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- CAT12.8.1 r1980: 1/1: ./condor/execute/dir_52137/ds/sub-06/sub-06_T1w.n
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- SANLM denoising (medium): 63s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 10s
- Initial correction 10s
- Refine background 4s
- Final correction 7s
- Final scaling 7s
- 54s
- Correct center-of-mass 6s
- Affine registration 12s
- SPM preprocessing 1 (estimate 1 - TPM registration): 94s
- SPM preprocessing 1 (estimate 2): 74s
- SPM preprocessing 2 (write):
- Write Segmentation 23s
- Update Segmentation 25s
- Update Skull-Stripping 53s
- Update probability maps 10s
- 111s
- Global intensity correction: 19s
- SANLM denoising after intensity normalization (medium): 14s
- Fast Optimized Shooting registration 42s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.00) 19s
- Estimate local tissue thresholds (WM) 25s
- Estimate local tissue thresholds (GM) 36s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 38s
- 131s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 4s
- Ventricle detection 21s
- Blood vessel detection 13s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.04) 32s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 5s
- Final corrections 6s
- 93s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 40s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.07,0.990.04]
- 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
- 15s
- 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 | 0.0820 0.0000 0.0820 | 32.0000
- 2 | 2.50 | 0.0797 0.0010 0.0807 | 29.4886
- 3 | 2.50 | 0.0790 0.0016 0.0806 | 26.9772
- 4 | 2.50 | 0.0787 0.0018 0.0805 | 24.6107
- 5 | 2.50 | 0.0785 0.0019 0.0804 | 22.6548
- 6 | 2.50 | 0.0782 0.0020 0.0802 | 20.6989
- 7 | 2.50 | 0.0780 0.0020 0.0800 | 18.9688
- 8 | 2.50 | 0.0778 0.0021 0.0799 | 17.4455
- 9 | 2.50 | 0.0775 0.0022 0.0797 | 15.9223
- 10 | 2.50 | 0.0772 0.0023 0.0795 | 14.6627
- 11 | 2.50 | 0.0770 0.0023 0.0793 | 13.4764
- 12 | 2.50 | 0.0767 0.0024 0.0791 | 12.3015
- 13 | 2.50 | 0.0764 0.0025 0.0789 | 11.3776
- 14 | 2.50 | 0.0762 0.0025 0.0787 | 10.4537
- 15 | 2.25 | 0.0751 0.0026 0.0777 | 9.5920
- 16 | 2.25 | 0.0724 0.0040 0.0764 | 8.8725
- 29 | 2.00 | 0.0742 0.0018 0.0760 | 3.3283
- 30 | 2.00 | 0.0680 0.0043 0.0723 | 3.1221
- 31 | 2.00 | 0.0660 0.0053 0.0713 | 2.9160
- 43 | 1.75 | 0.0650 0.0030 0.0681 | 1.5785
- 44 | 1.75 | 0.0605 0.0055 0.0659 | 1.5194
- 45 | 1.75 | 0.0590 0.0063 0.0653 | 1.4626
- 57 | 1.50 | 0.0575 0.0046 0.0620 | 1.0900
- 58 | 1.50 | 0.0542 0.0067 0.0609 | 1.0730
- 59 | 1.50 | 0.0531 0.0073 0.0604 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 204s
- Prepare output 15s
- 219s
- Jacobian determinant (RMS): 0.011 0.038 0.056 0.078 0.100 | 0.106721
- Template Matching: 0.082 0.217 0.198 0.177 0.159 | 0.159261
- Write result maps: 29s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 40s
- CSF distance: 21s
- PBT2x thickness: 60s
- 129s
- Create initial surface 105s
- Topology correction: 132s
- Surface refinement: 168s
- Reduction of surface collisions with optimization: 162s
- Spherical mapping with areal smoothing 108s
- Spherical registration 318s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 49s
- CSF distance: 20s
- PBT2x thickness: 57s
- 132s
- Create initial surface 97s
- Topology correction: 111s
- Surface refinement: 123s
- Reduction of surface collisions with optimization: 82s
- Spherical mapping with areal smoothing 101s
- Spherical registration 303s
- Final surface processing results:
- Average thickness (FS): 2.5717 0.6339 mm
- Surface intensity / position RMSE: 0.0663 / 0.0753
- Euler number / defect number / defect size: 18.0 / 18.0 / 1.06%
- Display thickness: /var/lib/condor/execute/dir_52137/ds/sub-06/surf/lh.thickness.sub-06_T1w
- Display thickness: /var/lib/condor/execute/dir_52137/ds/sub-06/surf/rh.thickness.sub-06_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_52137/ds/sub-06/sub-06_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 2185s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 32s
- ROI estimation of 'lpba40' atlas 9s
- ROI estimation of 'hammers' atlas 21s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 8s
- ROI estimation of 'aal3' atlas 12s
- ROI estimation of 'mori' atlas 19s
- ROI estimation of 'anatomy3' atlas 34s
- ROI estimation of 'julichbrain' atlas 42s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 31s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 72s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 84s
- Write results 85s
- 393s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_52137/ds/sub-06/report/catreport_sub-06_T1w.pdf
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- CAT preprocessing takes 61 minute(s) and 34 second(s).
- Image Quality Rating (IQR): 83.55% (B)
- GM volume (GMV): 47.26% (717.10 / 1517.20 ml)
- GM thickness (GMT): 2.57 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_52137/ds/sub-06/mri
- Reports are saved in /var/lib/condor/execute/dir_52137/ds/sub-06/report
- Labels are saved in /var/lib/condor/execute/dir_52137/ds/sub-06/label
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