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- CAT12.8.1 r1980: 1/1: ./execute/dir_7856/ds/sub-sc017/sub-sc017_T1w.n
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- SANLM denoising (medium): 33s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 6s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 38s
- Correct center-of-mass 5s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 93s
- SPM preprocessing 1 (estimate 2): 59s
- SPM preprocessing 2 (write):
- Write Segmentation 17s
- Update Segmentation 20s
- Update Skull-Stripping 44s
- Update probability maps 10s
- 91s
- Global intensity correction: 17s
- SANLM denoising after intensity normalization (medium): 13s
- Fast Optimized Shooting registration 33s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.12) 15s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 23s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 9s
- 75s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 18s
- Blood vessel detection 9s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 26s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 75s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 34s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 3s
- 12s
- 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 | 0.0818 0.0000 0.0818 | 32.0000
- 2 | 2.50 | 0.0799 0.0010 0.0809 | 29.4886
- 3 | 2.50 | 0.0794 0.0014 0.0808 | 26.9772
- 4 | 2.50 | 0.0791 0.0016 0.0807 | 24.6107
- 5 | 2.50 | 0.0789 0.0017 0.0806 | 22.6548
- 6 | 2.50 | 0.0786 0.0018 0.0804 | 20.6989
- 7 | 2.50 | 0.0784 0.0019 0.0803 | 18.9688
- 8 | 2.50 | 0.0782 0.0019 0.0801 | 17.4455
- 9 | 2.50 | 0.0780 0.0020 0.0800 | 15.9223
- 10 | 2.50 | 0.0777 0.0021 0.0798 | 14.6627
- 11 | 2.50 | 0.0775 0.0022 0.0796 | 13.4764
- 12 | 2.50 | 0.0772 0.0022 0.0794 | 12.3015
- 13 | 2.50 | 0.0769 0.0023 0.0792 | 11.3776
- 14 | 2.50 | 0.0767 0.0024 0.0790 | 10.4537
- 15 | 2.25 | 0.0763 0.0024 0.0787 | 9.5920
- 16 | 2.25 | 0.0735 0.0038 0.0773 | 8.8725
- 29 | 2.00 | 0.0756 0.0017 0.0773 | 3.3283
- 30 | 2.00 | 0.0694 0.0042 0.0736 | 3.1221
- 31 | 2.00 | 0.0673 0.0052 0.0725 | 2.9160
- 43 | 1.75 | 0.0663 0.0030 0.0693 | 1.5785
- 44 | 1.75 | 0.0618 0.0054 0.0672 | 1.5194
- 45 | 1.75 | 0.0603 0.0062 0.0665 | 1.4626
- 57 | 1.50 | 0.0589 0.0045 0.0634 | 1.0900
- 58 | 1.50 | 0.0557 0.0066 0.0623 | 1.0730
- 59 | 1.50 | 0.0546 0.0073 0.0619 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 172s
- Prepare output 11s
- 183s
- Jacobian determinant (RMS): 0.010 0.034 0.052 0.077 0.102 | 0.109843
- Template Matching: 0.082 0.220 0.202 0.181 0.164 | 0.163854
- Write result maps: 25s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 36s
- CSF distance: 16s
- PBT2x thickness: 48s
- 107s
- Create initial surface 93s
- Topology correction: 108s
- Surface refinement: 105s
- Reduction of surface collisions with optimization: 87s
- Spherical mapping with areal smoothing 112s
- Spherical registration 310s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 30s
- CSF distance: 16s
- PBT2x thickness: 47s
- 99s
- Create initial surface 92s
- Topology correction: 102s
- Surface refinement: 118s
- Reduction of surface collisions with optimization: 87s
- Spherical mapping with areal smoothing 100s
- Spherical registration 308s
- Final surface processing results:
- Average thickness (FS): 2.5001 0.5845 mm
- Surface intensity / position RMSE: 0.0654 / 0.0696
- Euler number / defect number / defect size: 20.0 / 11.5 / 0.76%
- Display thickness: /var/lib/condor/execute/dir_7856/ds/sub-sc017/surf/lh.thickness.sub-sc017_T1w
- Display thickness: /var/lib/condor/execute/dir_7856/ds/sub-sc017/surf/rh.thickness.sub-sc017_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_7856/ds/sub-sc017/sub-sc017_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1929s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 32s
- ROI estimation of 'lpba40' atlas 9s
- ROI estimation of 'hammers' atlas 22s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 8s
- ROI estimation of 'aal3' atlas 13s
- ROI estimation of 'mori' atlas 18s
- ROI estimation of 'anatomy3' atlas 27s
- ROI estimation of 'julichbrain' atlas 35s
- 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 58s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 88s
- Write results 90s
- 360s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_7856/ds/sub-sc017/report/catreport_sub-sc017_T1w.pdf
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- CAT preprocessing takes 53 minute(s) and 5 second(s).
- Image Quality Rating (IQR): 80.56% (B-)
- GM volume (GMV): 49.75% (777.74 / 1563.34 ml)
- GM thickness (GMT): 2.50 0.58 mm
- Segmentations are saved in /var/lib/condor/execute/dir_7856/ds/sub-sc017/mri
- Reports are saved in /var/lib/condor/execute/dir_7856/ds/sub-sc017/report
- Labels are saved in /var/lib/condor/execute/dir_7856/ds/sub-sc017/label
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