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- CAT12.8.1 r1980: 1/1: ./dir_7765/ds/sub-0696/sub-0696_ses-01_T1w.n
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- SANLM denoising (medium): 221s
- APP: Rough bias correction:
- Initialize 11s
- Estimate background 12s
- Initial correction 27s
- Refine background 6s
- Final correction 14s
- Final scaling 10s
- 89s
- Correct center-of-mass 6s
- Affine registration 25s
- SPM preprocessing 1 (estimate 1 - TPM registration): 113s
- SPM preprocessing 1 (estimate 2): 77s
- SPM preprocessing 2 (write):
- Write Segmentation 28s
- Update Segmentation 29s
- Update Skull-Stripping 69s
- Update probability maps 14s
- 141s
- Global intensity correction: 27s
- SANLM denoising after intensity normalization (medium): 23s
- Fast Optimized Shooting registration 47s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 6s
- Prepare partitions 9s
- Prepare segments (LASmod = 1.10) 24s
- Estimate local tissue thresholds (WM) 35s
- Estimate local tissue thresholds (GM) 49s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 59s
- 188s
- ROI segmentation (partitioning):
- Atlas -> subject space 12s
- Major structures 5s
- Ventricle detection 23s
- Blood vessel detection 17s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 44s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 6s
- Final corrections 7s
- 117s
- Blood vessel correction (BVCstr=0.50): 3s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 47s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 7s
- Level 1 cleanup (brain masking) 4s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 4s
- 17s
- 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 | 0.0799 0.0000 0.0799 | 32.0000
- 2 | 2.50 | 0.0780 0.0009 0.0789 | 29.4886
- 3 | 2.50 | 0.0775 0.0014 0.0788 | 26.9772
- 4 | 2.50 | 0.0772 0.0015 0.0787 | 24.6107
- 5 | 2.50 | 0.0770 0.0016 0.0786 | 22.6548
- 6 | 2.50 | 0.0769 0.0016 0.0785 | 20.6989
- 7 | 2.50 | 0.0767 0.0016 0.0784 | 18.9688
- 8 | 2.50 | 0.0765 0.0017 0.0782 | 17.4455
- 9 | 2.50 | 0.0764 0.0017 0.0781 | 15.9223
- 10 | 2.50 | 0.0762 0.0018 0.0779 | 14.6627
- 11 | 2.50 | 0.0760 0.0018 0.0778 | 13.4764
- 12 | 2.50 | 0.0758 0.0018 0.0776 | 12.3015
- 13 | 2.50 | 0.0756 0.0018 0.0775 | 11.3776
- 14 | 2.50 | 0.0754 0.0019 0.0773 | 10.4537
- 15 | 2.25 | 0.0739 0.0019 0.0758 | 9.5920
- 16 | 2.25 | 0.0716 0.0029 0.0745 | 8.8725
- 29 | 2.00 | 0.0731 0.0013 0.0744 | 3.3283
- 30 | 2.00 | 0.0677 0.0034 0.0711 | 3.1221
- 31 | 2.00 | 0.0659 0.0043 0.0702 | 2.9160
- 43 | 1.75 | 0.0651 0.0025 0.0676 | 1.5785
- 44 | 1.75 | 0.0610 0.0046 0.0656 | 1.5194
- 45 | 1.75 | 0.0596 0.0054 0.0650 | 1.4626
- 57 | 1.50 | 0.0583 0.0039 0.0622 | 1.0900
- 58 | 1.50 | 0.0553 0.0058 0.0612 | 1.0730
- Shooting registration with 2.50:-0.25:1.50 mm takes: 167s
- Prepare output 16s
- 184s
- Jacobian determinant (RMS): 0.007 0.023 0.039 0.066 0.093 | 0.098439
- Template Matching: 0.080 0.215 0.198 0.179 0.166 | 0.166047
- Write result maps: 44s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 39s
- CSF distance: 21s
- PBT2x thickness: 62s
- 130s
- Create initial surface 109s
- Topology correction: 118s
- Surface refinement: 86s
- Reduction of surface collisions with optimization: 86s
- Spherical mapping with areal smoothing 103s
- Spherical registration 339s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 41s
- CSF distance: 20s
- PBT2x thickness: 60s
- 128s
- Create initial surface 103s
- Topology correction: 113s
- Surface refinement: 89s
- Reduction of surface collisions with optimization: 82s
- Spherical mapping with areal smoothing 99s
- Spherical registration 338s
- Final surface processing results:
- Average thickness (FS): 2.6455 0.6345 mm
- Surface intensity / position RMSE: 0.0770 / 0.0782
- Euler number / defect number / defect size: 34.0 / 27.5 / 0.89%
- Display thickness: /var/lib/condor/execute/dir_7765/ds/sub-0696/surf/lh.thickness.sub-0696_ses-01_T1w
- Display thickness: /var/lib/condor/execute/dir_7765/ds/sub-0696/surf/rh.thickness.sub-0696_ses-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_7765/ds/sub-0696/sub-0696_ses-01_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 2054s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 13s
- ROI estimation of 'neuromorphometrics' atlas 48s
- ROI estimation of 'lpba40' atlas 14s
- ROI estimation of 'hammers' atlas 34s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 12s
- ROI estimation of 'aal3' atlas 20s
- ROI estimation of 'mori' atlas 30s
- ROI estimation of 'anatomy3' atlas 43s
- ROI estimation of 'julichbrain' atlas 57s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 22s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 39s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 91s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 139s
- Write results 141s
- 568s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_7765/ds/sub-0696/report/catreport_sub-0696_ses-01_T1w.pdf
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- CAT preprocessing takes 69 minute(s) and 13 second(s).
- Image Quality Rating (IQR): 82.18% (B-)
- GM volume (GMV): 50.01% (762.63 / 1524.86 ml)
- GM thickness (GMT): 2.65 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_7765/ds/sub-0696/mri
- Reports are saved in /var/lib/condor/execute/dir_7765/ds/sub-0696/report
- Labels are saved in /var/lib/condor/execute/dir_7765/ds/sub-0696/label
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