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- CAT12.8.1 r1980: 1/1: ./execute/dir_24888/ds/sub-sc020/sub-sc020_T1w.n
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- SANLM denoising (medium): 10s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 8s
- Initial correction 5s
- Refine background 3s
- Final correction 4s
- Final scaling 5s
- 36s
- Correct center-of-mass 5s
- Affine registration 9s
- SPM preprocessing 1 (estimate 1 - TPM registration): 8s
- Use initial fine affine registration. 60s
- SPM preprocessing 1 (estimate 2): 58s
- SPM preprocessing 2 (write):
- Write Segmentation 15s
- Update Segmentation 17s
- Update Skull-Stripping 36s
- Update probability maps 8s
- 76s
- Global intensity correction: 14s
- SANLM denoising after intensity normalization (medium): 11s
- Fast Optimized Shooting registration 32s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.19) 12s
- Estimate local tissue thresholds (WM) 16s
- Estimate local tissue thresholds (GM) 20s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 16s
- 74s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 10s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.06) 23s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 59s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 29s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 10s
- 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 | 0.0828 0.0000 0.0828 | 32.0000
- 2 | 2.50 | 0.0801 0.0012 0.0813 | 29.4886
- 3 | 2.50 | 0.0793 0.0018 0.0811 | 26.9772
- 4 | 2.50 | 0.0789 0.0021 0.0810 | 24.6107
- 5 | 2.50 | 0.0786 0.0022 0.0808 | 22.6548
- 6 | 2.50 | 0.0783 0.0023 0.0806 | 20.6989
- 7 | 2.50 | 0.0780 0.0024 0.0804 | 18.9688
- 8 | 2.50 | 0.0777 0.0026 0.0802 | 17.4455
- 9 | 2.50 | 0.0774 0.0026 0.0800 | 15.9223
- 10 | 2.50 | 0.0770 0.0028 0.0798 | 14.6627
- 11 | 2.50 | 0.0767 0.0029 0.0796 | 13.4764
- 12 | 2.50 | 0.0763 0.0029 0.0793 | 12.3015
- 13 | 2.50 | 0.0760 0.0031 0.0790 | 11.3776
- 14 | 2.50 | 0.0756 0.0031 0.0788 | 10.4537
- 15 | 2.25 | 0.0752 0.0032 0.0785 | 9.5920
- 16 | 2.25 | 0.0719 0.0049 0.0768 | 8.8725
- 29 | 2.00 | 0.0728 0.0022 0.0751 | 3.3283
- 30 | 2.00 | 0.0660 0.0050 0.0710 | 3.1221
- 31 | 2.00 | 0.0637 0.0060 0.0698 | 2.9160
- 43 | 1.75 | 0.0624 0.0035 0.0659 | 1.5785
- 44 | 1.75 | 0.0581 0.0057 0.0638 | 1.5194
- 45 | 1.75 | 0.0566 0.0065 0.0631 | 1.4626
- 57 | 1.50 | 0.0550 0.0047 0.0598 | 1.0900
- 58 | 1.50 | 0.0521 0.0066 0.0587 | 1.0730
- 59 | 1.50 | 0.0512 0.0072 0.0584 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 161s
- Prepare output 9s
- 171s
- Jacobian determinant (RMS): 0.011 0.043 0.067 0.093 0.116 | 0.122845
- Template Matching: 0.083 0.216 0.191 0.170 0.154 | 0.153621
- Write result maps: 24s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 35s
- CSF distance: 12s
- PBT2x thickness: 37s
- 90s
- Create initial surface 72s
- Topology correction: 74s
- Surface refinement: 68s
- Reduction of surface collisions with optimization: 58s
- Spherical mapping with areal smoothing 76s
- Spherical registration 299s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 25s
- CSF distance: 12s
- PBT2x thickness: 38s
- 80s
- Create initial surface 72s
- Topology correction: 71s
- Surface refinement: 85s
- Reduction of surface collisions with optimization: 57s
- Spherical mapping with areal smoothing 75s
- Spherical registration 294s
- Final surface processing results:
- Average thickness (FS): 2.4200 0.5950 mm
- Surface intensity / position RMSE: 0.0636 / 0.0634
- Euler number / defect number / defect size: 8.0 / 8.5 / 0.08%
- Display thickness: /var/lib/condor/execute/dir_24888/ds/sub-sc020/surf/lh.thickness.sub-sc020_T1w
- Display thickness: /var/lib/condor/execute/dir_24888/ds/sub-sc020/surf/rh.thickness.sub-sc020_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_24888/ds/sub-sc020/sub-sc020_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1556s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 26s
- 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 11s
- ROI estimation of 'mori' atlas 15s
- ROI estimation of 'anatomy3' atlas 22s
- ROI estimation of 'julichbrain' atlas 28s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 48s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 72s
- Write results 73s
- 296s
- Quality check: 5s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_24888/ds/sub-sc020/report/catreport_sub-sc020_T1w.pdf
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- CAT preprocessing takes 44 minute(s) and 27 second(s).
- Image Quality Rating (IQR): 86.37% (B)
- GM volume (GMV): 46.35% (570.45 / 1230.87 ml)
- GM thickness (GMT): 2.42 0.60 mm
- Segmentations are saved in /var/lib/condor/execute/dir_24888/ds/sub-sc020/mri
- Reports are saved in /var/lib/condor/execute/dir_24888/ds/sub-sc020/report
- Labels are saved in /var/lib/condor/execute/dir_24888/ds/sub-sc020/label
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