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- CAT12.8.1 r1980: 1/1: ./sub-NC250_ses-20190814_acq-highres_run-02_T1w.n
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- SANLM denoising (medium): 53s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 10s
- Initial correction 8s
- Refine background 5s
- Final correction 7s
- Final scaling 8s
- 53s
- Correct center-of-mass 4s
- Affine registration 13s
- SPM preprocessing 1 (estimate 1 - TPM registration): 90s
- SPM preprocessing 1 (estimate 2): 91s
- SPM preprocessing 2 (write):
- Write Segmentation 22s
- Update Segmentation 24s
- Update Skull-Stripping 52s
- Update probability maps 10s
- 108s
- Global intensity correction: 20s
- SANLM denoising after intensity normalization (medium): 11s
- Fast Optimized Shooting registration 45s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.15) 20s
- Estimate local tissue thresholds (WM) 22s
- Estimate local tissue thresholds (GM) 28s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 27s
- 109s
- ROI segmentation (partitioning):
- Atlas -> subject space 11s
- Major structures 5s
- Ventricle detection 20s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.05) 28s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 6s
- 88s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 49s
- 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 | 0.0867 0.0000 0.0867 | 32.0000
- 2 | 2.50 | 0.0838 0.0013 0.0850 | 29.4886
- 3 | 2.50 | 0.0829 0.0019 0.0848 | 26.9772
- 4 | 2.50 | 0.0825 0.0021 0.0847 | 24.6107
- 5 | 2.50 | 0.0822 0.0023 0.0845 | 22.6548
- 6 | 2.50 | 0.0819 0.0023 0.0843 | 20.6989
- 7 | 2.50 | 0.0816 0.0024 0.0841 | 18.9688
- 8 | 2.50 | 0.0813 0.0025 0.0839 | 17.4455
- 9 | 2.50 | 0.0810 0.0026 0.0836 | 15.9223
- 10 | 2.50 | 0.0807 0.0027 0.0834 | 14.6627
- 11 | 2.50 | 0.0804 0.0028 0.0832 | 13.4764
- 12 | 2.50 | 0.0801 0.0028 0.0829 | 12.3015
- 13 | 2.50 | 0.0798 0.0029 0.0826 | 11.3776
- 14 | 2.50 | 0.0794 0.0029 0.0824 | 10.4537
- 15 | 2.25 | 0.0791 0.0030 0.0821 | 9.5920
- 16 | 2.25 | 0.0762 0.0044 0.0806 | 8.8725
- 17 | 2.25 | 0.0751 0.0049 0.0800 | 8.1530
- 18 | 2.25 | 0.0744 0.0051 0.0795 | 7.5234
- 29 | 2.00 | 0.0766 0.0024 0.0790 | 3.3283
- 30 | 2.00 | 0.0713 0.0047 0.0761 | 3.1221
- 31 | 2.00 | 0.0696 0.0056 0.0752 | 2.9160
- 43 | 1.75 | 0.0690 0.0032 0.0722 | 1.5785
- 44 | 1.75 | 0.0645 0.0055 0.0701 | 1.5194
- 45 | 1.75 | 0.0631 0.0064 0.0695 | 1.4626
- 57 | 1.50 | 0.0622 0.0046 0.0668 | 1.0900
- 58 | 1.50 | 0.0588 0.0068 0.0657 | 1.0730
- 59 | 1.50 | 0.0578 0.0075 0.0653 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 237s
- Prepare output 12s
- 249s
- Jacobian determinant (RMS): 0.011 0.039 0.059 0.081 0.105 | 0.110663
- Template Matching: 0.087 0.223 0.209 0.189 0.173 | 0.173289
- Write result maps: 37s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 39s
- CSF distance: 20s
- PBT2x thickness: 64s
- 135s
- Create initial surface 120s
- Topology correction: 150s
- Surface refinement: 170s
- Reduction of surface collisions with optimization: 205s
- Spherical mapping with areal smoothing 119s
- Spherical registration 280s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 39s
- CSF distance: 20s
- PBT2x thickness: 65s
- 135s
- Create initial surface 121s
- Topology correction: 146s
- Surface refinement: 141s
- Reduction of surface collisions with optimization: 112s
- Spherical mapping with areal smoothing 116s
- Spherical registration 289s
- Final surface processing results:
- Average thickness (FS): 2.3066 0.6969 mm
- Surface intensity / position RMSE: 0.0961 / 0.1411
- Euler number / defect number / defect size: 182.0 / 61.0 / 5.81%
- Display thickness: /var/lib/condor/execute/dir_28111/ds/sub-NC250/surf/lh.thickness.sub-NC250_ses-20190814_acq-highres_run-02_T1w
- Display thickness: /var/lib/condor/execute/dir_28111/ds/sub-NC250/surf/rh.thickness.sub-NC250_ses-20190814_acq-highres_run-02_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_28111/ds/sub-NC250/sub-NC250_ses-20190814_acq-highres_run-02_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 2365s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 17s
- ROI estimation of 'neuromorphometrics' atlas 57s
- ROI estimation of 'lpba40' atlas 17s
- ROI estimation of 'hammers' atlas 43s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 16s
- ROI estimation of 'aal3' atlas 26s
- ROI estimation of 'mori' atlas 39s
- ROI estimation of 'anatomy3' atlas 54s
- ROI estimation of 'julichbrain' atlas 74s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 28s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 42s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 116s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 153s
- Write results 154s
- 688s
- Quality check: 7s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_28111/ds/sub-NC250/report/catreport_sub-NC250_ses-20190814_acq-highres_run-02_T1w.pdf
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- CAT preprocessing takes 70 minute(s) and 7 second(s).
- Image Quality Rating (IQR): 66.89% (D+)
- GM volume (GMV): 47.33% (723.33 / 1528.39 ml)
- GM thickness (GMT): 2.31 0.70 mm
- Segmentations are saved in /var/lib/condor/execute/dir_28111/ds/sub-NC250/mri
- Reports are saved in /var/lib/condor/execute/dir_28111/ds/sub-NC250/report
- Labels are saved in /var/lib/condor/execute/dir_28111/ds/sub-NC250/label
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