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- CAT12.8.1 r1980: 1/1: ./execute/dir_28845/ds/sub-105/sub-105_T1w.n
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- SANLM denoising (medium): 105s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 11s
- Initial correction 8s
- Refine background 5s
- Final correction 6s
- Final scaling 9s
- 50s
- Correct center-of-mass 3s
- Affine registration 11s
- SPM preprocessing 1 (estimate 1 - TPM registration): 61s
- SPM preprocessing 1 (estimate 2): 60s
- SPM preprocessing 2 (write):
- Write Segmentation 15s
- Update Segmentation 18s
- Update Skull-Stripping 41s
- Update probability maps 9s
- 84s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 24s
- Fast Optimized Shooting registration 33s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 15s
- Estimate local tissue thresholds (WM) 20s
- Estimate local tissue thresholds (GM) 27s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 36s
- 107s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 4s
- Ventricle detection 18s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.48 > WMHCstr'=0.19) 26s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 4s
- 76s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 34s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.990.04]
- Final cleanup (gcutstr=0.24):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 3s
- 11s
- 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 | 0.0870 0.0000 0.0870 | 32.0000
- 2 | 2.50 | 0.0838 0.0013 0.0851 | 29.4886
- 3 | 2.50 | 0.0828 0.0021 0.0848 | 26.9772
- 4 | 2.50 | 0.0823 0.0023 0.0846 | 24.6107
- 5 | 2.50 | 0.0819 0.0025 0.0844 | 22.6548
- 6 | 2.50 | 0.0816 0.0027 0.0842 | 20.6989
- 7 | 2.50 | 0.0812 0.0028 0.0840 | 18.9688
- 8 | 2.50 | 0.0808 0.0029 0.0838 | 17.4455
- 9 | 2.50 | 0.0805 0.0030 0.0835 | 15.9223
- 10 | 2.50 | 0.0801 0.0031 0.0832 | 14.6627
- 11 | 2.50 | 0.0797 0.0032 0.0829 | 13.4764
- 12 | 2.50 | 0.0793 0.0033 0.0826 | 12.3015
- 13 | 2.50 | 0.0789 0.0034 0.0823 | 11.3776
- 14 | 2.50 | 0.0785 0.0035 0.0820 | 10.4537
- 15 | 2.25 | 0.0791 0.0036 0.0827 | 9.5920
- 16 | 2.25 | 0.0758 0.0052 0.0810 | 8.8725
- 17 | 2.25 | 0.0745 0.0058 0.0803 | 8.1530
- 29 | 2.00 | 0.0764 0.0027 0.0791 | 3.3283
- 30 | 2.00 | 0.0704 0.0052 0.0756 | 3.1221
- 31 | 2.00 | 0.0682 0.0062 0.0745 | 2.9160
- 43 | 1.75 | 0.0672 0.0036 0.0708 | 1.5785
- 44 | 1.75 | 0.0627 0.0060 0.0687 | 1.5194
- 45 | 1.75 | 0.0611 0.0069 0.0680 | 1.4626
- 57 | 1.50 | 0.0598 0.0050 0.0649 | 1.0900
- 58 | 1.50 | 0.0565 0.0072 0.0637 | 1.0730
- 59 | 1.50 | 0.0554 0.0079 0.0632 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 164s
- Prepare output 10s
- 174s
- Jacobian determinant (RMS): 0.011 0.041 0.062 0.085 0.108 | 0.115154
- Template Matching: 0.087 0.223 0.205 0.183 0.166 | 0.166122
- Write result maps: 23s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 40s
- CSF distance: 18s
- PBT2x thickness: 50s
- 114s
- Create initial surface 94s
- Topology correction: 100s
- Surface refinement: 79s
- Reduction of surface collisions with optimization: 74s
- Spherical mapping with areal smoothing 94s
- Spherical registration 283s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 53s
- CSF distance: 16s
- PBT2x thickness: 47s
- 123s
- Create initial surface 90s
- Topology correction: 96s
- Surface refinement: 104s
- Reduction of surface collisions with optimization: 73s
- Spherical mapping with areal smoothing 86s
- Spherical registration 287s
- Final surface processing results:
- Average thickness (FS): 2.4678 0.5876 mm
- Surface intensity / position RMSE: 0.0641 / 0.0649
- Euler number / defect number / defect size: 24.0 / 16.0 / 0.61%
- Display thickness: /var/lib/condor/execute/dir_28845/ds/sub-105/surf/lh.thickness.sub-105_T1w
- Display thickness: /var/lib/condor/execute/dir_28845/ds/sub-105/surf/rh.thickness.sub-105_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_28845/ds/sub-105/sub-105_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1795s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 8s
- ROI estimation of 'neuromorphometrics' atlas 28s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 20s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 11s
- ROI estimation of 'mori' atlas 16s
- ROI estimation of 'anatomy3' atlas 23s
- ROI estimation of 'julichbrain' atlas 30s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 47s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 70s
- Write results 71s
- 303s
- Quality check: 5s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_28845/ds/sub-105/report/catreport_sub-105_T1w.pdf
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- CAT preprocessing takes 50 minute(s) and 58 second(s).
- Image Quality Rating (IQR): 81.99% (B-)
- GM volume (GMV): 41.25% (726.30 / 1760.87 ml)
- GM thickness (GMT): 2.47 0.59 mm
- Segmentations are saved in /var/lib/condor/execute/dir_28845/ds/sub-105/mri
- Reports are saved in /var/lib/condor/execute/dir_28845/ds/sub-105/report
- Labels are saved in /var/lib/condor/execute/dir_28845/ds/sub-105/label
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