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- CAT12.8.1 r1980: 1/1: ./sub-season212_ses-3_acq-MPrageHiRes_T1w.n
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- SANLM denoising (medium): 50s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 8s
- Initial correction 11s
- Refine background 4s
- Final correction 9s
- Final scaling 9s
- 57s
- Correct center-of-mass 6s
- Affine registration 13s
- SPM preprocessing 1 (estimate 1 - TPM registration): 95s
- SPM preprocessing 1 (estimate 2): 98s
- SPM preprocessing 2 (write):
- Write Segmentation 21s
- Update Segmentation 25s
- Update Skull-Stripping 56s
- Update probability maps 11s
- 113s
- Global intensity correction: 20s
- SANLM denoising after intensity normalization (medium): 21s
- Fast Optimized Shooting registration 37s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 6s
- Prepare partitions 4s
- Prepare segments (LASmod = 1.03) 20s
- Estimate local tissue thresholds (WM) 23s
- Estimate local tissue thresholds (GM) 32s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 30s
- 118s
- ROI segmentation (partitioning):
- Atlas -> subject space 10s
- Major structures 5s
- Ventricle detection 26s
- Blood vessel detection 12s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.04) 38s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 5s
- Final corrections 5s
- 104s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 41s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 6s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 4s
- 14s
- 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 | 0.0793 0.0012 0.0805 | 29.4886
- 3 | 2.50 | 0.0785 0.0019 0.0804 | 26.9772
- 4 | 2.50 | 0.0781 0.0021 0.0802 | 24.6107
- 5 | 2.50 | 0.0778 0.0023 0.0800 | 22.6548
- 6 | 2.50 | 0.0775 0.0024 0.0799 | 20.6989
- 7 | 2.50 | 0.0772 0.0025 0.0797 | 18.9688
- 8 | 2.50 | 0.0769 0.0026 0.0795 | 17.4455
- 9 | 2.50 | 0.0766 0.0027 0.0792 | 15.9223
- 10 | 2.50 | 0.0762 0.0028 0.0790 | 14.6627
- 11 | 2.50 | 0.0759 0.0029 0.0788 | 13.4764
- 12 | 2.50 | 0.0756 0.0030 0.0785 | 12.3015
- 13 | 2.50 | 0.0752 0.0031 0.0783 | 11.3776
- 14 | 2.50 | 0.0749 0.0032 0.0780 | 10.4537
- 15 | 2.25 | 0.0735 0.0032 0.0767 | 9.5920
- 16 | 2.25 | 0.0706 0.0047 0.0753 | 8.8725
- 29 | 2.00 | 0.0715 0.0021 0.0736 | 3.3283
- 30 | 2.00 | 0.0652 0.0045 0.0697 | 3.1221
- 31 | 2.00 | 0.0630 0.0056 0.0686 | 2.9160
- 43 | 1.75 | 0.0617 0.0032 0.0650 | 1.5785
- 44 | 1.75 | 0.0576 0.0053 0.0630 | 1.5194
- 45 | 1.75 | 0.0562 0.0061 0.0623 | 1.4626
- 57 | 1.50 | 0.0544 0.0044 0.0589 | 1.0900
- 58 | 1.50 | 0.0515 0.0063 0.0578 | 1.0730
- 59 | 1.50 | 0.0506 0.0069 0.0575 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 163s
- Prepare output 12s
- 175s
- Jacobian determinant (RMS): 0.013 0.046 0.066 0.089 0.109 | 0.115099
- Template Matching: 0.082 0.212 0.189 0.169 0.152 | 0.151774
- Write result maps: 29s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 36s
- CSF distance: 13s
- PBT2x thickness: 38s
- 93s
- Create initial surface 73s
- Topology correction: 88s
- Surface refinement: 65s
- Reduction of surface collisions with optimization: 60s
- Spherical mapping with areal smoothing 72s
- Spherical registration 300s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 52s
- CSF distance: 14s
- PBT2x thickness: 41s
- 114s
- Create initial surface 80s
- Topology correction: 89s
- Surface refinement: 83s
- Reduction of surface collisions with optimization: 57s
- Spherical mapping with areal smoothing 70s
- Spherical registration 282s
- Final surface processing results:
- Average thickness (FS): 2.4837 0.5847 mm
- Surface intensity / position RMSE: 0.0654 / 0.0672
- Euler number / defect number / defect size: 10.0 / 9.0 / 0.23%
- Display thickness: /var/lib/condor/execute/dir_21558/ds/sub-season212/surf/lh.thickness.sub-season212_ses-3_acq-MPrageHiRes_T1w
- Display thickness: /var/lib/condor/execute/dir_21558/ds/sub-season212/surf/rh.thickness.sub-season212_ses-3_acq-MPrageHiRes_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_21558/ds/sub-season212/sub-season212_ses-3_acq-MPrageHiRes_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1619s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 34s
- ROI estimation of 'lpba40' atlas 10s
- ROI estimation of 'hammers' atlas 24s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 8s
- ROI estimation of 'aal3' atlas 14s
- ROI estimation of 'mori' atlas 20s
- ROI estimation of 'anatomy3' atlas 30s
- ROI estimation of 'julichbrain' atlas 40s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 16s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 29s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 64s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 98s
- Write results 98s
- 399s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_21558/ds/sub-season212/report/catreport_sub-season212_ses-3_acq-MPrageHiRes_T1w.pdf
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- CAT preprocessing takes 52 minute(s) and 18 second(s).
- Image Quality Rating (IQR): 86.96% (B+)
- GM volume (GMV): 47.39% (637.20 / 1344.56 ml)
- GM thickness (GMT): 2.48 0.58 mm
- Segmentations are saved in /var/lib/condor/execute/dir_21558/ds/sub-season212/mri
- Reports are saved in /var/lib/condor/execute/dir_21558/ds/sub-season212/report
- Labels are saved in /var/lib/condor/execute/dir_21558/ds/sub-season212/label
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