- SPM preprocessing 1 (estimate 2): 57s
- SPM preprocessing 2 (write):
- Write Segmentation 16s
- Update Segmentation 17s
- Update Skull-Stripping 41s
- Update probability maps 9s
- 83s
- Global intensity correction: 17s
- SANLM denoising after intensity normalization (medium): 13s
- Fast Optimized Shooting registration 36s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 13s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 22s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 8s
- 70s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 17s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 21s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 5s
- 65s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 29s
- AMAP peaks: [CSF,GM,WM] = [0.360.07,0.680.07,0.990.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 10s
- 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 | 0.0824 0.0000 0.0824 | 32.0000
- 2 | 2.50 | 0.0799 0.0011 0.0811 | 29.4886
- 3 | 2.50 | 0.0792 0.0017 0.0809 | 26.9772
- 4 | 2.50 | 0.0789 0.0019 0.0808 | 24.6107
- 5 | 2.50 | 0.0786 0.0021 0.0807 | 22.6548
- 6 | 2.50 | 0.0783 0.0022 0.0805 | 20.6989
- 7 | 2.50 | 0.0781 0.0022 0.0803 | 18.9688
- 8 | 2.50 | 0.0778 0.0023 0.0802 | 17.4455
- 9 | 2.50 | 0.0776 0.0024 0.0800 | 15.9223
- 10 | 2.50 | 0.0773 0.0025 0.0798 | 14.6627
- 11 | 2.50 | 0.0770 0.0026 0.0796 | 13.4764
- 12 | 2.50 | 0.0767 0.0026 0.0793 | 12.3015
- 13 | 2.50 | 0.0764 0.0027 0.0791 | 11.3776
- 14 | 2.50 | 0.0761 0.0028 0.0789 | 10.4537
- 15 | 2.25 | 0.0739 0.0028 0.0768 | 9.5920
- 16 | 2.25 | 0.0711 0.0042 0.0753 | 8.8725
- 29 | 2.00 | 0.0719 0.0019 0.0738 | 3.3283
- 30 | 2.00 | 0.0663 0.0042 0.0705 | 3.1221
- 31 | 2.00 | 0.0645 0.0051 0.0695 | 2.9160
- 43 | 1.75 | 0.0634 0.0029 0.0663 | 1.5785
- 44 | 1.75 | 0.0594 0.0050 0.0644 | 1.5194
- 45 | 1.75 | 0.0581 0.0057 0.0638 | 1.4626
- 57 | 1.50 | 0.0564 0.0041 0.0606 | 1.0900
- 58 | 1.50 | 0.0536 0.0060 0.0596 | 1.0730
- Shooting registration with 2.50:-0.25:1.50 mm takes: 145s
- Prepare output 10s
- 155s
- Jacobian determinant (RMS): 0.012 0.042 0.060 0.081 0.103 | 0.107600
- Template Matching: 0.082 0.213 0.193 0.174 0.161 | 0.160795
- Write result maps: 26s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 26s
- CSF distance: 14s
- PBT2x thickness: 39s
- 86s
- Create initial surface 74s
- Topology correction: 72s
- Surface refinement: 93s
- Reduction of surface collisions with optimization: 57s
- Spherical mapping with areal smoothing 71s
- Spherical registration 309s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 24s
- CSF distance: 14s
- PBT2x thickness: 41s
- 84s
- Create initial surface 76s
- Topology correction: 74s
- Surface refinement: 95s
- Reduction of surface collisions with optimization: 57s
- Spherical mapping with areal smoothing 72s
- Spherical registration 303s
- Final surface processing results:
- Average thickness (FS): 2.6252 0.6261 mm
- Surface intensity / position RMSE: 0.0614 / 0.0578
- Euler number / defect number / defect size: 6.0 / 8.0 / 0.06%
- Display thickness: /var/lib/condor/execute/dir_7854/ds/sub-sc004/surf/lh.thickness.sub-sc004_T1w
- Display thickness: /var/lib/condor/execute/dir_7854/ds/sub-sc004/surf/rh.thickness.sub-sc004_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_7854/ds/sub-sc004/sub-sc004_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1613s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 31s
- ROI estimation of 'lpba40' atlas 9s
- ROI estimation of 'hammers' atlas 22s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 8s
- ROI estimation of 'aal3' atlas 13s
- ROI estimation of 'mori' atlas 21s
- ROI estimation of 'anatomy3' atlas 28s
- ROI estimation of 'julichbrain' atlas 38s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 27s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 60s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 89s
- Write results 90s
- 373s
- Quality check: 5s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_7854/ds/sub-sc004/report/catreport_sub-sc004_T1w.pdf
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- CAT preprocessing takes 46 minute(s) and 21 second(s).
- Image Quality Rating (IQR): 80.76% (B-)
- GM volume (GMV): 50.10% (643.22 / 1283.84 ml)
- GM thickness (GMT): 2.63 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_7854/ds/sub-sc004/mri
- Reports are saved in /var/lib/condor/execute/dir_7854/ds/sub-sc004/report
- Labels are saved in /var/lib/condor/execute/dir_7854/ds/sub-sc004/label
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