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- CAT12.8.1 r2040: 1/1: ./sub-0027274/ses-2/sub-0027274_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 70s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 6s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 36s
- Correct center-of-mass 4s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 81s
- SPM preprocessing 1 (estimate 2): 59s
- SPM preprocessing 2 (write):
- Write Segmentation 16s
- Update Segmentation 20s
- Update Skull-Stripping 40s
- Update probability maps 8s
- 83s
- Global intensity correction: 14s
- SANLM denoising after intensity normalization (medium): 33s
- Fast Optimized Shooting registration 31s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.00) 16s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 29s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 40s
- 113s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 4s
- Ventricle detection 18s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 28s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 4s
- 79s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 38s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 5s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 3s
- 12s
- 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 | 0.0861 0.0000 0.0861 | 32.0000
- 2 | 2.50 | 0.0835 0.0012 0.0847 | 29.4886
- 3 | 2.50 | 0.0827 0.0018 0.0845 | 26.9772
- 4 | 2.50 | 0.0823 0.0020 0.0843 | 24.6107
- 5 | 2.50 | 0.0820 0.0022 0.0842 | 22.6548
- 6 | 2.50 | 0.0817 0.0023 0.0840 | 20.6989
- 7 | 2.50 | 0.0815 0.0024 0.0838 | 18.9688
- 8 | 2.50 | 0.0812 0.0025 0.0836 | 17.4455
- 9 | 2.50 | 0.0809 0.0025 0.0834 | 15.9223
- 10 | 2.50 | 0.0806 0.0026 0.0832 | 14.6627
- 11 | 2.50 | 0.0803 0.0027 0.0830 | 13.4764
- 12 | 2.50 | 0.0800 0.0027 0.0827 | 12.3015
- 13 | 2.50 | 0.0797 0.0028 0.0825 | 11.3776
- 14 | 2.50 | 0.0794 0.0029 0.0822 | 10.4537
- 15 | 2.25 | 0.0792 0.0029 0.0822 | 9.5920
- 16 | 2.25 | 0.0762 0.0044 0.0806 | 8.8725
- 17 | 2.25 | 0.0750 0.0049 0.0799 | 8.1530
- 18 | 2.25 | 0.0743 0.0051 0.0794 | 7.5234
- 29 | 2.00 | 0.0764 0.0024 0.0788 | 3.3283
- 30 | 2.00 | 0.0713 0.0046 0.0759 | 3.1221
- 31 | 2.00 | 0.0696 0.0054 0.0750 | 2.9160
- 43 | 1.75 | 0.0690 0.0031 0.0721 | 1.5785
- 44 | 1.75 | 0.0648 0.0053 0.0701 | 1.5194
- 45 | 1.75 | 0.0634 0.0061 0.0695 | 1.4626
- 57 | 1.50 | 0.0624 0.0044 0.0668 | 1.0900
- 58 | 1.50 | 0.0591 0.0066 0.0658 | 1.0730
- 59 | 1.50 | 0.0580 0.0073 0.0653 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 182s
- Prepare output 11s
- 193s
- Jacobian determinant (RMS): 0.010 0.035 0.054 0.076 0.102 | 0.107802
- Template Matching: 0.086 0.223 0.209 0.190 0.174 | 0.174126
- Write result maps: 31s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 37s
- CSF distance: 19s
- PBT2x thickness: 57s
- 120s
- Create initial surface 108s
- Topology correction: 114s
- Surface refinement: 91s
- Reduction of surface collisions with optimization: 101s
- Spherical mapping with areal smoothing 99s
- Spherical registration 282s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 40s
- CSF distance: 19s
- PBT2x thickness: 55s
- 121s
- Create initial surface 108s
- Topology correction: 113s
- Surface refinement: 143s
- Reduction of surface collisions with optimization: 98s
- Spherical mapping with areal smoothing 117s
- Spherical registration 357s
- Final surface processing results:
- Average thickness (FS): 2.6129 0.6413 mm
- Surface intensity / position RMSE: 0.0740 / 0.0726
- Euler number / defect number / defect size: 16.0 / 15.0 / 0.35%
- Display thickness: /var/lib/condor/execute/dir_2614931/ds/UWM/sub-0027274/ses-2/surf/lh.thickness.sub-0027274_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2614931/ds/UWM/sub-0027274/ses-2/surf/rh.thickness.sub-0027274_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2614931/ds/UWM/sub-0027274/ses-2/sub-0027274_ses-2_run-1_T1w.nii
- Surface ROI estimation: 14s
- Surface and thickness estimation takes: 2095s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 13s
- ROI estimation of 'neuromorphometrics' atlas 40s
- ROI estimation of 'lpba40' atlas 11s
- ROI estimation of 'hammers' atlas 30s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 9s
- ROI estimation of 'aal3' atlas 14s
- ROI estimation of 'mori' atlas 20s
- ROI estimation of 'anatomy3' atlas 29s
- ROI estimation of 'julichbrain' atlas 36s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 14s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 26s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 55s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 83s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s
- Write results 8s
- 392s
- Quality check: 12s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2614931/ds/UWM/sub-0027274/ses-2/report/catreport_sub-0027274_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 57 minute(s) and 54 second(s).
- Image Quality Rating (IQR): 80.44% (B-)
- GM volume (GMV): 50.69% (898.20 / 1772.02 ml)
- GM thickness (GMT): 2.61 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2614931/ds/UWM/sub-0027274/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_2614931/ds/UWM/sub-0027274/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_2614931/ds/UWM/sub-0027274/ses-2/label
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