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- CAT12.8.1 r1980: 1/1: ./condor/execute/dir_26029/ds/sub-11/sub-11_T1w.n
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- SANLM denoising (medium): 34s
- APP: Rough bias correction:
- Initialize 4s
- Estimate background 7s
- Initial correction 5s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 33s
- Correct center-of-mass 6s
- Affine registration 11s
- SPM preprocessing 1 (estimate 1 - TPM registration): 6s
- Use initial fine affine registration. 66s
- SPM preprocessing 1 (estimate 2): 55s
- SPM preprocessing 2 (write):
- Write Segmentation 14s
- Update Segmentation 20s
- Update Skull-Stripping 34s
- Update probability maps 6s
- 75s
- Global intensity correction: 12s
- SANLM denoising after intensity normalization (medium): 12s
- Fast Optimized Shooting registration 41s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.05) 18s
- Estimate local tissue thresholds (WM) 14s
- Estimate local tissue thresholds (GM) 22s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 17s
- 81s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 16s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 31s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 5s
- Final corrections 3s
- 80s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 50s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 5s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 3s
- 13s
- 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 | 0.0825 0.0000 0.0825 | 32.0000
- 2 | 2.50 | 0.0802 0.0011 0.0813 | 29.4886
- 3 | 2.50 | 0.0795 0.0017 0.0812 | 26.9772
- 4 | 2.50 | 0.0792 0.0019 0.0810 | 24.6107
- 5 | 2.50 | 0.0789 0.0020 0.0809 | 22.6548
- 6 | 2.50 | 0.0787 0.0020 0.0807 | 20.6989
- 7 | 2.50 | 0.0785 0.0021 0.0806 | 18.9688
- 8 | 2.50 | 0.0782 0.0022 0.0804 | 17.4455
- 9 | 2.50 | 0.0780 0.0023 0.0802 | 15.9223
- 10 | 2.50 | 0.0777 0.0023 0.0801 | 14.6627
- 11 | 2.50 | 0.0775 0.0024 0.0799 | 13.4764
- 12 | 2.50 | 0.0772 0.0024 0.0796 | 12.3015
- 13 | 2.50 | 0.0769 0.0025 0.0794 | 11.3776
- 14 | 2.50 | 0.0766 0.0026 0.0792 | 10.4537
- 15 | 2.25 | 0.0762 0.0026 0.0788 | 9.5920
- 16 | 2.25 | 0.0734 0.0040 0.0774 | 8.8725
- 29 | 2.00 | 0.0749 0.0018 0.0767 | 3.3283
- 30 | 2.00 | 0.0689 0.0042 0.0731 | 3.1221
- 31 | 2.00 | 0.0668 0.0052 0.0720 | 2.9160
- 43 | 1.75 | 0.0658 0.0030 0.0688 | 1.5785
- 44 | 1.75 | 0.0615 0.0053 0.0667 | 1.5194
- 45 | 1.75 | 0.0600 0.0061 0.0661 | 1.4626
- 57 | 1.50 | 0.0587 0.0044 0.0632 | 1.0900
- 58 | 1.50 | 0.0556 0.0064 0.0621 | 1.0730
- 59 | 1.50 | 0.0546 0.0071 0.0617 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 260s
- Prepare output 11s
- 271s
- Jacobian determinant (RMS): 0.010 0.035 0.052 0.075 0.098 | 0.105467
- Template Matching: 0.083 0.220 0.200 0.180 0.164 | 0.163718
- Write result maps: 21s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 54s
- CSF distance: 20s
- PBT2x thickness: 60s
- 143s
- Create initial surface 109s
- Topology correction: 120s
- Surface refinement: 120s
- Reduction of surface collisions with optimization: 94s
- Spherical mapping with areal smoothing 107s
- Spherical registration 317s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 41s
- CSF distance: 19s
- PBT2x thickness: 59s
- 128s
- Create initial surface 109s
- Topology correction: 119s
- Surface refinement: 132s
- Reduction of surface collisions with optimization: 92s
- Spherical mapping with areal smoothing 107s
- Spherical registration 307s
- Final surface processing results:
- Average thickness (FS): 2.5189 0.6769 mm
- Surface intensity / position RMSE: 0.0737 / 0.0827
- Euler number / defect number / defect size: 26.0 / 14.0 / 1.37%
- Display thickness: /var/lib/condor/execute/dir_26029/ds/sub-11/surf/lh.thickness.sub-11_T1w
- Display thickness: /var/lib/condor/execute/dir_26029/ds/sub-11/surf/rh.thickness.sub-11_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_26029/ds/sub-11/sub-11_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 2104s
- 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 33s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 16s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 54s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 81s
- Write results 82s
- 328s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_26029/ds/sub-11/report/catreport_sub-11_T1w.pdf
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- CAT preprocessing takes 57 minute(s) and 24 second(s).
- Image Quality Rating (IQR): 82.47% (B-)
- GM volume (GMV): 49.27% (659.27 / 1338.07 ml)
- GM thickness (GMT): 2.52 0.68 mm
- Segmentations are saved in /var/lib/condor/execute/dir_26029/ds/sub-11/mri
- Reports are saved in /var/lib/condor/execute/dir_26029/ds/sub-11/report
- Labels are saved in /var/lib/condor/execute/dir_26029/ds/sub-11/label
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