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- CAT12.8.1 r2040: 1/1: ./ds/CMU_a/sub-0050646/sub-0050646_T1w.n
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- SANLM denoising (medium): 55s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 8s
- Initial correction 7s
- Refine background 3s
- Final correction 6s
- Final scaling 6s
- 39s
- Correct center-of-mass 4s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 85s
- SPM preprocessing 1 (estimate 2): 82s
- SPM preprocessing 2 (write):
- Write Segmentation 16s
- Update Segmentation 22s
- Update Skull-Stripping 41s
- Update probability maps 9s
- 88s
- Global intensity correction: 14s
- SANLM denoising after intensity normalization (medium): 35s
- Fast Optimized Shooting registration 40s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 20s
- Estimate local tissue thresholds (WM) 22s
- Estimate local tissue thresholds (GM) 36s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 50s
- 139s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 5s
- Ventricle detection 21s
- Blood vessel detection 15s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.09) 42s
- Manual stroke lesion detection 0s
- Closing of deep structures 3s
- Side alignment 5s
- Final corrections 4s
- 104s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 42s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 6s
- Level 1 cleanup (brain masking) 4s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 4s
- 16s
- 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 | 0.0871 0.0000 0.0871 | 32.0000
- 2 | 2.50 | 0.0850 0.0010 0.0860 | 29.4886
- 3 | 2.50 | 0.0843 0.0015 0.0859 | 26.9772
- 4 | 2.50 | 0.0840 0.0017 0.0857 | 24.6107
- 5 | 2.50 | 0.0838 0.0018 0.0856 | 22.6548
- 6 | 2.50 | 0.0836 0.0019 0.0855 | 20.6989
- 7 | 2.50 | 0.0833 0.0020 0.0853 | 18.9688
- 8 | 2.50 | 0.0831 0.0021 0.0852 | 17.4455
- 9 | 2.50 | 0.0828 0.0022 0.0850 | 15.9223
- 10 | 2.50 | 0.0826 0.0023 0.0848 | 14.6627
- 11 | 2.50 | 0.0823 0.0023 0.0847 | 13.4764
- 12 | 2.50 | 0.0820 0.0024 0.0844 | 12.3015
- 13 | 2.50 | 0.0817 0.0025 0.0843 | 11.3776
- 14 | 2.50 | 0.0815 0.0026 0.0840 | 10.4537
- 15 | 2.25 | 0.0838 0.0026 0.0865 | 9.5920
- 16 | 2.25 | 0.0806 0.0042 0.0848 | 8.8725
- 17 | 2.25 | 0.0792 0.0048 0.0840 | 8.1530
- 18 | 2.25 | 0.0782 0.0052 0.0834 | 7.5234
- 19 | 2.25 | 0.0775 0.0054 0.0829 | 6.9630
- 20 | 2.25 | 0.0769 0.0055 0.0823 | 6.4027
- 21 | 2.25 | 0.0762 0.0056 0.0818 | 5.9447
- 22 | 2.25 | 0.0757 0.0056 0.0813 | 5.5083
- 23 | 2.25 | 0.0752 0.0056 0.0808 | 5.0803
- 24 | 2.25 | 0.0747 0.0057 0.0804 | 4.7404
- 29 | 2.00 | 0.0772 0.0041 0.0813 | 3.3283
- 30 | 2.00 | 0.0734 0.0060 0.0793 | 3.1221
- 43 | 1.75 | 0.0726 0.0033 0.0759 | 1.5785
- 44 | 1.75 | 0.0671 0.0062 0.0733 | 1.5194
- 45 | 1.75 | 0.0653 0.0072 0.0725 | 1.4626
- 57 | 1.50 | 0.0643 0.0052 0.0695 | 1.0900
- 58 | 1.50 | 0.0605 0.0078 0.0682 | 1.0730
- 59 | 1.50 | 0.0592 0.0085 0.0677 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 242s
- Prepare output 13s
- 255s
- Jacobian determinant (RMS): 0.010 0.036 0.064 0.088 0.119 | 0.127048
- Template Matching: 0.087 0.224 0.220 0.196 0.178 | 0.177630
- Write result maps: 29s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 50s
- CSF distance: 24s
- PBT2x thickness: 69s
- 151s
- Create initial surface 116s
- Topology correction: 125s
- Surface refinement: 111s
- Reduction of surface collisions with optimization: 99s
- Spherical mapping with areal smoothing 116s
- Spherical registration 341s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 64s
- CSF distance: 23s
- PBT2x thickness: 67s
- 162s
- Create initial surface 114s
- Topology correction: 126s
- Surface refinement: 130s
- Reduction of surface collisions with optimization: 99s
- Spherical mapping with areal smoothing 118s
- Spherical registration 329s
- Final surface processing results:
- Average thickness (FS): 2.5946 0.6588 mm
- Surface intensity / position RMSE: 0.0711 / 0.0819
- Euler number / defect number / defect size: 30.0 / 18.0 / 1.08%
- Display thickness: /var/lib/condor/execute/dir_3346852/ds/CMU_a/sub-0050646/surf/lh.thickness.sub-0050646_T1w
- Display thickness: /var/lib/condor/execute/dir_3346852/ds/CMU_a/sub-0050646/surf/rh.thickness.sub-0050646_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3346852/ds/CMU_a/sub-0050646/sub-0050646_T1w.nii
- Surface ROI estimation: 11s
- Surface and thickness estimation takes: 2256s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 26s
- ROI estimation of 'lpba40' atlas 7s
- ROI estimation of 'hammers' atlas 18s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 6s
- ROI estimation of 'aal3' atlas 11s
- ROI estimation of 'mori' atlas 15s
- ROI estimation of 'anatomy3' atlas 23s
- ROI estimation of 'julichbrain' atlas 29s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 24s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 48s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 68s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s
- Write results 7s
- 303s
- Quality check: 13s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3346852/ds/CMU_a/sub-0050646/report/catreport_sub-0050646_T1w.pdf
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- CAT preprocessing takes 61 minute(s) and 53 second(s).
- Image Quality Rating (IQR): 79.37% (C+)
- GM volume (GMV): 47.78% (832.85 / 1742.93 ml)
- GM thickness (GMT): 2.59 0.66 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3346852/ds/CMU_a/sub-0050646/mri
- Reports are saved in /var/lib/condor/execute/dir_3346852/ds/CMU_a/sub-0050646/report
- Labels are saved in /var/lib/condor/execute/dir_3346852/ds/CMU_a/sub-0050646/label
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