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- CAT12.8.1 r1980: 1/1: ./dir_6132/ds/sub-0845/sub-0845_ses-01_T1w.n
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- SANLM denoising (medium): 143s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 5s
- Initial correction 11s
- Refine background 3s
- Final correction 7s
- Final scaling 6s
- 45s
- Correct center-of-mass 3s
- Affine registration 12s
- SPM preprocessing 1 (estimate 1 - TPM registration): 7s
- Use initial fine affine registration. 56s
- SPM preprocessing 1 (estimate 2): 52s
- SPM preprocessing 2 (write):
- Write Segmentation 17s
- Update Segmentation 17s
- Update Skull-Stripping 42s
- Update probability maps 9s
- 86s
- Global intensity correction: 17s
- SANLM denoising after intensity normalization (medium): 18s
- Fast Optimized Shooting registration 31s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.12) 11s
- Estimate local tissue thresholds (WM) 17s
- Estimate local tissue thresholds (GM) 24s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 35s
- 98s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 3s
- Ventricle detection 11s
- Blood vessel detection 7s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 22s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 5s
- 60s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 22s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 3s
- Level 1 cleanup (brain masking) 2s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 9s
- 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 | 0.0854 0.0000 0.0854 | 32.0000
- 2 | 2.50 | 0.0823 0.0013 0.0835 | 29.4886
- 3 | 2.50 | 0.0814 0.0019 0.0833 | 26.9772
- 4 | 2.50 | 0.0809 0.0022 0.0831 | 24.6107
- 5 | 2.50 | 0.0806 0.0023 0.0829 | 22.6548
- 6 | 2.50 | 0.0803 0.0024 0.0827 | 20.6989
- 7 | 2.50 | 0.0801 0.0025 0.0825 | 18.9688
- 8 | 2.50 | 0.0798 0.0026 0.0823 | 17.4455
- 9 | 2.50 | 0.0795 0.0026 0.0821 | 15.9223
- 10 | 2.50 | 0.0791 0.0027 0.0818 | 14.6627
- 11 | 2.50 | 0.0788 0.0028 0.0816 | 13.4764
- 12 | 2.50 | 0.0785 0.0028 0.0813 | 12.3015
- 13 | 2.50 | 0.0782 0.0029 0.0811 | 11.3776
- 14 | 2.50 | 0.0779 0.0029 0.0808 | 10.4537
- 15 | 2.25 | 0.0784 0.0030 0.0814 | 9.5920
- 16 | 2.25 | 0.0753 0.0045 0.0798 | 8.8725
- 17 | 2.25 | 0.0741 0.0050 0.0792 | 8.1530
- 29 | 2.00 | 0.0767 0.0023 0.0790 | 3.3283
- 30 | 2.00 | 0.0711 0.0046 0.0758 | 3.1221
- 31 | 2.00 | 0.0693 0.0055 0.0748 | 2.9160
- 43 | 1.75 | 0.0690 0.0032 0.0721 | 1.5785
- 44 | 1.75 | 0.0645 0.0056 0.0701 | 1.5194
- 45 | 1.75 | 0.0631 0.0064 0.0694 | 1.4626
- 57 | 1.50 | 0.0623 0.0046 0.0670 | 1.0900
- 58 | 1.50 | 0.0589 0.0069 0.0658 | 1.0730
- 59 | 1.50 | 0.0578 0.0076 0.0654 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 138s
- Prepare output 9s
- 147s
- Jacobian determinant (RMS): 0.011 0.038 0.060 0.089 0.119 | 0.126481
- Template Matching: 0.085 0.222 0.208 0.189 0.173 | 0.173429
- Write result maps: 28s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 22s
- CSF distance: 11s
- PBT2x thickness: 34s
- 72s
- Create initial surface 54s
- Topology correction: 72s
- Surface refinement: 69s
- Reduction of surface collisions with optimization: 43s
- Spherical mapping with areal smoothing 58s
- Spherical registration 178s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 20s
- CSF distance: 11s
- PBT2x thickness: 34s
- 69s
- Create initial surface 53s
- Topology correction: 67s
- Surface refinement: 55s
- Reduction of surface collisions with optimization: 42s
- Spherical mapping with areal smoothing 57s
- Spherical registration 182s
- Final surface processing results:
- Average thickness (FS): 2.4387 0.6707 mm
- Surface intensity / position RMSE: 0.0929 / 0.1198
- Euler number / defect number / defect size: 116.0 / 49.0 / 3.90%
- Display thickness: /var/lib/condor/execute/dir_6132/ds/sub-0845/surf/lh.thickness.sub-0845_ses-01_T1w
- Display thickness: /var/lib/condor/execute/dir_6132/ds/sub-0845/surf/rh.thickness.sub-0845_ses-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_6132/ds/sub-0845/sub-0845_ses-01_T1w.nii
- Surface ROI estimation: 6s
- Surface and thickness estimation takes: 1152s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 15s
- ROI estimation of 'neuromorphometrics' atlas 56s
- ROI estimation of 'lpba40' atlas 16s
- ROI estimation of 'hammers' atlas 38s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 13s
- ROI estimation of 'aal3' atlas 21s
- ROI estimation of 'mori' atlas 31s
- ROI estimation of 'anatomy3' atlas 45s
- ROI estimation of 'julichbrain' atlas 60s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 21s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 24s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 99s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 150s
- Write results 151s
- 595s
- Quality check: 4s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_6132/ds/sub-0845/report/catreport_sub-0845_ses-01_T1w.pdf
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- CAT preprocessing takes 44 minute(s) and 22 second(s).
- Image Quality Rating (IQR): 81.17% (B-)
- GM volume (GMV): 54.71% (678.15 / 1239.50 ml)
- GM thickness (GMT): 2.44 0.67 mm
- Segmentations are saved in /var/lib/condor/execute/dir_6132/ds/sub-0845/mri
- Reports are saved in /var/lib/condor/execute/dir_6132/ds/sub-0845/report
- Labels are saved in /var/lib/condor/execute/dir_6132/ds/sub-0845/label
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