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- CAT12.8.1 r1980: 1/1: ./execute/dir_19497/ds/sub-140/sub-140_T1w.n
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- SANLM denoising (medium): 69s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 10s
- Initial correction 11s
- Refine background 5s
- Final correction 8s
- Final scaling 9s
- 58s
- Correct center-of-mass 5s
- Affine registration 12s
- SPM preprocessing 1 (estimate 1 - TPM registration): 85s
- SPM preprocessing 1 (estimate 2): 56s
- SPM preprocessing 2 (write):
- Write Segmentation 21s
- Update Segmentation 21s
- Update Skull-Stripping 50s
- Update probability maps 11s
- 102s
- Global intensity correction: 19s
- SANLM denoising after intensity normalization (medium): 11s
- Fast Optimized Shooting registration 42s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.14) 16s
- Estimate local tissue thresholds (WM) 27s
- Estimate local tissue thresholds (GM) 36s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 18s
- 107s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 4s
- Ventricle detection 16s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.48 > WMHCstr'=0.02) 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 0.05): 36s
- AMAP peaks: [CSF,GM,WM] = [0.360.07,0.680.07,0.990.04]
- Final cleanup (gcutstr=0.24):
- Level 1 cleanup (ROI estimation) 5s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 3s
- 13s
- 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 | 0.0851 0.0000 0.0851 | 32.0000
- 2 | 2.50 | 0.0826 0.0011 0.0837 | 29.4886
- 3 | 2.50 | 0.0819 0.0017 0.0836 | 26.9772
- 4 | 2.50 | 0.0815 0.0019 0.0834 | 24.6107
- 5 | 2.50 | 0.0812 0.0021 0.0833 | 22.6548
- 6 | 2.50 | 0.0809 0.0022 0.0831 | 20.6989
- 7 | 2.50 | 0.0806 0.0023 0.0829 | 18.9688
- 8 | 2.50 | 0.0803 0.0024 0.0827 | 17.4455
- 9 | 2.50 | 0.0800 0.0025 0.0825 | 15.9223
- 10 | 2.50 | 0.0797 0.0026 0.0823 | 14.6627
- 11 | 2.50 | 0.0794 0.0027 0.0821 | 13.4764
- 12 | 2.50 | 0.0791 0.0028 0.0818 | 12.3015
- 13 | 2.50 | 0.0787 0.0029 0.0816 | 11.3776
- 14 | 2.50 | 0.0784 0.0030 0.0814 | 10.4537
- 15 | 2.25 | 0.0782 0.0030 0.0812 | 9.5920
- 16 | 2.25 | 0.0752 0.0045 0.0797 | 8.8725
- 17 | 2.25 | 0.0739 0.0051 0.0791 | 8.1530
- 29 | 2.00 | 0.0754 0.0024 0.0778 | 3.3283
- 30 | 2.00 | 0.0694 0.0049 0.0743 | 3.1221
- 31 | 2.00 | 0.0673 0.0059 0.0732 | 2.9160
- 43 | 1.75 | 0.0661 0.0034 0.0695 | 1.5785
- 44 | 1.75 | 0.0617 0.0058 0.0674 | 1.5194
- 45 | 1.75 | 0.0602 0.0066 0.0667 | 1.4626
- 57 | 1.50 | 0.0586 0.0048 0.0634 | 1.0900
- 58 | 1.50 | 0.0555 0.0068 0.0623 | 1.0730
- 59 | 1.50 | 0.0544 0.0075 0.0619 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 204s
- Prepare output 13s
- 217s
- Jacobian determinant (RMS): 0.011 0.043 0.067 0.094 0.119 | 0.126727
- Template Matching: 0.085 0.222 0.202 0.180 0.163 | 0.163138
- Write result maps: 31s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 36s
- CSF distance: 18s
- PBT2x thickness: 56s
- 117s
- Create initial surface 103s
- Topology correction: 106s
- Surface refinement: 106s
- Reduction of surface collisions with optimization: 72s
- Spherical mapping with areal smoothing 97s
- Spherical registration 340s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 46s
- CSF distance: 18s
- PBT2x thickness: 55s
- 126s
- Create initial surface 97s
- Topology correction: 107s
- Surface refinement: 89s
- Reduction of surface collisions with optimization: 72s
- Spherical mapping with areal smoothing 97s
- Spherical registration 339s
- Final surface processing results:
- Average thickness (FS): 2.5660 0.5953 mm
- Surface intensity / position RMSE: 0.0619 / 0.0621
- Euler number / defect number / defect size: 8.0 / 8.5 / 0.30%
- Display thickness: /var/lib/condor/execute/dir_19497/ds/sub-140/surf/lh.thickness.sub-140_T1w
- Display thickness: /var/lib/condor/execute/dir_19497/ds/sub-140/surf/rh.thickness.sub-140_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_19497/ds/sub-140/sub-140_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1977s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 30s
- ROI estimation of 'lpba40' atlas 9s
- ROI estimation of 'hammers' atlas 21s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 8s
- ROI estimation of 'aal3' atlas 13s
- ROI estimation of 'mori' atlas 19s
- ROI estimation of 'anatomy3' atlas 30s
- ROI estimation of 'julichbrain' atlas 38s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 26s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 61s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 90s
- Write results 91s
- 372s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_19497/ds/sub-140/report/catreport_sub-140_T1w.pdf
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- CAT preprocessing takes 56 minute(s) and 30 second(s).
- Image Quality Rating (IQR): 80.92% (B-)
- GM volume (GMV): 48.25% (668.27 / 1385.12 ml)
- GM thickness (GMT): 2.57 0.60 mm
- Segmentations are saved in /var/lib/condor/execute/dir_19497/ds/sub-140/mri
- Reports are saved in /var/lib/condor/execute/dir_19497/ds/sub-140/report
- Labels are saved in /var/lib/condor/execute/dir_19497/ds/sub-140/label
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