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- CAT12.8.1 r1980: 1/1: ./condor/execute/dir_29671/ds/sub-07/sub-07_T1w.n
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- SANLM denoising (medium): 37s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 6s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 6s
- 38s
- Correct center-of-mass 5s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 12s
- Use initial fine affine registration. 77s
- SPM preprocessing 1 (estimate 2): 70s
- SPM preprocessing 2 (write):
- Write Segmentation 17s
- Update Segmentation 21s
- Update Skull-Stripping 43s
- Update probability maps 9s
- 89s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 16s
- Fast Optimized Shooting registration 32s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 5s
- Prepare segments (LASmod = 1.00) 15s
- Estimate local tissue thresholds (WM) 19s
- Estimate local tissue thresholds (GM) 27s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 27s
- 101s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 18s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.02) 31s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 4s
- 81s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 37s
- 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) 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 | 0.0873 0.0000 0.0873 | 32.0000
- 2 | 2.50 | 0.0837 0.0015 0.0851 | 29.4886
- 3 | 2.50 | 0.0826 0.0023 0.0848 | 26.9772
- 4 | 2.50 | 0.0820 0.0026 0.0846 | 24.6107
- 5 | 2.50 | 0.0816 0.0028 0.0844 | 22.6548
- 6 | 2.50 | 0.0812 0.0029 0.0841 | 20.6989
- 7 | 2.50 | 0.0808 0.0031 0.0839 | 18.9688
- 8 | 2.50 | 0.0804 0.0032 0.0836 | 17.4455
- 9 | 2.50 | 0.0800 0.0033 0.0833 | 15.9223
- 10 | 2.50 | 0.0796 0.0034 0.0830 | 14.6627
- 11 | 2.50 | 0.0792 0.0035 0.0827 | 13.4764
- 12 | 2.50 | 0.0787 0.0036 0.0824 | 12.3015
- 13 | 2.50 | 0.0783 0.0038 0.0821 | 11.3776
- 14 | 2.50 | 0.0779 0.0038 0.0817 | 10.4537
- 15 | 2.25 | 0.0777 0.0040 0.0816 | 9.5920
- 16 | 2.25 | 0.0743 0.0056 0.0799 | 8.8725
- 29 | 2.00 | 0.0755 0.0025 0.0780 | 3.3283
- 30 | 2.00 | 0.0691 0.0051 0.0742 | 3.1221
- 31 | 2.00 | 0.0670 0.0061 0.0730 | 2.9160
- 43 | 1.75 | 0.0660 0.0035 0.0695 | 1.5785
- 44 | 1.75 | 0.0618 0.0057 0.0675 | 1.5194
- 45 | 1.75 | 0.0604 0.0065 0.0669 | 1.4626
- 57 | 1.50 | 0.0593 0.0048 0.0641 | 1.0900
- 58 | 1.50 | 0.0562 0.0067 0.0630 | 1.0730
- 59 | 1.50 | 0.0552 0.0074 0.0626 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 157s
- Prepare output 11s
- 168s
- Jacobian determinant (RMS): 0.014 0.049 0.072 0.097 0.121 | 0.128716
- Template Matching: 0.087 0.223 0.201 0.181 0.166 | 0.165607
- Write result maps: 24s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 26s
- CSF distance: 13s
- PBT2x thickness: 39s
- 83s
- Create initial surface 64s
- Topology correction: 73s
- Surface refinement: 74s
- Reduction of surface collisions with optimization: 57s
- Spherical mapping with areal smoothing 70s
- Spherical registration 301s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 30s
- CSF distance: 13s
- PBT2x thickness: 39s
- 88s
- Create initial surface 64s
- Topology correction: 75s
- Surface refinement: 83s
- Reduction of surface collisions with optimization: 56s
- Spherical mapping with areal smoothing 69s
- Spherical registration 292s
- Final surface processing results:
- Average thickness (FS): 2.4431 0.6362 mm
- Surface intensity / position RMSE: 0.0774 / 0.0849
- Euler number / defect number / defect size: 42.0 / 20.0 / 1.58%
- Display thickness: /var/lib/condor/execute/dir_29671/ds/sub-07/surf/lh.thickness.sub-07_T1w
- Display thickness: /var/lib/condor/execute/dir_29671/ds/sub-07/surf/rh.thickness.sub-07_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_29671/ds/sub-07/sub-07_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1534s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 8s
- ROI estimation of 'neuromorphometrics' atlas 29s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 20s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 12s
- ROI estimation of 'mori' atlas 17s
- ROI estimation of 'anatomy3' atlas 25s
- ROI estimation of 'julichbrain' atlas 34s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 14s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 24s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 54s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 81s
- Write results 82s
- 335s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_29671/ds/sub-07/report/catreport_sub-07_T1w.pdf
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- CAT preprocessing takes 46 minute(s) and 32 second(s).
- Image Quality Rating (IQR): 76.80% (C+)
- GM volume (GMV): 48.56% (624.73 / 1286.55 ml)
- GM thickness (GMT): 2.44 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_29671/ds/sub-07/mri
- Reports are saved in /var/lib/condor/execute/dir_29671/ds/sub-07/report
- Labels are saved in /var/lib/condor/execute/dir_29671/ds/sub-07/label
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