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- CAT12.8.1 r1980: 1/1: ./execute/dir_23543/ds/sub-sc033/sub-sc033_T1w.n
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- SANLM denoising (medium): 24s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 6s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 39s
- Correct center-of-mass 5s
- Affine registration 9s
- SPM preprocessing 1 (estimate 1 - TPM registration): 88s
- SPM preprocessing 1 (estimate 2): 49s
- SPM preprocessing 2 (write):
- Write Segmentation 17s
- Update Segmentation 18s
- Update Skull-Stripping 40s
- Update probability maps 9s
- 83s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 8s
- Fast Optimized Shooting registration 32s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.05) 14s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 23s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 13s
- 77s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 13s
- Blood vessel detection 9s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 25s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 3s
- Final corrections 5s
- 68s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 32s
- AMAP peaks: [CSF,GM,WM] = [0.360.07,0.680.07,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 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 | 0.0813 0.0000 0.0813 | 32.0000
- 2 | 2.50 | 0.0791 0.0010 0.0802 | 29.4886
- 3 | 2.50 | 0.0785 0.0016 0.0800 | 26.9772
- 4 | 2.50 | 0.0782 0.0018 0.0799 | 24.6107
- 5 | 2.50 | 0.0779 0.0019 0.0798 | 22.6548
- 6 | 2.50 | 0.0777 0.0020 0.0796 | 20.6989
- 7 | 2.50 | 0.0774 0.0021 0.0795 | 18.9688
- 8 | 2.50 | 0.0772 0.0022 0.0793 | 17.4455
- 9 | 2.50 | 0.0769 0.0022 0.0791 | 15.9223
- 10 | 2.50 | 0.0766 0.0023 0.0790 | 14.6627
- 11 | 2.50 | 0.0764 0.0024 0.0788 | 13.4764
- 12 | 2.50 | 0.0761 0.0025 0.0786 | 12.3015
- 13 | 2.50 | 0.0758 0.0026 0.0784 | 11.3776
- 14 | 2.50 | 0.0755 0.0026 0.0781 | 10.4537
- 15 | 2.25 | 0.0744 0.0027 0.0771 | 9.5920
- 16 | 2.25 | 0.0718 0.0041 0.0758 | 8.8725
- 29 | 2.00 | 0.0731 0.0018 0.0749 | 3.3283
- 30 | 2.00 | 0.0674 0.0042 0.0716 | 3.1221
- 31 | 2.00 | 0.0654 0.0051 0.0705 | 2.9160
- 43 | 1.75 | 0.0644 0.0029 0.0673 | 1.5785
- 44 | 1.75 | 0.0602 0.0051 0.0653 | 1.5194
- 45 | 1.75 | 0.0588 0.0059 0.0647 | 1.4626
- 57 | 1.50 | 0.0573 0.0043 0.0616 | 1.0900
- 58 | 1.50 | 0.0542 0.0063 0.0605 | 1.0730
- 59 | 1.50 | 0.0532 0.0069 0.0601 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 173s
- Prepare output 10s
- 183s
- Jacobian determinant (RMS): 0.011 0.041 0.062 0.087 0.112 | 0.118493
- Template Matching: 0.081 0.215 0.196 0.176 0.160 | 0.159628
- Write result maps: 26s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 28s
- CSF distance: 15s
- PBT2x thickness: 45s
- 94s
- Create initial surface 84s
- Topology correction: 91s
- Surface refinement: 81s
- Reduction of surface collisions with optimization: 77s
- Spherical mapping with areal smoothing 84s
- Spherical registration 298s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 32s
- CSF distance: 16s
- PBT2x thickness: 45s
- 98s
- Create initial surface 86s
- Topology correction: 97s
- Surface refinement: 89s
- Reduction of surface collisions with optimization: 73s
- Spherical mapping with areal smoothing 82s
- Spherical registration 315s
- Final surface processing results:
- Average thickness (FS): 2.7030 0.6430 mm
- Surface intensity / position RMSE: 0.0694 / 0.0687
- Euler number / defect number / defect size: 18.0 / 15.5 / 0.94%
- Display thickness: /var/lib/condor/execute/dir_23543/ds/sub-sc033/surf/lh.thickness.sub-sc033_T1w
- Display thickness: /var/lib/condor/execute/dir_23543/ds/sub-sc033/surf/rh.thickness.sub-sc033_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_23543/ds/sub-sc033/sub-sc033_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1748s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 34s
- 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 20s
- ROI estimation of 'anatomy3' atlas 28s
- ROI estimation of 'julichbrain' atlas 36s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 26s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 57s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 88s
- Write results 89s
- 372s
- Quality check: 5s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_23543/ds/sub-sc033/report/catreport_sub-sc033_T1w.pdf
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- CAT preprocessing takes 49 minute(s) and 23 second(s).
- Image Quality Rating (IQR): 81.25% (B-)
- GM volume (GMV): 53.32% (759.89 / 1425.17 ml)
- GM thickness (GMT): 2.70 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_23543/ds/sub-sc033/mri
- Reports are saved in /var/lib/condor/execute/dir_23543/ds/sub-sc033/report
- Labels are saved in /var/lib/condor/execute/dir_23543/ds/sub-sc033/label
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