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- CAT12.8.1 r1980: 1/1: ./dir_14707/ds/sub-022/sub-022_ses-t0_T1w.n
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- SANLM denoising (medium): 10s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 5s
- Initial correction 5s
- Refine background 2s
- Final correction 4s
- Final scaling 5s
- 31s
- Correct center-of-mass 2s
- Affine registration 8s
- SPM preprocessing 1 (estimate 1 - TPM registration): 57s
- SPM preprocessing 1 (estimate 2): 44s
- SPM preprocessing 2 (write):
- Write Segmentation 12s
- Update Segmentation 16s
- Update Skull-Stripping 33s
- Update probability maps 6s
- 68s
- Global intensity correction: 12s
- SANLM denoising after intensity normalization (medium): 6s
- Fast Optimized Shooting registration 25s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 1s
- Prepare segments (LASmod = 1.10) 13s
- Estimate local tissue thresholds (WM) 14s
- Estimate local tissue thresholds (GM) 18s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 13s
- 66s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 3s
- Ventricle detection 12s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.06) 24s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 3s
- 61s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 31s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 2s
- 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 | 0.0830 0.0000 0.0830 | 32.0000
- 2 | 2.50 | 0.0805 0.0011 0.0816 | 29.4886
- 3 | 2.50 | 0.0797 0.0017 0.0815 | 26.9772
- 4 | 2.50 | 0.0794 0.0020 0.0813 | 24.6107
- 5 | 2.50 | 0.0791 0.0021 0.0812 | 22.6548
- 6 | 2.50 | 0.0788 0.0022 0.0810 | 20.6989
- 7 | 2.50 | 0.0786 0.0023 0.0808 | 18.9688
- 8 | 2.50 | 0.0783 0.0024 0.0807 | 17.4455
- 9 | 2.50 | 0.0780 0.0024 0.0804 | 15.9223
- 10 | 2.50 | 0.0777 0.0025 0.0802 | 14.6627
- 11 | 2.50 | 0.0774 0.0026 0.0800 | 13.4764
- 12 | 2.50 | 0.0771 0.0027 0.0798 | 12.3015
- 13 | 2.50 | 0.0768 0.0028 0.0795 | 11.3776
- 14 | 2.50 | 0.0765 0.0028 0.0793 | 10.4537
- 15 | 2.25 | 0.0753 0.0029 0.0782 | 9.5920
- 16 | 2.25 | 0.0724 0.0043 0.0767 | 8.8725
- 29 | 2.00 | 0.0737 0.0019 0.0756 | 3.3283
- 30 | 2.00 | 0.0678 0.0043 0.0721 | 3.1221
- 31 | 2.00 | 0.0659 0.0053 0.0711 | 2.9160
- 43 | 1.75 | 0.0651 0.0030 0.0681 | 1.5785
- 44 | 1.75 | 0.0609 0.0052 0.0661 | 1.5194
- 45 | 1.75 | 0.0594 0.0060 0.0655 | 1.4626
- 57 | 1.50 | 0.0581 0.0044 0.0625 | 1.0900
- 58 | 1.50 | 0.0549 0.0064 0.0614 | 1.0730
- 59 | 1.50 | 0.0539 0.0071 0.0610 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 131s
- Prepare output 8s
- 139s
- Jacobian determinant (RMS): 0.011 0.039 0.057 0.081 0.105 | 0.111812
- Template Matching: 0.083 0.217 0.198 0.178 0.162 | 0.161594
- Write result maps: 18s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 34s
- CSF distance: 14s
- PBT2x thickness: 40s
- 94s
- Create initial surface 79s
- Topology correction: 91s
- Surface refinement: 79s
- Reduction of surface collisions with optimization: 67s
- Spherical mapping with areal smoothing 72s
- Spherical registration 246s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 38s
- CSF distance: 14s
- PBT2x thickness: 40s
- 97s
- Create initial surface 79s
- Topology correction: 91s
- Surface refinement: 104s
- Reduction of surface collisions with optimization: 70s
- Spherical mapping with areal smoothing 73s
- Spherical registration 243s
- Final surface processing results:
- Average thickness (FS): 2.4362 0.6731 mm
- Surface intensity / position RMSE: 0.0765 / 0.0844
- Euler number / defect number / defect size: 86.0 / 48.0 / 2.45%
- Display thickness: /var/lib/condor/execute/dir_14707/ds/sub-022/surf/lh.thickness.sub-022_ses-t0_T1w
- Display thickness: /var/lib/condor/execute/dir_14707/ds/sub-022/surf/rh.thickness.sub-022_ses-t0_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_14707/ds/sub-022/sub-022_ses-t0_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1561s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 6s
- ROI estimation of 'neuromorphometrics' atlas 21s
- ROI estimation of 'lpba40' atlas 6s
- ROI estimation of 'hammers' atlas 15s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 5s
- ROI estimation of 'aal3' atlas 9s
- ROI estimation of 'mori' atlas 13s
- ROI estimation of 'anatomy3' atlas 19s
- ROI estimation of 'julichbrain' atlas 25s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 10s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 18s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 40s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 60s
- Write results 61s
- 250s
- Quality check: 4s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_14707/ds/sub-022/report/catreport_sub-022_ses-t0_T1w.pdf
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- CAT preprocessing takes 41 minute(s) and 18 second(s).
- Image Quality Rating (IQR): 81.01% (B-)
- GM volume (GMV): 45.36% (738.95 / 1629.18 ml)
- GM thickness (GMT): 2.44 0.67 mm
- Segmentations are saved in /var/lib/condor/execute/dir_14707/ds/sub-022/mri
- Reports are saved in /var/lib/condor/execute/dir_14707/ds/sub-022/report
- Labels are saved in /var/lib/condor/execute/dir_14707/ds/sub-022/label
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