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- CAT12.8.1 r1980: 1/1: ./execute/dir_7214/ds/sub-sc017/sub-sc017_T1w.n
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- SANLM denoising (medium): 29s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 7s
- Initial correction 7s
- Refine background 3s
- Final correction 5s
- Final scaling 6s
- 39s
- Correct center-of-mass 2s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 73s
- SPM preprocessing 1 (estimate 2): 63s
- SPM preprocessing 2 (write):
- Write Segmentation 15s
- Update Segmentation 21s
- Update Skull-Stripping 41s
- Update probability maps 8s
- 85s
- Global intensity correction: 15s
- SANLM denoising after intensity normalization (medium): 13s
- Fast Optimized Shooting registration 30s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.12) 17s
- Estimate local tissue thresholds (WM) 19s
- Estimate local tissue thresholds (GM) 26s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 20s
- 93s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 18s
- Blood vessel detection 12s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.06) 37s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 5s
- Final corrections 4s
- 90s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 38s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.04]
- 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
- 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 | 0.0861 0.0000 0.0861 | 32.0000
- 2 | 2.50 | 0.0833 0.0012 0.0846 | 29.4886
- 3 | 2.50 | 0.0825 0.0019 0.0844 | 26.9772
- 4 | 2.50 | 0.0821 0.0021 0.0842 | 24.6107
- 5 | 2.50 | 0.0818 0.0022 0.0841 | 22.6548
- 6 | 2.50 | 0.0815 0.0023 0.0839 | 20.6989
- 7 | 2.50 | 0.0813 0.0024 0.0837 | 18.9688
- 8 | 2.50 | 0.0809 0.0025 0.0835 | 17.4455
- 9 | 2.50 | 0.0806 0.0026 0.0832 | 15.9223
- 10 | 2.50 | 0.0803 0.0027 0.0830 | 14.6627
- 11 | 2.50 | 0.0800 0.0028 0.0828 | 13.4764
- 12 | 2.50 | 0.0796 0.0029 0.0825 | 12.3015
- 13 | 2.50 | 0.0792 0.0030 0.0822 | 11.3776
- 14 | 2.50 | 0.0789 0.0030 0.0819 | 10.4537
- 15 | 2.25 | 0.0798 0.0031 0.0830 | 9.5920
- 16 | 2.25 | 0.0764 0.0048 0.0811 | 8.8725
- 17 | 2.25 | 0.0750 0.0054 0.0804 | 8.1530
- 29 | 2.00 | 0.0777 0.0025 0.0802 | 3.3283
- 30 | 2.00 | 0.0714 0.0051 0.0765 | 3.1221
- 31 | 2.00 | 0.0692 0.0061 0.0754 | 2.9160
- 43 | 1.75 | 0.0687 0.0035 0.0722 | 1.5785
- 44 | 1.75 | 0.0639 0.0061 0.0699 | 1.5194
- 45 | 1.75 | 0.0623 0.0070 0.0692 | 1.4626
- 57 | 1.50 | 0.0611 0.0051 0.0662 | 1.0900
- 58 | 1.50 | 0.0576 0.0074 0.0650 | 1.0730
- 59 | 1.50 | 0.0564 0.0081 0.0646 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 163s
- Prepare output 10s
- 173s
- Jacobian determinant (RMS): 0.011 0.039 0.061 0.087 0.113 | 0.119495
- Template Matching: 0.086 0.225 0.208 0.187 0.169 | 0.169258
- Write result maps: 21s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 52s
- CSF distance: 23s
- PBT2x thickness: 57s
- 140s
- Create initial surface 114s
- Topology correction: 128s
- Surface refinement: 175s
- Reduction of surface collisions with optimization: 116s
- Spherical mapping with areal smoothing 139s
- Spherical registration 301s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 45s
- CSF distance: 24s
- PBT2x thickness: 58s
- 135s
- Create initial surface 114s
- Topology correction: 132s
- Surface refinement: 143s
- Reduction of surface collisions with optimization: 121s
- Spherical mapping with areal smoothing 153s
- Spherical registration 294s
- Final surface processing results:
- Average thickness (FS): 2.4353 0.6289 mm
- Surface intensity / position RMSE: 0.0723 / 0.0974
- Euler number / defect number / defect size: 28.0 / 18.0 / 1.57%
- Display thickness: /var/lib/condor/execute/dir_7214/ds/sub-sc017/surf/lh.thickness.sub-sc017_T1w
- Display thickness: /var/lib/condor/execute/dir_7214/ds/sub-sc017/surf/rh.thickness.sub-sc017_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_7214/ds/sub-sc017/sub-sc017_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 2313s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 25s
- 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 10s
- ROI estimation of 'mori' atlas 15s
- ROI estimation of 'anatomy3' atlas 22s
- ROI estimation of 'julichbrain' atlas 29s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 22s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 48s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 71s
- Write results 72s
- 296s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_7214/ds/sub-sc017/report/catreport_sub-sc017_T1w.pdf
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- CAT preprocessing takes 58 minute(s) and 45 second(s).
- Image Quality Rating (IQR): 84.31% (B)
- GM volume (GMV): 45.56% (889.86 / 1953.28 ml)
- GM thickness (GMT): 2.44 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_7214/ds/sub-sc017/mri
- Reports are saved in /var/lib/condor/execute/dir_7214/ds/sub-sc017/report
- Labels are saved in /var/lib/condor/execute/dir_7214/ds/sub-sc017/label
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