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- CAT12.8.1 r2040: 1/1: ./sub-0026189/ses-2/sub-0026189_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 38s
- APP: Rough bias correction:
- Initialize 4s
- Estimate background 4s
- Initial correction 4s
- Refine background 2s
- Final correction 4s
- Final scaling 4s
- 27s
- Correct center-of-mass 3s
- Affine registration 8s
- SPM preprocessing 1 (estimate 1 - TPM registration): 58s
- SPM preprocessing 1 (estimate 2): 41s
- SPM preprocessing 2 (write):
- Write Segmentation 12s
- Update Segmentation 14s
- Update Skull-Stripping 31s
- Update probability maps 7s
- 64s
- Global intensity correction: 12s
- SANLM denoising after intensity normalization (medium): 18s
- Fast Optimized Shooting registration 25s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.15) 10s
- Estimate local tissue thresholds (WM) 13s
- Estimate local tissue thresholds (GM) 19s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 28s
- 77s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 2s
- Ventricle detection 9s
- Blood vessel detection 6s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.18) 14s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 4s
- 45s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 26s
- 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
- 8s
- 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 | 0.0908 0.0000 0.0908 | 32.0000
- 2 | 2.50 | 0.0882 0.0012 0.0894 | 29.4886
- 3 | 2.50 | 0.0874 0.0018 0.0892 | 26.9772
- 4 | 2.50 | 0.0870 0.0021 0.0891 | 24.6107
- 5 | 2.50 | 0.0867 0.0022 0.0889 | 22.6548
- 6 | 2.50 | 0.0864 0.0023 0.0887 | 20.6989
- 7 | 2.50 | 0.0861 0.0024 0.0886 | 18.9688
- 8 | 2.50 | 0.0858 0.0025 0.0884 | 17.4455
- 9 | 2.50 | 0.0855 0.0026 0.0881 | 15.9223
- 10 | 2.50 | 0.0852 0.0027 0.0879 | 14.6627
- 11 | 2.50 | 0.0849 0.0028 0.0877 | 13.4764
- 12 | 2.50 | 0.0845 0.0029 0.0875 | 12.3015
- 13 | 2.50 | 0.0842 0.0030 0.0872 | 11.3776
- 14 | 2.50 | 0.0839 0.0031 0.0870 | 10.4537
- 15 | 2.25 | 0.0841 0.0032 0.0873 | 9.5920
- 16 | 2.25 | 0.0807 0.0048 0.0856 | 8.8725
- 17 | 2.25 | 0.0794 0.0054 0.0848 | 8.1530
- 18 | 2.25 | 0.0785 0.0057 0.0842 | 7.5234
- 19 | 2.25 | 0.0779 0.0058 0.0837 | 6.9630
- 20 | 2.25 | 0.0773 0.0058 0.0832 | 6.4027
- 21 | 2.25 | 0.0768 0.0059 0.0827 | 5.9447
- 22 | 2.25 | 0.0763 0.0059 0.0822 | 5.5083
- 23 | 2.25 | 0.0758 0.0058 0.0817 | 5.0803
- 24 | 2.25 | 0.0754 0.0059 0.0812 | 4.7404
- 25 | 2.25 | 0.0749 0.0058 0.0808 | 4.4005
- 29 | 2.00 | 0.0767 0.0045 0.0813 | 3.3283
- 30 | 2.00 | 0.0734 0.0061 0.0795 | 3.1221
- 43 | 1.75 | 0.0722 0.0033 0.0756 | 1.5785
- 44 | 1.75 | 0.0671 0.0060 0.0731 | 1.5194
- 45 | 1.75 | 0.0654 0.0070 0.0724 | 1.4626
- 57 | 1.50 | 0.0639 0.0051 0.0689 | 1.0900
- 58 | 1.50 | 0.0604 0.0074 0.0678 | 1.0730
- 59 | 1.50 | 0.0592 0.0081 0.0673 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 147s
- Prepare output 7s
- 154s
- Jacobian determinant (RMS): 0.012 0.044 0.073 0.095 0.123 | 0.131076
- Template Matching: 0.091 0.225 0.220 0.196 0.178 | 0.177566
- Write result maps: 28s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 23s
- CSF distance: 12s
- PBT2x thickness: 31s
- 70s
- Create initial surface 59s
- Topology correction: 68s
- Surface refinement: 57s
- Reduction of surface collisions with optimization: 47s
- Spherical mapping with areal smoothing 65s
- Spherical registration 202s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 20s
- CSF distance: 11s
- PBT2x thickness: 30s
- 66s
- Create initial surface 54s
- Topology correction: 67s
- Surface refinement: 65s
- Reduction of surface collisions with optimization: 43s
- Spherical mapping with areal smoothing 73s
- Spherical registration 219s
- Final surface processing results:
- Average thickness (FS): 2.3660 0.6334 mm
- Surface intensity / position RMSE: 0.0627 / 0.0609
- Euler number / defect number / defect size: 18.0 / 15.5 / 0.48%
- Display thickness: /var/lib/condor/execute/dir_3556103/ds/UM/sub-0026189/ses-2/surf/lh.thickness.sub-0026189_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3556103/ds/UM/sub-0026189/ses-2/surf/rh.thickness.sub-0026189_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3556103/ds/UM/sub-0026189/ses-2/sub-0026189_ses-2_run-1_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1227s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 24s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 19s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 11s
- ROI estimation of 'mori' atlas 15s
- ROI estimation of 'anatomy3' atlas 21s
- ROI estimation of 'julichbrain' atlas 29s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 27s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 53s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 79s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s
- Write results 9s
- 327s
- Quality check: 9s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3556103/ds/UM/sub-0026189/ses-2/report/catreport_sub-0026189_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 37 minute(s) and 57 second(s).
- Image Quality Rating (IQR): 75.37% (C)
- GM volume (GMV): 45.14% (637.62 / 1412.54 ml)
- GM thickness (GMT): 2.37 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3556103/ds/UM/sub-0026189/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_3556103/ds/UM/sub-0026189/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_3556103/ds/UM/sub-0026189/ses-2/label
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