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- CAT12.8.1 r1980: 1/1: ./ds/sub-f5416zj/sub-f5416zj_ses-wave1bas_T1w.n
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- SANLM denoising (medium): 166s
- APP: Rough bias correction:
- Initialize 14s
- Estimate background 13s
- Initial correction 16s
- Refine background 7s
- Final correction 13s
- Final scaling 15s
- 93s
- Correct center-of-mass 6s
- Affine registration 20s
- SPM preprocessing 1 (estimate 1 - TPM registration): 164s
- SPM preprocessing 1 (estimate 2): 63s
- SPM preprocessing 2 (write):
- Write Segmentation 34s
- Update Segmentation 39s
- Update Skull-Stripping 91s
- Update probability maps 18s
- 183s
- Global intensity correction: 36s
- SANLM denoising after intensity normalization (medium): 29s
- Fast Optimized Shooting registration 51s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 10s
- Prepare partitions 4s
- Prepare segments (LASmod = 1.04) 34s
- Estimate local tissue thresholds (WM) 42s
- Estimate local tissue thresholds (GM) 60s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 59s
- 215s
- ROI segmentation (partitioning):
- Atlas -> subject space 15s
- Major structures 7s
- Ventricle detection 29s
- Blood vessel detection 25s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.11) 60s
- Manual stroke lesion detection 0s
- Closing of deep structures 4s
- Side alignment 8s
- Final corrections 9s
- 157s
- Blood vessel correction (BVCstr=0.50): 3s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 64s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 10s
- Level 1 cleanup (brain masking) 6s
- Level 2 cleanup (CSF correction) 3s
- Level 3 cleanup (CSF/WM PVE) 7s
- 26s
- 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 | 0.0871 0.0000 0.0871 | 32.0000
- 2 | 2.50 | 0.0830 0.0016 0.0846 | 29.4886
- 3 | 2.50 | 0.0817 0.0025 0.0842 | 26.9772
- 4 | 2.50 | 0.0811 0.0028 0.0840 | 24.6107
- 5 | 2.50 | 0.0807 0.0030 0.0837 | 22.6548
- 6 | 2.50 | 0.0802 0.0032 0.0834 | 20.6989
- 7 | 2.50 | 0.0798 0.0033 0.0831 | 18.9688
- 8 | 2.50 | 0.0794 0.0035 0.0828 | 17.4455
- 9 | 2.50 | 0.0789 0.0036 0.0825 | 15.9223
- 10 | 2.50 | 0.0784 0.0037 0.0822 | 14.6627
- 11 | 2.50 | 0.0780 0.0039 0.0818 | 13.4764
- 12 | 2.50 | 0.0775 0.0040 0.0814 | 12.3015
- 13 | 2.50 | 0.0770 0.0041 0.0811 | 11.3776
- 14 | 2.50 | 0.0765 0.0042 0.0807 | 10.4537
- 15 | 2.25 | 0.0759 0.0044 0.0803 | 9.5920
- 16 | 2.25 | 0.0721 0.0063 0.0783 | 8.8725
- 29 | 2.00 | 0.0720 0.0028 0.0748 | 3.3283
- 30 | 2.00 | 0.0645 0.0058 0.0703 | 3.1221
- 31 | 2.00 | 0.0619 0.0070 0.0689 | 2.9160
- 43 | 1.75 | 0.0602 0.0041 0.0642 | 1.5785
- 44 | 1.75 | 0.0559 0.0063 0.0622 | 1.5194
- 45 | 1.75 | 0.0545 0.0071 0.0616 | 1.4626
- 57 | 1.50 | 0.0525 0.0052 0.0578 | 1.0900
- 58 | 1.50 | 0.0497 0.0071 0.0568 | 1.0730
- 59 | 1.50 | 0.0488 0.0076 0.0565 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 199s
- Prepare output 20s
- 219s
- Jacobian determinant (RMS): 0.015 0.054 0.080 0.109 0.133 | 0.140263
- Template Matching: 0.087 0.216 0.186 0.163 0.147 | 0.146508
- Write result maps: 117s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 59s
- CSF distance: 19s
- PBT2x thickness: 54s
- 140s
- Create initial surface 94s
- Topology correction: 90s
- Surface refinement: 112s
- Reduction of surface collisions with optimization: 81s
- Spherical mapping with areal smoothing 96s
- Spherical registration 352s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 52s
- CSF distance: 17s
- PBT2x thickness: 50s
- 126s
- Create initial surface 103s
- Topology correction: 89s
- Surface refinement: 89s
- Reduction of surface collisions with optimization: 69s
- Spherical mapping with areal smoothing 104s
- Spherical registration 326s
- Final surface processing results:
- Average thickness (FS): 2.4918 0.6483 mm
- Surface intensity / position RMSE: 0.0612 / 0.0569
- Euler number / defect number / defect size: 8.0 / 5.5 / 0.10%
- Display thickness: /var/lib/condor/execute/dir_52325/ds/sub-f5416zj/surf/lh.thickness.sub-f5416zj_ses-wave1bas_T1w
- Display thickness: /var/lib/condor/execute/dir_52325/ds/sub-f5416zj/surf/rh.thickness.sub-f5416zj_ses-wave1bas_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_52325/ds/sub-f5416zj/sub-f5416zj_ses-wave1bas_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 2032s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 19s
- ROI estimation of 'neuromorphometrics' atlas 68s
- ROI estimation of 'lpba40' atlas 19s
- ROI estimation of 'hammers' atlas 44s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 16s
- ROI estimation of 'aal3' atlas 24s
- ROI estimation of 'mori' atlas 34s
- ROI estimation of 'anatomy3' atlas 48s
- ROI estimation of 'julichbrain' atlas 66s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 27s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 50s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 123s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 175s
- Write results 177s
- 717s
- Quality check: 11s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_52325/ds/sub-f5416zj/report/catreport_sub-f5416zj_ses-wave1bas_T1w.pdf
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- CAT preprocessing takes 76 minute(s) and 11 second(s).
- Image Quality Rating (IQR): 82.12% (B-)
- GM volume (GMV): 43.20% (606.90 / 1404.94 ml)
- GM thickness (GMT): 2.49 0.65 mm
- Segmentations are saved in /var/lib/condor/execute/dir_52325/ds/sub-f5416zj/mri
- Reports are saved in /var/lib/condor/execute/dir_52325/ds/sub-f5416zj/report
- Labels are saved in /var/lib/condor/execute/dir_52325/ds/sub-f5416zj/label
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