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- CAT12.8.1 r2040: 1/1: ./sub-0025954/ses-2/sub-0025954_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 41s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 4s
- Initial correction 4s
- Refine background 3s
- Final correction 4s
- Final scaling 4s
- 30s
- Correct center-of-mass 3s
- Affine registration 7s
- SPM preprocessing 1 (estimate 1 - TPM registration): 62s
- SPM preprocessing 1 (estimate 2): 51s
- SPM preprocessing 2 (write):
- Write Segmentation 14s
- Update Segmentation 15s
- Update Skull-Stripping 34s
- Update probability maps 8s
- 71s
- Global intensity correction: 12s
- SANLM denoising after intensity normalization (medium): 21s
- Fast Optimized Shooting registration 26s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.10) 11s
- Estimate local tissue thresholds (WM) 14s
- Estimate local tissue thresholds (GM) 21s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 29s
- 84s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 3s
- Ventricle detection 9s
- Blood vessel detection 7s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 20s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 53s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 27s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.07,0.980.05]
- 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 | 0.0813 0.0000 0.0813 | 32.0000
- 2 | 2.50 | 0.0788 0.0011 0.0799 | 29.4886
- 3 | 2.50 | 0.0781 0.0017 0.0798 | 26.9772
- 4 | 2.50 | 0.0778 0.0019 0.0796 | 24.6107
- 5 | 2.50 | 0.0775 0.0020 0.0795 | 22.6548
- 6 | 2.50 | 0.0772 0.0021 0.0793 | 20.6989
- 7 | 2.50 | 0.0770 0.0022 0.0792 | 18.9688
- 8 | 2.50 | 0.0767 0.0023 0.0790 | 17.4455
- 9 | 2.50 | 0.0764 0.0024 0.0788 | 15.9223
- 10 | 2.50 | 0.0761 0.0025 0.0786 | 14.6627
- 11 | 2.50 | 0.0758 0.0025 0.0784 | 13.4764
- 12 | 2.50 | 0.0756 0.0026 0.0782 | 12.3015
- 13 | 2.50 | 0.0752 0.0027 0.0779 | 11.3776
- 14 | 2.50 | 0.0750 0.0028 0.0777 | 10.4537
- 15 | 2.25 | 0.0735 0.0028 0.0763 | 9.5920
- 16 | 2.25 | 0.0707 0.0042 0.0749 | 8.8725
- 29 | 2.00 | 0.0715 0.0019 0.0734 | 3.3283
- 30 | 2.00 | 0.0657 0.0042 0.0699 | 3.1221
- 31 | 2.00 | 0.0637 0.0051 0.0689 | 2.9160
- 43 | 1.75 | 0.0626 0.0030 0.0656 | 1.5785
- 44 | 1.75 | 0.0586 0.0050 0.0637 | 1.5194
- 45 | 1.75 | 0.0573 0.0058 0.0631 | 1.4626
- 57 | 1.50 | 0.0558 0.0042 0.0600 | 1.0900
- 58 | 1.50 | 0.0529 0.0061 0.0589 | 1.0730
- 59 | 1.50 | 0.0519 0.0067 0.0586 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 153s
- Prepare output 8s
- 161s
- Jacobian determinant (RMS): 0.011 0.040 0.058 0.079 0.100 | 0.106906
- Template Matching: 0.081 0.212 0.191 0.172 0.156 | 0.155812
- Write result maps: 43s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 22s
- CSF distance: 12s
- PBT2x thickness: 35s
- 74s
- Create initial surface 66s
- Topology correction: 73s
- Surface refinement: 58s
- Reduction of surface collisions with optimization: 56s
- Spherical mapping with areal smoothing 64s
- Spherical registration 209s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 20s
- CSF distance: 12s
- PBT2x thickness: 35s
- 72s
- Create initial surface 65s
- Topology correction: 73s
- Surface refinement: 54s
- Reduction of surface collisions with optimization: 55s
- Spherical mapping with areal smoothing 90s
- Spherical registration 248s
- Final surface processing results:
- Average thickness (FS): 2.7016 0.6425 mm
- Surface intensity / position RMSE: 0.0699 / 0.0699
- Euler number / defect number / defect size: 26.0 / 14.5 / 1.03%
- Display thickness: /var/lib/condor/execute/dir_105506/ds/BNU_2/sub-0025954/ses-2/surf/lh.thickness.sub-0025954_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_105506/ds/BNU_2/sub-0025954/ses-2/surf/rh.thickness.sub-0025954_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_105506/ds/BNU_2/sub-0025954/ses-2/sub-0025954_ses-2_run-1_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1344s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 21s
- ROI estimation of 'neuromorphometrics' atlas 79s
- ROI estimation of 'lpba40' atlas 23s
- ROI estimation of 'hammers' atlas 52s
- ROI estimation of 'thalamus' atlas 4s
- ROI estimation of 'ibsr' atlas 19s
- ROI estimation of 'aal3' atlas 32s
- ROI estimation of 'mori' atlas 43s
- ROI estimation of 'anatomy3' atlas 59s
- ROI estimation of 'julichbrain' atlas 62s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 28s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 41s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 66s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 92s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s
- Write results 9s
- 632s
- Quality check: 9s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_105506/ds/BNU_2/sub-0025954/ses-2/report/catreport_sub-0025954_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 45 minute(s) and 45 second(s).
- Image Quality Rating (IQR): 79.56% (C+)
- GM volume (GMV): 50.86% (749.76 / 1474.30 ml)
- GM thickness (GMT): 2.70 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_105506/ds/BNU_2/sub-0025954/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_105506/ds/BNU_2/sub-0025954/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_105506/ds/BNU_2/sub-0025954/ses-2/label
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