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- CAT12.8.1 r1980: 1/1: ./condor/execute/dir_26020/ds/sub-49/sub-49_T1w.n
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- SANLM denoising (medium): 28s
- APP: Rough bias correction:
- Initialize 3s
- Estimate background 6s
- Initial correction 4s
- Refine background 2s
- Final correction 4s
- Final scaling 4s
- 26s
- Correct center-of-mass 6s
- Affine registration 9s
- SPM preprocessing 1 (estimate 1 - TPM registration): 11s
- Use initial fine affine registration. 61s
- SPM preprocessing 1 (estimate 2): 57s
- SPM preprocessing 2 (write):
- Write Segmentation 12s
- Update Segmentation 18s
- Update Skull-Stripping 29s
- Update probability maps 5s
- 64s
- Global intensity correction: 9s
- SANLM denoising after intensity normalization (medium): 12s
- Fast Optimized Shooting registration 40s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 1s
- Prepare segments (LASmod = 1.00) 16s
- Estimate local tissue thresholds (WM) 12s
- Estimate local tissue thresholds (GM) 20s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 14s
- 71s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 4s
- Ventricle detection 13s
- Blood vessel detection 10s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.05) 29s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 3s
- 73s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 41s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 5s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 1s
- 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 | 0.0839 0.0000 0.0839 | 32.0000
- 2 | 2.50 | 0.0812 0.0012 0.0824 | 29.4886
- 3 | 2.50 | 0.0804 0.0018 0.0822 | 26.9772
- 4 | 2.50 | 0.0800 0.0020 0.0821 | 24.6107
- 5 | 2.50 | 0.0797 0.0022 0.0819 | 22.6548
- 6 | 2.50 | 0.0794 0.0023 0.0817 | 20.6989
- 7 | 2.50 | 0.0791 0.0024 0.0815 | 18.9688
- 8 | 2.50 | 0.0788 0.0025 0.0814 | 17.4455
- 9 | 2.50 | 0.0785 0.0026 0.0811 | 15.9223
- 10 | 2.50 | 0.0782 0.0027 0.0809 | 14.6627
- 11 | 2.50 | 0.0779 0.0028 0.0807 | 13.4764
- 12 | 2.50 | 0.0775 0.0029 0.0804 | 12.3015
- 13 | 2.50 | 0.0772 0.0030 0.0802 | 11.3776
- 14 | 2.50 | 0.0768 0.0031 0.0799 | 10.4537
- 15 | 2.25 | 0.0765 0.0032 0.0797 | 9.5920
- 16 | 2.25 | 0.0734 0.0047 0.0781 | 8.8725
- 29 | 2.00 | 0.0748 0.0021 0.0769 | 3.3283
- 30 | 2.00 | 0.0686 0.0046 0.0732 | 3.1221
- 31 | 2.00 | 0.0664 0.0056 0.0719 | 2.9160
- 43 | 1.75 | 0.0651 0.0033 0.0684 | 1.5785
- 44 | 1.75 | 0.0608 0.0055 0.0663 | 1.5194
- 45 | 1.75 | 0.0593 0.0062 0.0655 | 1.4626
- 57 | 1.50 | 0.0578 0.0046 0.0624 | 1.0900
- 58 | 1.50 | 0.0548 0.0065 0.0613 | 1.0730
- 59 | 1.50 | 0.0538 0.0071 0.0609 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 260s
- Prepare output 10s
- 269s
- Jacobian determinant (RMS): 0.012 0.044 0.063 0.087 0.110 | 0.115184
- Template Matching: 0.084 0.220 0.199 0.178 0.161 | 0.161322
- Write result maps: 20s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 47s
- CSF distance: 18s
- PBT2x thickness: 56s
- 129s
- Create initial surface 100s
- Topology correction: 90s
- Surface refinement: 99s
- Reduction of surface collisions with optimization: 73s
- Spherical mapping with areal smoothing 96s
- Spherical registration 290s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 42s
- CSF distance: 18s
- PBT2x thickness: 55s
- 122s
- Create initial surface 97s
- Topology correction: 91s
- Surface refinement: 85s
- Reduction of surface collisions with optimization: 75s
- Spherical mapping with areal smoothing 94s
- Spherical registration 299s
- Final surface processing results:
- Average thickness (FS): 2.6186 0.6832 mm
- Surface intensity / position RMSE: 0.0703 / 0.0768
- Euler number / defect number / defect size: 16.0 / 14.5 / 0.58%
- Display thickness: /var/lib/condor/execute/dir_26020/ds/sub-49/surf/lh.thickness.sub-49_T1w
- Display thickness: /var/lib/condor/execute/dir_26020/ds/sub-49/surf/rh.thickness.sub-49_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_26020/ds/sub-49/sub-49_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1832s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 6s
- ROI estimation of 'neuromorphometrics' atlas 23s
- ROI estimation of 'lpba40' atlas 6s
- ROI estimation of 'hammers' atlas 16s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 6s
- ROI estimation of 'aal3' atlas 9s
- ROI estimation of 'mori' atlas 14s
- ROI estimation of 'anatomy3' atlas 20s
- ROI estimation of 'julichbrain' atlas 26s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 10s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 13s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 42s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 63s
- Write results 64s
- 256s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_26020/ds/sub-49/report/catreport_sub-49_T1w.pdf
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- CAT preprocessing takes 49 minute(s) and 52 second(s).
- Image Quality Rating (IQR): 82.90% (B-)
- GM volume (GMV): 48.43% (609.10 / 1257.61 ml)
- GM thickness (GMT): 2.62 0.68 mm
- Segmentations are saved in /var/lib/condor/execute/dir_26020/ds/sub-49/mri
- Reports are saved in /var/lib/condor/execute/dir_26020/ds/sub-49/report
- Labels are saved in /var/lib/condor/execute/dir_26020/ds/sub-49/label
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