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- CAT12.8.1 r1980: 1/1: ./execute/dir_2753110/ds/sub-72/sub-72_T1w.n
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- SANLM denoising (medium): 81s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 13s
- Initial correction 10s
- Refine background 5s
- Final correction 8s
- Final scaling 9s
- 60s
- Correct center-of-mass 6s
- Affine registration 11s
- SPM preprocessing 1 (estimate 1 - TPM registration): 85s
- SPM preprocessing 1 (estimate 2): 57s
- SPM preprocessing 2 (write):
- Write Segmentation 20s
- Update Segmentation 22s
- Update Skull-Stripping 50s
- Update probability maps 11s
- 103s
- Global intensity correction: 19s
- SANLM denoising after intensity normalization (medium): 9s
- Fast Optimized Shooting registration 42s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.00) 16s
- Estimate local tissue thresholds (WM) 26s
- Estimate local tissue thresholds (GM) 37s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 36s
- 127s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 15s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.48 > WMHCstr'=0.01) 27s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 77s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 37s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.07,0.980.05]
- Final cleanup (gcutstr=0.24):
- 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
- 13s
- 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 | 0.0879 0.0000 0.0879 | 32.0000
- 2 | 2.50 | 0.0847 0.0013 0.0860 | 29.4886
- 3 | 2.50 | 0.0837 0.0020 0.0857 | 26.9772
- 4 | 2.50 | 0.0832 0.0023 0.0855 | 24.6107
- 5 | 2.50 | 0.0828 0.0025 0.0853 | 22.6548
- 6 | 2.50 | 0.0824 0.0026 0.0851 | 20.6989
- 7 | 2.50 | 0.0821 0.0027 0.0848 | 18.9688
- 8 | 2.50 | 0.0817 0.0029 0.0846 | 17.4455
- 9 | 2.50 | 0.0814 0.0030 0.0843 | 15.9223
- 10 | 2.50 | 0.0810 0.0031 0.0840 | 14.6627
- 11 | 2.50 | 0.0806 0.0032 0.0838 | 13.4764
- 12 | 2.50 | 0.0802 0.0033 0.0834 | 12.3015
- 13 | 2.50 | 0.0797 0.0034 0.0831 | 11.3776
- 14 | 2.50 | 0.0794 0.0035 0.0828 | 10.4537
- 15 | 2.25 | 0.0797 0.0036 0.0833 | 9.5920
- 16 | 2.25 | 0.0763 0.0053 0.0815 | 8.8725
- 17 | 2.25 | 0.0748 0.0059 0.0807 | 8.1530
- 29 | 2.00 | 0.0769 0.0027 0.0796 | 3.3283
- 30 | 2.00 | 0.0704 0.0054 0.0758 | 3.1221
- 31 | 2.00 | 0.0681 0.0065 0.0746 | 2.9160
- 43 | 1.75 | 0.0670 0.0038 0.0708 | 1.5785
- 44 | 1.75 | 0.0624 0.0062 0.0686 | 1.5194
- 45 | 1.75 | 0.0608 0.0070 0.0679 | 1.4626
- 57 | 1.50 | 0.0594 0.0052 0.0646 | 1.0900
- 58 | 1.50 | 0.0562 0.0072 0.0635 | 1.0730
- 59 | 1.50 | 0.0552 0.0079 0.0631 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 202s
- Prepare output 13s
- 216s
- Jacobian determinant (RMS): 0.011 0.044 0.068 0.098 0.126 | 0.134389
- Template Matching: 0.088 0.224 0.204 0.183 0.166 | 0.165505
- Write result maps: 28s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 36s
- CSF distance: 20s
- PBT2x thickness: 59s
- 122s
- Create initial surface 104s
- Topology correction: 109s
- Surface refinement: 118s
- Reduction of surface collisions with optimization: 76s
- Spherical mapping with areal smoothing 97s
- Spherical registration 339s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 39s
- CSF distance: 19s
- PBT2x thickness: 56s
- 121s
- Create initial surface 98s
- Topology correction: 106s
- Surface refinement: 90s
- Reduction of surface collisions with optimization: 72s
- Spherical mapping with areal smoothing 90s
- Spherical registration 336s
- Final surface processing results:
- Average thickness (FS): 2.5675 0.6185 mm
- Surface intensity / position RMSE: 0.0655 / 0.0651
- Euler number / defect number / defect size: 8.0 / 6.5 / 0.18%
- Display thickness: /var/lib/condor/execute/dir_2753110/ds/sub-72/surf/lh.thickness.sub-72_T1w
- Display thickness: /var/lib/condor/execute/dir_2753110/ds/sub-72/surf/rh.thickness.sub-72_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2753110/ds/sub-72/sub-72_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 1987s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 10s
- ROI estimation of 'neuromorphometrics' atlas 34s
- ROI estimation of 'lpba40' atlas 10s
- ROI estimation of 'hammers' atlas 23s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 8s
- ROI estimation of 'aal3' atlas 14s
- ROI estimation of 'mori' atlas 19s
- ROI estimation of 'anatomy3' atlas 28s
- ROI estimation of 'julichbrain' atlas 36s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 14s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 25s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 57s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 83s
- Write results 84s
- 363s
- Quality check: 5s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2753110/ds/sub-72/report/catreport_sub-72_T1w.pdf
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- CAT preprocessing takes 57 minute(s) and 5 second(s).
- Image Quality Rating (IQR): 82.15% (B-)
- GM volume (GMV): 47.52% (664.99 / 1399.46 ml)
- GM thickness (GMT): 2.57 0.62 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2753110/ds/sub-72/mri
- Reports are saved in /var/lib/condor/execute/dir_2753110/ds/sub-72/report
- Labels are saved in /var/lib/condor/execute/dir_2753110/ds/sub-72/label
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