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- CAT12.8.1 r1980: 1/1: ./execute/dir_16923/ds/sub-006/sub-006_T1w.n
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- SANLM denoising (medium): 119s
- APP: Rough bias correction:
- Initialize 9s
- Estimate background 9s
- Initial correction 8s
- Refine background 4s
- Final correction 7s
- Final scaling 9s
- 55s
- Correct center-of-mass 4s
- Affine registration 15s
- SPM preprocessing 1 (estimate 1 - TPM registration): 5s
- Use initial fine affine registration. 4s
- Use previous fine affine registration. 107s
- SPM preprocessing 1 (estimate 2): 47s
- SPM preprocessing 2 (write):
- Write Segmentation 23s
- Update Segmentation 30s
- Update Skull-Stripping 64s
- Update probability maps 12s
- 129s
- Global intensity correction: 23s
- SANLM denoising after intensity normalization (medium): 45s
- Fast Optimized Shooting registration 37s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 7s
- Prepare partitions 7s
- Prepare segments (LASmod = 1.00) 26s
- Estimate local tissue thresholds (WM) 27s
- Estimate local tissue thresholds (GM) 39s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 53s
- 164s
- ROI segmentation (partitioning):
- Atlas -> subject space 12s
- Major structures 6s
- Ventricle detection 29s
- Blood vessel detection 18s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.11) 46s
- Manual stroke lesion detection 0s
- Closing of deep structures 3s
- Side alignment 7s
- Final corrections 6s
- 127s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 52s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 8s
- Level 1 cleanup (brain masking) 4s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 5s
- 19s
- 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 | 0.0837 0.0000 0.0837 | 32.0000
- 2 | 2.50 | 0.0815 0.0011 0.0826 | 29.4886
- 3 | 2.50 | 0.0808 0.0016 0.0825 | 26.9772
- 4 | 2.50 | 0.0805 0.0018 0.0824 | 24.6107
- 5 | 2.50 | 0.0802 0.0020 0.0822 | 22.6548
- 6 | 2.50 | 0.0800 0.0021 0.0821 | 20.6989
- 7 | 2.50 | 0.0798 0.0022 0.0819 | 18.9688
- 8 | 2.50 | 0.0795 0.0023 0.0818 | 17.4455
- 9 | 2.50 | 0.0792 0.0023 0.0816 | 15.9223
- 10 | 2.50 | 0.0790 0.0024 0.0814 | 14.6627
- 11 | 2.50 | 0.0787 0.0025 0.0812 | 13.4764
- 12 | 2.50 | 0.0784 0.0026 0.0810 | 12.3015
- 13 | 2.50 | 0.0781 0.0027 0.0808 | 11.3776
- 14 | 2.50 | 0.0778 0.0027 0.0805 | 10.4537
- 15 | 2.25 | 0.0778 0.0028 0.0807 | 9.5920
- 16 | 2.25 | 0.0748 0.0043 0.0791 | 8.8725
- 29 | 2.00 | 0.0768 0.0019 0.0787 | 3.3283
- 30 | 2.00 | 0.0699 0.0047 0.0746 | 3.1221
- 31 | 2.00 | 0.0675 0.0059 0.0733 | 2.9160
- 43 | 1.75 | 0.0665 0.0034 0.0699 | 1.5785
- 44 | 1.75 | 0.0615 0.0060 0.0675 | 1.5194
- 45 | 1.75 | 0.0598 0.0069 0.0667 | 1.4626
- 57 | 1.50 | 0.0582 0.0050 0.0632 | 1.0900
- 58 | 1.50 | 0.0547 0.0073 0.0619 | 1.0730
- 59 | 1.50 | 0.0535 0.0080 0.0615 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 152s
- Prepare output 13s
- 165s
- Jacobian determinant (RMS): 0.010 0.036 0.056 0.083 0.108 | 0.115282
- Template Matching: 0.084 0.224 0.202 0.179 0.160 | 0.160350
- Write result maps: 31s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 44s
- CSF distance: 13s
- PBT2x thickness: 39s
- 102s
- Create initial surface 73s
- Topology correction: 83s
- Surface refinement: 64s
- Reduction of surface collisions with optimization: 60s
- Spherical mapping with areal smoothing 67s
- Spherical registration 253s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 37s
- CSF distance: 12s
- PBT2x thickness: 36s
- 90s
- Create initial surface 67s
- Topology correction: 79s
- Surface refinement: 56s
- Reduction of surface collisions with optimization: 57s
- Spherical mapping with areal smoothing 68s
- Spherical registration 259s
- Final surface processing results:
- Average thickness (FS): 2.5489 0.5836 mm
- Surface intensity / position RMSE: 0.0670 / 0.0672
- Euler number / defect number / defect size: 12.0 / 8.0 / 0.73%
- Display thickness: /var/lib/condor/execute/dir_16923/ds/sub-006/surf/lh.thickness.sub-006_T1w
- Display thickness: /var/lib/condor/execute/dir_16923/ds/sub-006/surf/rh.thickness.sub-006_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_16923/ds/sub-006/sub-006_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1470s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 11s
- ROI estimation of 'neuromorphometrics' atlas 39s
- ROI estimation of 'lpba40' atlas 11s
- ROI estimation of 'hammers' atlas 27s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 10s
- ROI estimation of 'aal3' atlas 15s
- ROI estimation of 'mori' atlas 22s
- ROI estimation of 'anatomy3' atlas 31s
- ROI estimation of 'julichbrain' atlas 42s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 30s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 68s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 102s
- Write results 103s
- 428s
- Quality check: 7s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_16923/ds/sub-006/report/catreport_sub-006_T1w.pdf
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- CAT preprocessing takes 52 minute(s) and 52 second(s).
- Image Quality Rating (IQR): 87.84% (B+)
- GM volume (GMV): 47.94% (667.98 / 1393.32 ml)
- GM thickness (GMT): 2.55 0.58 mm
- Segmentations are saved in /var/lib/condor/execute/dir_16923/ds/sub-006/mri
- Reports are saved in /var/lib/condor/execute/dir_16923/ds/sub-006/report
- Labels are saved in /var/lib/condor/execute/dir_16923/ds/sub-006/label
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