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- CAT12.8.1 r2040: 1/1: ./sub-0025991/ses-5/sub-0025991_ses-5_run-1_T1w.n
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- SANLM denoising (medium): 48s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 5s
- Initial correction 5s
- Refine background 3s
- Final correction 4s
- Final scaling 5s
- 34s
- Correct center-of-mass 4s
- Affine registration 8s
- SPM preprocessing 1 (estimate 1 - TPM registration): 65s
- SPM preprocessing 1 (estimate 2): 54s
- SPM preprocessing 2 (write):
- Write Segmentation 16s
- Update Segmentation 17s
- Update Skull-Stripping 39s
- Update probability maps 8s
- 81s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 22s
- Fast Optimized Shooting registration 31s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 13s
- Estimate local tissue thresholds (WM) 17s
- Estimate local tissue thresholds (GM) 24s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 42s
- 105s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 12s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.03) 23s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 62s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 33s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- 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 | 0.0819 0.0000 0.0819 | 32.0000
- 2 | 2.50 | 0.0797 0.0010 0.0807 | 29.4886
- 3 | 2.50 | 0.0790 0.0016 0.0805 | 26.9772
- 4 | 2.50 | 0.0786 0.0018 0.0804 | 24.6107
- 5 | 2.50 | 0.0783 0.0020 0.0803 | 22.6548
- 6 | 2.50 | 0.0781 0.0020 0.0801 | 20.6989
- 7 | 2.50 | 0.0778 0.0021 0.0799 | 18.9688
- 8 | 2.50 | 0.0776 0.0022 0.0798 | 17.4455
- 9 | 2.50 | 0.0773 0.0023 0.0796 | 15.9223
- 10 | 2.50 | 0.0770 0.0024 0.0794 | 14.6627
- 11 | 2.50 | 0.0767 0.0025 0.0792 | 13.4764
- 12 | 2.50 | 0.0764 0.0025 0.0790 | 12.3015
- 13 | 2.50 | 0.0761 0.0026 0.0788 | 11.3776
- 14 | 2.50 | 0.0758 0.0027 0.0785 | 10.4537
- 15 | 2.25 | 0.0749 0.0027 0.0777 | 9.5920
- 16 | 2.25 | 0.0721 0.0041 0.0762 | 8.8725
- 29 | 2.00 | 0.0735 0.0019 0.0754 | 3.3283
- 30 | 2.00 | 0.0677 0.0042 0.0719 | 3.1221
- 31 | 2.00 | 0.0656 0.0052 0.0708 | 2.9160
- 43 | 1.75 | 0.0645 0.0030 0.0675 | 1.5785
- 44 | 1.75 | 0.0603 0.0052 0.0655 | 1.5194
- 45 | 1.75 | 0.0588 0.0060 0.0649 | 1.4626
- 57 | 1.50 | 0.0573 0.0044 0.0617 | 1.0900
- 58 | 1.50 | 0.0543 0.0064 0.0607 | 1.0730
- 59 | 1.50 | 0.0533 0.0070 0.0603 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 166s
- Prepare output 10s
- 176s
- Jacobian determinant (RMS): 0.010 0.038 0.055 0.079 0.101 | 0.109085
- Template Matching: 0.082 0.216 0.197 0.177 0.160 | 0.159767
- Write result maps: 32s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 37s
- CSF distance: 13s
- PBT2x thickness: 40s
- 96s
- Create initial surface 81s
- Topology correction: 89s
- Surface refinement: 76s
- Reduction of surface collisions with optimization: 64s
- Spherical mapping with areal smoothing 82s
- Spherical registration 291s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 24s
- CSF distance: 12s
- PBT2x thickness: 38s
- 80s
- Create initial surface 78s
- Topology correction: 85s
- Surface refinement: 94s
- Reduction of surface collisions with optimization: 59s
- Spherical mapping with areal smoothing 76s
- Spherical registration 304s
- Final surface processing results:
- Average thickness (FS): 2.3988 0.6098 mm
- Surface intensity / position RMSE: 0.0634 / 0.0651
- Euler number / defect number / defect size: 18.0 / 10.0 / 0.38%
- Display thickness: /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-5/surf/lh.thickness.sub-0025991_ses-5_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-5/surf/rh.thickness.sub-0025991_ses-5_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-5/sub-0025991_ses-5_run-1_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1644s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 8s
- ROI estimation of 'neuromorphometrics' atlas 29s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 21s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 12s
- ROI estimation of 'mori' atlas 18s
- ROI estimation of 'anatomy3' atlas 26s
- ROI estimation of 'julichbrain' atlas 34s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 14s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 25s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 55s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 85s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s
- Write results 8s
- 353s
- Quality check: 11s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-5/report/catreport_sub-0025991_ses-5_run-1_T1w.pdf
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- CAT preprocessing takes 48 minute(s) and 1 second(s).
- Image Quality Rating (IQR): 82.73% (B-)
- GM volume (GMV): 45.85% (618.98 / 1349.95 ml)
- GM thickness (GMT): 2.40 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-5/mri
- Reports are saved in /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-5/report
- Labels are saved in /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-5/label
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