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- CAT12.8.1 r1980: 1/1: ./dir_15073/ds/sub-1268/sub-1268_ses-01_T1w.n
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- SANLM denoising (medium): 211s
- APP: Rough bias correction:
- Initialize 11s
- Estimate background 12s
- Initial correction 21s
- Refine background 6s
- Final correction 12s
- Final scaling 11s
- 86s
- Correct center-of-mass 6s
- Affine registration 24s
- SPM preprocessing 1 (estimate 1 - TPM registration): 123s
- SPM preprocessing 1 (estimate 2): 114s
- SPM preprocessing 2 (write):
- Write Segmentation 30s
- Update Segmentation 33s
- Update Skull-Stripping 77s
- Update probability maps 17s
- 157s
- Global intensity correction: 31s
- SANLM denoising after intensity normalization (medium): 34s
- Fast Optimized Shooting registration 53s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 7s
- Prepare partitions 5s
- Prepare segments (LASmod = 1.22) 24s
- Estimate local tissue thresholds (WM) 30s
- Estimate local tissue thresholds (GM) 42s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 55s
- 172s
- ROI segmentation (partitioning):
- Atlas -> subject space 16s
- Major structures 6s
- Ventricle detection 27s
- Blood vessel detection 14s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.13) 42s
- Manual stroke lesion detection 0s
- Closing of deep structures 3s
- Side alignment 6s
- Final corrections 9s
- 124s
- Blood vessel correction (BVCstr=0.50): 3s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 58s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 7s
- Level 1 cleanup (brain masking) 5s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 4s
- 18s
- 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 | 0.0883 0.0000 0.0883 | 32.0000
- 2 | 2.50 | 0.0854 0.0013 0.0867 | 29.4886
- 3 | 2.50 | 0.0845 0.0019 0.0865 | 26.9772
- 4 | 2.50 | 0.0841 0.0022 0.0863 | 24.6107
- 5 | 2.50 | 0.0838 0.0023 0.0861 | 22.6548
- 6 | 2.50 | 0.0835 0.0024 0.0859 | 20.6989
- 7 | 2.50 | 0.0832 0.0025 0.0857 | 18.9688
- 8 | 2.50 | 0.0828 0.0026 0.0855 | 17.4455
- 9 | 2.50 | 0.0825 0.0027 0.0852 | 15.9223
- 10 | 2.50 | 0.0821 0.0028 0.0850 | 14.6627
- 11 | 2.50 | 0.0818 0.0029 0.0847 | 13.4764
- 12 | 2.50 | 0.0814 0.0030 0.0844 | 12.3015
- 13 | 2.50 | 0.0811 0.0031 0.0841 | 11.3776
- 14 | 2.50 | 0.0807 0.0032 0.0839 | 10.4537
- 15 | 2.25 | 0.0825 0.0033 0.0857 | 9.5920
- 16 | 2.25 | 0.0787 0.0051 0.0838 | 8.8725
- 17 | 2.25 | 0.0772 0.0058 0.0830 | 8.1530
- 18 | 2.25 | 0.0763 0.0061 0.0824 | 7.5234
- 19 | 2.25 | 0.0755 0.0063 0.0818 | 6.9630
- 20 | 2.25 | 0.0749 0.0063 0.0812 | 6.4027
- 29 | 2.00 | 0.0772 0.0035 0.0807 | 3.3283
- 30 | 2.00 | 0.0719 0.0060 0.0779 | 3.1221
- 31 | 2.00 | 0.0700 0.0069 0.0769 | 2.9160
- 43 | 1.75 | 0.0694 0.0039 0.0733 | 1.5785
- 44 | 1.75 | 0.0644 0.0066 0.0710 | 1.5194
- 45 | 1.75 | 0.0628 0.0074 0.0703 | 1.4626
- 57 | 1.50 | 0.0617 0.0055 0.0672 | 1.0900
- 58 | 1.50 | 0.0581 0.0078 0.0659 | 1.0730
- 59 | 1.50 | 0.0570 0.0085 0.0655 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 255s
- Prepare output 15s
- 269s
- Jacobian determinant (RMS): 0.010 0.040 0.073 0.105 0.135 | 0.143358
- Template Matching: 0.088 0.225 0.210 0.188 0.171 | 0.170926
- Write result maps: 54s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 39s
- CSF distance: 20s
- PBT2x thickness: 64s
- 132s
- Create initial surface 112s
- Topology correction: 124s
- Surface refinement: 117s
- Reduction of surface collisions with optimization: 101s
- Spherical mapping with areal smoothing 112s
- Spherical registration 292s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 42s
- CSF distance: 21s
- PBT2x thickness: 63s
- 135s
- Create initial surface 112s
- Topology correction: 123s
- Surface refinement: 146s
- Reduction of surface collisions with optimization: 95s
- Spherical mapping with areal smoothing 108s
- Spherical registration 283s
- Final surface processing results:
- Average thickness (FS): 2.5792 0.6494 mm
- Surface intensity / position RMSE: 0.0792 / 0.0814
- Euler number / defect number / defect size: 50.0 / 35.5 / 1.03%
- Display thickness: /var/lib/condor/execute/dir_15073/ds/sub-1268/surf/lh.thickness.sub-1268_ses-01_T1w
- Display thickness: /var/lib/condor/execute/dir_15073/ds/sub-1268/surf/rh.thickness.sub-1268_ses-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_15073/ds/sub-1268/sub-1268_ses-01_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 2122s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 26s
- ROI estimation of 'neuromorphometrics' atlas 92s
- ROI estimation of 'lpba40' atlas 25s
- ROI estimation of 'hammers' atlas 63s
- ROI estimation of 'thalamus' atlas 5s
- ROI estimation of 'ibsr' atlas 22s
- ROI estimation of 'aal3' atlas 37s
- ROI estimation of 'mori' atlas 57s
- ROI estimation of 'anatomy3' atlas 82s
- ROI estimation of 'julichbrain' atlas 112s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 42s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 59s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 178s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 221s
- Write results 223s
- 1024s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_15073/ds/sub-1268/report/catreport_sub-1268_ses-01_T1w.pdf
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- CAT preprocessing takes 80 minute(s) and 25 second(s).
- Image Quality Rating (IQR): 80.80% (B-)
- GM volume (GMV): 49.23% (760.19 / 1544.02 ml)
- GM thickness (GMT): 2.58 0.65 mm
- Segmentations are saved in /var/lib/condor/execute/dir_15073/ds/sub-1268/mri
- Reports are saved in /var/lib/condor/execute/dir_15073/ds/sub-1268/report
- Labels are saved in /var/lib/condor/execute/dir_15073/ds/sub-1268/label
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