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- CAT12.8.1 r1980: 1/1: ./execute/dir_29720/ds/sub-12/sub-12_ses-01_T1w.n
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- SANLM denoising (medium): 59s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 4s
- Initial correction 5s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 32s
- Correct center-of-mass 2s
- Affine registration 8s
- SPM preprocessing 1 (estimate 1 - TPM registration): 71s
- SPM preprocessing 1 (estimate 2): 42s
- SPM preprocessing 2 (write):
- Write Segmentation 12s
- Update Segmentation 14s
- Update Skull-Stripping 31s
- Update probability maps 6s
- 64s
- Global intensity correction: 11s
- SANLM denoising after intensity normalization (medium): 7s
- Fast Optimized Shooting registration 25s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 10s
- Estimate local tissue thresholds (WM) 13s
- Estimate local tissue thresholds (GM) 18s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 17s
- 66s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 3s
- Ventricle detection 10s
- Blood vessel detection 7s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.13) 22s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 3s
- 55s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 21s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.670.07,0.980.05]
- 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
- 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 | 0.0861 0.0000 0.0861 | 32.0000
- 2 | 2.50 | 0.0838 0.0011 0.0849 | 29.4886
- 3 | 2.50 | 0.0831 0.0016 0.0848 | 26.9772
- 4 | 2.50 | 0.0828 0.0018 0.0846 | 24.6107
- 5 | 2.50 | 0.0825 0.0020 0.0845 | 22.6548
- 6 | 2.50 | 0.0823 0.0021 0.0843 | 20.6989
- 7 | 2.50 | 0.0820 0.0022 0.0842 | 18.9688
- 8 | 2.50 | 0.0817 0.0023 0.0840 | 17.4455
- 9 | 2.50 | 0.0815 0.0023 0.0838 | 15.9223
- 10 | 2.50 | 0.0812 0.0025 0.0836 | 14.6627
- 11 | 2.50 | 0.0809 0.0025 0.0834 | 13.4764
- 12 | 2.50 | 0.0806 0.0026 0.0832 | 12.3015
- 13 | 2.50 | 0.0802 0.0027 0.0830 | 11.3776
- 14 | 2.50 | 0.0799 0.0028 0.0827 | 10.4537
- 15 | 2.25 | 0.0809 0.0028 0.0837 | 9.5920
- 16 | 2.25 | 0.0779 0.0043 0.0822 | 8.8725
- 17 | 2.25 | 0.0766 0.0049 0.0815 | 8.1530
- 18 | 2.25 | 0.0758 0.0052 0.0810 | 7.5234
- 19 | 2.25 | 0.0752 0.0053 0.0805 | 6.9630
- 20 | 2.25 | 0.0746 0.0054 0.0800 | 6.4027
- 29 | 2.00 | 0.0773 0.0030 0.0803 | 3.3283
- 30 | 2.00 | 0.0723 0.0053 0.0775 | 3.1221
- 31 | 2.00 | 0.0704 0.0062 0.0766 | 2.9160
- 43 | 1.75 | 0.0697 0.0035 0.0732 | 1.5785
- 44 | 1.75 | 0.0647 0.0062 0.0709 | 1.5194
- 45 | 1.75 | 0.0631 0.0071 0.0702 | 1.4626
- 57 | 1.50 | 0.0619 0.0051 0.0670 | 1.0900
- 58 | 1.50 | 0.0582 0.0075 0.0658 | 1.0730
- 59 | 1.50 | 0.0570 0.0083 0.0653 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 166s
- Prepare output 8s
- 174s
- Jacobian determinant (RMS): 0.010 0.038 0.061 0.085 0.111 | 0.118315
- Template Matching: 0.086 0.224 0.211 0.189 0.171 | 0.171059
- Write result maps: 24s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 35s
- CSF distance: 15s
- PBT2x thickness: 42s
- 98s
- Create initial surface 72s
- Topology correction: 80s
- Surface refinement: 63s
- Reduction of surface collisions with optimization: 51s
- Spherical mapping with areal smoothing 69s
- Spherical registration 189s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 46s
- CSF distance: 14s
- PBT2x thickness: 41s
- 107s
- Create initial surface 64s
- Topology correction: 75s
- Surface refinement: 70s
- Reduction of surface collisions with optimization: 59s
- Spherical mapping with areal smoothing 73s
- Spherical registration 179s
- Final surface processing results:
- Average thickness (FS): 2.5386 0.6711 mm
- Surface intensity / position RMSE: 0.0732 / 0.1011
- Euler number / defect number / defect size: 16.0 / 11.5 / 1.44%
- Display thickness: /var/lib/condor/execute/dir_29720/ds/sub-12/surf/lh.thickness.sub-12_ses-01_T1w
- Display thickness: /var/lib/condor/execute/dir_29720/ds/sub-12/surf/rh.thickness.sub-12_ses-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_29720/ds/sub-12/sub-12_ses-01_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1329s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 10s
- ROI estimation of 'neuromorphometrics' atlas 39s
- ROI estimation of 'lpba40' atlas 11s
- ROI estimation of 'hammers' atlas 27s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 9s
- ROI estimation of 'aal3' atlas 15s
- ROI estimation of 'mori' atlas 21s
- ROI estimation of 'anatomy3' atlas 31s
- ROI estimation of 'julichbrain' atlas 40s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 18s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 68s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 102s
- Write results 102s
- 409s
- Quality check: 4s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_29720/ds/sub-12/report/catreport_sub-12_ses-01_T1w.pdf
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- CAT preprocessing takes 41 minute(s) and 12 second(s).
- Image Quality Rating (IQR): 82.13% (B-)
- GM volume (GMV): 47.37% (808.56 / 1706.95 ml)
- GM thickness (GMT): 2.54 0.67 mm
- Segmentations are saved in /var/lib/condor/execute/dir_29720/ds/sub-12/mri
- Reports are saved in /var/lib/condor/execute/dir_29720/ds/sub-12/report
- Labels are saved in /var/lib/condor/execute/dir_29720/ds/sub-12/label
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