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- CAT12.8.1 r1980: 1/1: ./dir_2537341/ds/sub-sc032/sub-sc032_T1w.n
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- SANLM denoising (medium): 13s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 8s
- Initial correction 9s
- Refine background 4s
- Final correction 7s
- Final scaling 6s
- 48s
- Correct center-of-mass 3s
- Affine registration 12s
- SPM preprocessing 1 (estimate 1 - TPM registration): 100s
- SPM preprocessing 1 (estimate 2): 81s
- SPM preprocessing 2 (write):
- Write Segmentation 21s
- Update Segmentation 26s
- Update Skull-Stripping 54s
- Update probability maps 12s
- 113s
- Global intensity correction: 20s
- SANLM denoising after intensity normalization (medium): 22s
- Fast Optimized Shooting registration 46s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.13) 21s
- Estimate local tissue thresholds (WM) 26s
- Estimate local tissue thresholds (GM) 38s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 27s
- 124s
- ROI segmentation (partitioning):
- Atlas -> subject space 11s
- Major structures 5s
- Ventricle detection 20s
- Blood vessel detection 15s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.03) 38s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 5s
- Final corrections 6s
- 102s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 44s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.04]
- 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
- 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 | 0.0816 0.0000 0.0816 | 32.0000
- 2 | 2.50 | 0.0793 0.0011 0.0804 | 29.4886
- 3 | 2.50 | 0.0786 0.0016 0.0803 | 26.9772
- 4 | 2.50 | 0.0783 0.0018 0.0801 | 24.6107
- 5 | 2.50 | 0.0780 0.0020 0.0800 | 22.6548
- 6 | 2.50 | 0.0778 0.0020 0.0798 | 20.6989
- 7 | 2.50 | 0.0775 0.0021 0.0796 | 18.9688
- 8 | 2.50 | 0.0773 0.0022 0.0795 | 17.4455
- 9 | 2.50 | 0.0770 0.0023 0.0793 | 15.9223
- 10 | 2.50 | 0.0767 0.0024 0.0791 | 14.6627
- 11 | 2.50 | 0.0764 0.0024 0.0789 | 13.4764
- 12 | 2.50 | 0.0762 0.0025 0.0786 | 12.3015
- 13 | 2.50 | 0.0759 0.0026 0.0784 | 11.3776
- 14 | 2.50 | 0.0756 0.0026 0.0782 | 10.4537
- 15 | 2.25 | 0.0740 0.0027 0.0767 | 9.5920
- 16 | 2.25 | 0.0714 0.0040 0.0754 | 8.8725
- 29 | 2.00 | 0.0726 0.0018 0.0744 | 3.3283
- 30 | 2.00 | 0.0672 0.0040 0.0712 | 3.1221
- 31 | 2.00 | 0.0654 0.0049 0.0703 | 2.9160
- 43 | 1.75 | 0.0646 0.0028 0.0674 | 1.5785
- 44 | 1.75 | 0.0605 0.0050 0.0654 | 1.5194
- 45 | 1.75 | 0.0591 0.0058 0.0649 | 1.4626
- 57 | 1.50 | 0.0577 0.0042 0.0619 | 1.0900
- 58 | 1.50 | 0.0546 0.0062 0.0608 | 1.0730
- 59 | 1.50 | 0.0536 0.0069 0.0604 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 205s
- Prepare output 15s
- 220s
- Jacobian determinant (RMS): 0.011 0.038 0.057 0.080 0.104 | 0.111481
- Template Matching: 0.082 0.214 0.196 0.177 0.161 | 0.160655
- Write result maps: 32s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 50s
- CSF distance: 24s
- PBT2x thickness: 69s
- 150s
- Create initial surface 127s
- Topology correction: 141s
- Surface refinement: 161s
- Reduction of surface collisions with optimization: 111s
- Spherical mapping with areal smoothing 127s
- Spherical registration 339s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 52s
- CSF distance: 23s
- PBT2x thickness: 69s
- 153s
- Create initial surface 124s
- Topology correction: 158s
- Surface refinement: 216s
- Reduction of surface collisions with optimization: 113s
- Spherical mapping with areal smoothing 127s
- Spherical registration 324s
- Final surface processing results:
- Average thickness (FS): 2.4833 0.5954 mm
- Surface intensity / position RMSE: 0.0652 / 0.0641
- Euler number / defect number / defect size: 22.0 / 18.5 / 0.47%
- Display thickness: /var/lib/condor/execute/dir_2537341/ds/sub-sc032/surf/lh.thickness.sub-sc032_T1w
- Display thickness: /var/lib/condor/execute/dir_2537341/ds/sub-sc032/surf/rh.thickness.sub-sc032_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2537341/ds/sub-sc032/sub-sc032_T1w.nii
- Surface ROI estimation: 11s
- Surface and thickness estimation takes: 2502s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 11s
- ROI estimation of 'neuromorphometrics' atlas 39s
- ROI estimation of 'lpba40' atlas 11s
- ROI estimation of 'hammers' atlas 29s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 10s
- ROI estimation of 'aal3' atlas 16s
- ROI estimation of 'mori' atlas 23s
- ROI estimation of 'anatomy3' atlas 34s
- ROI estimation of 'julichbrain' atlas 44s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 18s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 33s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 73s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 106s
- Write results 109s
- 452s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2537341/ds/sub-sc032/report/catreport_sub-sc032_T1w.pdf
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- CAT preprocessing takes 72 minute(s) and 34 second(s).
- Image Quality Rating (IQR): 85.99% (B)
- GM volume (GMV): 47.09% (818.50 / 1738.32 ml)
- GM thickness (GMT): 2.48 0.60 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2537341/ds/sub-sc032/mri
- Reports are saved in /var/lib/condor/execute/dir_2537341/ds/sub-sc032/report
- Labels are saved in /var/lib/condor/execute/dir_2537341/ds/sub-sc032/label
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