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- CAT12.8.1 r1980: 1/1: ./execute/dir_17509/ds/sub-025/sub-025_T1w.n
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- SANLM denoising (medium): 84s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 6s
- Initial correction 7s
- Refine background 4s
- Final correction 7s
- Final scaling 11s
- 49s
- Correct center-of-mass 2s
- Affine registration 11s
- SPM preprocessing 1 (estimate 1 - TPM registration): 94s
- SPM preprocessing 1 (estimate 2): 50s
- SPM preprocessing 2 (write):
- Write Segmentation 19s
- Update Segmentation 25s
- Update Skull-Stripping 50s
- Update probability maps 10s
- 104s
- Global intensity correction: 17s
- SANLM denoising after intensity normalization (medium): 24s
- Fast Optimized Shooting registration 31s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 6s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.00) 19s
- Estimate local tissue thresholds (WM) 22s
- Estimate local tissue thresholds (GM) 31s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 38s
- 125s
- ROI segmentation (partitioning):
- Atlas -> subject space 11s
- Major structures 6s
- Ventricle detection 21s
- Blood vessel detection 14s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 42s
- Manual stroke lesion detection 0s
- Closing of deep structures 3s
- Side alignment 6s
- Final corrections 5s
- 107s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 35s
- 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) 4s
- 16s
- 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 | 0.0828 0.0000 0.0828 | 32.0000
- 2 | 2.50 | 0.0796 0.0013 0.0809 | 29.4886
- 3 | 2.50 | 0.0787 0.0020 0.0807 | 26.9772
- 4 | 2.50 | 0.0783 0.0022 0.0805 | 24.6107
- 5 | 2.50 | 0.0780 0.0024 0.0803 | 22.6548
- 6 | 2.50 | 0.0777 0.0025 0.0801 | 20.6989
- 7 | 2.50 | 0.0774 0.0026 0.0799 | 18.9688
- 8 | 2.50 | 0.0770 0.0027 0.0797 | 17.4455
- 9 | 2.50 | 0.0767 0.0027 0.0794 | 15.9223
- 10 | 2.50 | 0.0763 0.0028 0.0792 | 14.6627
- 11 | 2.50 | 0.0760 0.0029 0.0789 | 13.4764
- 12 | 2.50 | 0.0757 0.0030 0.0786 | 12.3015
- 13 | 2.50 | 0.0753 0.0031 0.0784 | 11.3776
- 14 | 2.50 | 0.0750 0.0031 0.0781 | 10.4537
- 15 | 2.25 | 0.0747 0.0032 0.0779 | 9.5920
- 16 | 2.25 | 0.0715 0.0048 0.0763 | 8.8725
- 29 | 2.00 | 0.0733 0.0022 0.0755 | 3.3283
- 30 | 2.00 | 0.0671 0.0046 0.0718 | 3.1221
- 31 | 2.00 | 0.0650 0.0056 0.0706 | 2.9160
- 43 | 1.75 | 0.0643 0.0032 0.0675 | 1.5785
- 44 | 1.75 | 0.0598 0.0056 0.0654 | 1.5194
- 45 | 1.75 | 0.0582 0.0065 0.0647 | 1.4626
- 57 | 1.50 | 0.0569 0.0047 0.0616 | 1.0900
- 58 | 1.50 | 0.0535 0.0069 0.0604 | 1.0730
- 59 | 1.50 | 0.0524 0.0076 0.0600 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 133s
- Prepare output 10s
- 143s
- Jacobian determinant (RMS): 0.011 0.037 0.054 0.077 0.101 | 0.108962
- Template Matching: 0.083 0.214 0.195 0.175 0.157 | 0.157224
- Write result maps: 27s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 26s
- CSF distance: 12s
- PBT2x thickness: 36s
- 79s
- Create initial surface 60s
- Topology correction: 67s
- Surface refinement: 52s
- Reduction of surface collisions with optimization: 50s
- Spherical mapping with areal smoothing 64s
- Spherical registration 177s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 22s
- CSF distance: 12s
- PBT2x thickness: 35s
- 74s
- Create initial surface 58s
- Topology correction: 68s
- Surface refinement: 53s
- Reduction of surface collisions with optimization: 49s
- Spherical mapping with areal smoothing 62s
- Spherical registration 178s
- Final surface processing results:
- Average thickness (FS): 2.6262 0.5845 mm
- Surface intensity / position RMSE: 0.0710 / 0.0708
- Euler number / defect number / defect size: 30.0 / 25.0 / 0.71%
- Display thickness: /var/lib/condor/execute/dir_17509/ds/sub-025/surf/lh.thickness.sub-025_T1w
- Display thickness: /var/lib/condor/execute/dir_17509/ds/sub-025/surf/rh.thickness.sub-025_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_17509/ds/sub-025/sub-025_T1w.nii
- Surface ROI estimation: 6s
- Surface and thickness estimation takes: 1174s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 16s
- ROI estimation of 'neuromorphometrics' atlas 59s
- ROI estimation of 'lpba40' atlas 17s
- ROI estimation of 'hammers' atlas 41s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 14s
- ROI estimation of 'aal3' atlas 25s
- ROI estimation of 'mori' atlas 38s
- ROI estimation of 'anatomy3' atlas 56s
- ROI estimation of 'julichbrain' atlas 77s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 25s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 32s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 99s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 137s
- Write results 138s
- 640s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_17509/ds/sub-025/report/catreport_sub-025_T1w.pdf
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- CAT preprocessing takes 47 minute(s) and 23 second(s).
- Image Quality Rating (IQR): 87.83% (B+)
- GM volume (GMV): 50.85% (758.96 / 1492.40 ml)
- GM thickness (GMT): 2.63 0.58 mm
- Segmentations are saved in /var/lib/condor/execute/dir_17509/ds/sub-025/mri
- Reports are saved in /var/lib/condor/execute/dir_17509/ds/sub-025/report
- Labels are saved in /var/lib/condor/execute/dir_17509/ds/sub-025/label
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