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- CAT12.8.1 r1980: 1/1: ./dir_26088/ds/sub-1010/sub-1010_ses-01_T1w.n
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- SANLM denoising (medium): 112s
- APP: Rough bias correction:
- Initialize 11s
- Estimate background 12s
- Initial correction 22s
- Refine background 5s
- Final correction 11s
- Final scaling 8s
- 80s
- Correct center-of-mass 5s
- Affine registration 22s
- SPM preprocessing 1 (estimate 1 - TPM registration): 100s
- SPM preprocessing 1 (estimate 2): 73s
- SPM preprocessing 2 (write):
- Write Segmentation 28s
- Update Segmentation 28s
- Update Skull-Stripping 68s
- Update probability maps 14s
- 139s
- Global intensity correction: 26s
- SANLM denoising after intensity normalization (medium): 16s
- Fast Optimized Shooting registration 46s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 6s
- Prepare partitions 9s
- Prepare segments (LASmod = 1.25) 21s
- Estimate local tissue thresholds (WM) 31s
- Estimate local tissue thresholds (GM) 46s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 55s
- 174s
- ROI segmentation (partitioning):
- Atlas -> subject space 11s
- Major structures 5s
- Ventricle detection 21s
- Blood vessel detection 15s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 37s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 5s
- Final corrections 7s
- 103s
- Blood vessel correction (BVCstr=0.50): 3s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 46s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- 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) 4s
- 16s
- 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 | 0.0834 0.0000 0.0834 | 32.0000
- 2 | 2.50 | 0.0811 0.0011 0.0822 | 29.4886
- 3 | 2.50 | 0.0804 0.0016 0.0820 | 26.9772
- 4 | 2.50 | 0.0801 0.0018 0.0819 | 24.6107
- 5 | 2.50 | 0.0798 0.0019 0.0817 | 22.6548
- 6 | 2.50 | 0.0796 0.0020 0.0816 | 20.6989
- 7 | 2.50 | 0.0794 0.0021 0.0814 | 18.9688
- 8 | 2.50 | 0.0791 0.0021 0.0812 | 17.4455
- 9 | 2.50 | 0.0789 0.0022 0.0810 | 15.9223
- 10 | 2.50 | 0.0786 0.0023 0.0809 | 14.6627
- 11 | 2.50 | 0.0783 0.0023 0.0806 | 13.4764
- 12 | 2.50 | 0.0780 0.0024 0.0804 | 12.3015
- 13 | 2.50 | 0.0778 0.0025 0.0802 | 11.3776
- 14 | 2.50 | 0.0775 0.0025 0.0800 | 10.4537
- 15 | 2.25 | 0.0767 0.0026 0.0793 | 9.5920
- 16 | 2.25 | 0.0741 0.0038 0.0779 | 8.8725
- 29 | 2.00 | 0.0753 0.0017 0.0770 | 3.3283
- 30 | 2.00 | 0.0693 0.0041 0.0734 | 3.1221
- 31 | 2.00 | 0.0674 0.0051 0.0724 | 2.9160
- 43 | 1.75 | 0.0664 0.0029 0.0693 | 1.5785
- 44 | 1.75 | 0.0622 0.0052 0.0673 | 1.5194
- 45 | 1.75 | 0.0608 0.0059 0.0667 | 1.4626
- 57 | 1.50 | 0.0596 0.0043 0.0639 | 1.0900
- 58 | 1.50 | 0.0565 0.0063 0.0628 | 1.0730
- 59 | 1.50 | 0.0555 0.0069 0.0625 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 193s
- Prepare output 16s
- 209s
- Jacobian determinant (RMS): 0.010 0.037 0.056 0.083 0.107 | 0.114593
- Template Matching: 0.083 0.222 0.202 0.182 0.167 | 0.166567
- Write result maps: 38s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 37s
- CSF distance: 19s
- PBT2x thickness: 57s
- 120s
- Create initial surface 99s
- Topology correction: 133s
- Surface refinement: 91s
- Reduction of surface collisions with optimization: 73s
- Spherical mapping with areal smoothing 94s
- Spherical registration 332s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 35s
- CSF distance: 19s
- PBT2x thickness: 56s
- 117s
- Create initial surface 98s
- Topology correction: 117s
- Surface refinement: 88s
- Reduction of surface collisions with optimization: 75s
- Spherical mapping with areal smoothing 102s
- Spherical registration 348s
- Final surface processing results:
- Average thickness (FS): 2.5052 0.6968 mm
- Surface intensity / position RMSE: 0.0867 / 0.1146
- Euler number / defect number / defect size: 100.0 / 48.0 / 3.46%
- Display thickness: /var/lib/condor/execute/dir_26088/ds/sub-1010/surf/lh.thickness.sub-1010_ses-01_T1w
- Display thickness: /var/lib/condor/execute/dir_26088/ds/sub-1010/surf/rh.thickness.sub-1010_ses-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_26088/ds/sub-1010/sub-1010_ses-01_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 2004s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 14s
- ROI estimation of 'neuromorphometrics' atlas 49s
- ROI estimation of 'lpba40' atlas 14s
- ROI estimation of 'hammers' atlas 35s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 12s
- ROI estimation of 'aal3' atlas 19s
- ROI estimation of 'mori' atlas 30s
- ROI estimation of 'anatomy3' atlas 42s
- ROI estimation of 'julichbrain' atlas 56s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 22s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 38s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 90s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 133s
- Write results 135s
- 559s
- Quality check: 7s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_26088/ds/sub-1010/report/catreport_sub-1010_ses-01_T1w.pdf
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- CAT preprocessing takes 65 minute(s) and 4 second(s).
- Image Quality Rating (IQR): 79.30% (C+)
- GM volume (GMV): 51.25% (692.60 / 1351.33 ml)
- GM thickness (GMT): 2.51 0.70 mm
- Segmentations are saved in /var/lib/condor/execute/dir_26088/ds/sub-1010/mri
- Reports are saved in /var/lib/condor/execute/dir_26088/ds/sub-1010/report
- Labels are saved in /var/lib/condor/execute/dir_26088/ds/sub-1010/label
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