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- CAT12.8.1 r1980: 1/1: ./execute/dir_9674/ds/sub-sc016/sub-sc016_T1w.n
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- SANLM denoising (medium): 41s
- APP: Rough bias correction:
- Initialize 9s
- Estimate background 9s
- Initial correction 8s
- Refine background 4s
- Final correction 6s
- Final scaling 6s
- 52s
- Correct center-of-mass 3s
- Affine registration 13s
- SPM preprocessing 1 (estimate 1 - TPM registration): 105s
- SPM preprocessing 1 (estimate 2): 78s
- SPM preprocessing 2 (write):
- Write Segmentation 24s
- Update Segmentation 25s
- Update Skull-Stripping 57s
- Update probability maps 12s
- 118s
- Global intensity correction: 22s
- SANLM denoising after intensity normalization (medium): 13s
- Fast Optimized Shooting registration 44s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.08) 20s
- Estimate local tissue thresholds (WM) 26s
- Estimate local tissue thresholds (GM) 37s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 13s
- 108s
- ROI segmentation (partitioning):
- Atlas -> subject space 10s
- Major structures 5s
- Ventricle detection 15s
- Blood vessel detection 14s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.15) 31s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 5s
- Final corrections 6s
- 87s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 40s
- AMAP peaks: [CSF,GM,WM] = [0.360.07,0.680.07,0.980.04]
- 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) 3s
- 14s
- 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 | 0.0855 0.0000 0.0855 | 32.0000
- 2 | 2.50 | 0.0831 0.0011 0.0843 | 29.4886
- 3 | 2.50 | 0.0825 0.0017 0.0841 | 26.9772
- 4 | 2.50 | 0.0821 0.0019 0.0840 | 24.6107
- 5 | 2.50 | 0.0819 0.0020 0.0838 | 22.6548
- 6 | 2.50 | 0.0816 0.0021 0.0837 | 20.6989
- 7 | 2.50 | 0.0814 0.0021 0.0835 | 18.9688
- 8 | 2.50 | 0.0811 0.0022 0.0833 | 17.4455
- 9 | 2.50 | 0.0809 0.0023 0.0831 | 15.9223
- 10 | 2.50 | 0.0806 0.0024 0.0830 | 14.6627
- 11 | 2.50 | 0.0803 0.0024 0.0827 | 13.4764
- 12 | 2.50 | 0.0800 0.0025 0.0825 | 12.3015
- 13 | 2.50 | 0.0797 0.0026 0.0823 | 11.3776
- 14 | 2.50 | 0.0794 0.0026 0.0821 | 10.4537
- 15 | 2.25 | 0.0773 0.0027 0.0800 | 9.5920
- 16 | 2.25 | 0.0744 0.0041 0.0785 | 8.8725
- 29 | 2.00 | 0.0749 0.0018 0.0767 | 3.3283
- 30 | 2.00 | 0.0690 0.0043 0.0733 | 3.1221
- 31 | 2.00 | 0.0671 0.0052 0.0724 | 2.9160
- 43 | 1.75 | 0.0659 0.0030 0.0689 | 1.5785
- 44 | 1.75 | 0.0617 0.0053 0.0670 | 1.5194
- 45 | 1.75 | 0.0604 0.0060 0.0664 | 1.4626
- 57 | 1.50 | 0.0586 0.0043 0.0629 | 1.0900
- 58 | 1.50 | 0.0556 0.0063 0.0619 | 1.0730
- 59 | 1.50 | 0.0546 0.0069 0.0616 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 207s
- Prepare output 14s
- 221s
- Jacobian determinant (RMS): 0.010 0.038 0.059 0.086 0.111 | 0.118559
- Template Matching: 0.086 0.223 0.201 0.181 0.164 | 0.163950
- Write result maps: 68s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 55s
- CSF distance: 23s
- PBT2x thickness: 68s
- 155s
- Create initial surface 117s
- Topology correction: 119s
- Surface refinement: 132s
- Reduction of surface collisions with optimization: 89s
- Spherical mapping with areal smoothing 116s
- Spherical registration 338s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 44s
- CSF distance: 22s
- PBT2x thickness: 62s
- 136s
- Create initial surface 158s
- Topology correction: 133s
- Surface refinement: 157s
- Reduction of surface collisions with optimization: 82s
- Spherical mapping with areal smoothing 103s
- Spherical registration 339s
- Final surface processing results:
- Average thickness (FS): 2.6557 0.6384 mm
- Surface intensity / position RMSE: 0.0574 / 0.0552
- Euler number / defect number / defect size: 6.0 / 8.5 / 0.06%
- Display thickness: /var/lib/condor/execute/dir_9674/ds/sub-sc016/surf/lh.thickness.sub-sc016_T1w
- Display thickness: /var/lib/condor/execute/dir_9674/ds/sub-sc016/surf/rh.thickness.sub-sc016_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_9674/ds/sub-sc016/sub-sc016_T1w.nii
- Surface ROI estimation: 119s
- Surface and thickness estimation takes: 2489s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 14s
- ROI estimation of 'neuromorphometrics' atlas 48s
- ROI estimation of 'lpba40' atlas 15s
- ROI estimation of 'hammers' atlas 36s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 13s
- ROI estimation of 'aal3' atlas 22s
- ROI estimation of 'mori' atlas 32s
- ROI estimation of 'anatomy3' atlas 46s
- ROI estimation of 'julichbrain' atlas 58s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 24s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 43s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 95s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 136s
- Write results 137s
- 585s
- Quality check: 7s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_9674/ds/sub-sc016/report/catreport_sub-sc016_T1w.pdf
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- CAT preprocessing takes 70 minute(s) and 18 second(s).
- Image Quality Rating (IQR): 84.39% (B)
- GM volume (GMV): 46.94% (744.51 / 1586.07 ml)
- GM thickness (GMT): 2.66 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_9674/ds/sub-sc016/mri
- Reports are saved in /var/lib/condor/execute/dir_9674/ds/sub-sc016/report
- Labels are saved in /var/lib/condor/execute/dir_9674/ds/sub-sc016/label
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