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- CAT12.8.1 r1980: 1/1: ./execute/dir_1631/ds/sub-120/sub-120_T1w.n
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- SANLM denoising (medium): 24s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 8s
- Initial correction 8s
- Refine background 4s
- Final correction 6s
- Final scaling 9s
- 47s
- Correct center-of-mass 3s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 72s
- SPM preprocessing 1 (estimate 2): 46s
- SPM preprocessing 2 (write):
- Write Segmentation 15s
- Update Segmentation 18s
- Update Skull-Stripping 37s
- Update probability maps 8s
- 78s
- Global intensity correction: 14s
- SANLM denoising after intensity normalization (medium): 8s
- Fast Optimized Shooting registration 29s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.13) 13s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 24s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 22s
- 86s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 16s
- Blood vessel detection 9s
- WMH detection (WMHCstr=0.48 > WMHCstr'=0.10) 24s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 3s
- Final corrections 4s
- 68s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 30s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.24):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 3s
- 11s
- 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 | 0.0868 0.0000 0.0868 | 32.0000
- 2 | 2.50 | 0.0839 0.0013 0.0851 | 29.4886
- 3 | 2.50 | 0.0831 0.0018 0.0849 | 26.9772
- 4 | 2.50 | 0.0827 0.0021 0.0847 | 24.6107
- 5 | 2.50 | 0.0824 0.0022 0.0846 | 22.6548
- 6 | 2.50 | 0.0821 0.0023 0.0844 | 20.6989
- 7 | 2.50 | 0.0819 0.0023 0.0842 | 18.9688
- 8 | 2.50 | 0.0816 0.0024 0.0840 | 17.4455
- 9 | 2.50 | 0.0813 0.0025 0.0838 | 15.9223
- 10 | 2.50 | 0.0810 0.0026 0.0835 | 14.6627
- 11 | 2.50 | 0.0807 0.0026 0.0833 | 13.4764
- 12 | 2.50 | 0.0804 0.0027 0.0830 | 12.3015
- 13 | 2.50 | 0.0801 0.0027 0.0828 | 11.3776
- 14 | 2.50 | 0.0798 0.0028 0.0825 | 10.4537
- 15 | 2.25 | 0.0793 0.0029 0.0822 | 9.5920
- 16 | 2.25 | 0.0766 0.0042 0.0808 | 8.8725
- 17 | 2.25 | 0.0756 0.0046 0.0802 | 8.1530
- 18 | 2.25 | 0.0749 0.0048 0.0798 | 7.5234
- 29 | 2.00 | 0.0774 0.0023 0.0797 | 3.3283
- 30 | 2.00 | 0.0722 0.0045 0.0767 | 3.1221
- 31 | 2.00 | 0.0705 0.0054 0.0758 | 2.9160
- 43 | 1.75 | 0.0698 0.0030 0.0728 | 1.5785
- 44 | 1.75 | 0.0653 0.0054 0.0708 | 1.5194
- 45 | 1.75 | 0.0639 0.0063 0.0701 | 1.4626
- 57 | 1.50 | 0.0627 0.0045 0.0672 | 1.0900
- 58 | 1.50 | 0.0593 0.0068 0.0661 | 1.0730
- 59 | 1.50 | 0.0582 0.0075 0.0657 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 149s
- Prepare output 9s
- 158s
- Jacobian determinant (RMS): 0.010 0.034 0.053 0.076 0.099 | 0.105986
- Template Matching: 0.087 0.225 0.211 0.192 0.175 | 0.174578
- Write result maps: 20s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 45s
- CSF distance: 16s
- PBT2x thickness: 47s
- 114s
- Create initial surface 91s
- Topology correction: 101s
- Surface refinement: 94s
- Reduction of surface collisions with optimization: 81s
- Spherical mapping with areal smoothing 85s
- Spherical registration 273s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 38s
- CSF distance: 17s
- PBT2x thickness: 47s
- 109s
- Create initial surface 93s
- Topology correction: 106s
- Surface refinement: 93s
- Reduction of surface collisions with optimization: 79s
- Spherical mapping with areal smoothing 86s
- Spherical registration 277s
- Final surface processing results:
- Average thickness (FS): 2.3651 0.5669 mm
- Surface intensity / position RMSE: 0.0671 / 0.0728
- Euler number / defect number / defect size: 42.0 / 22.5 / 1.67%
- Display thickness: /var/lib/condor/execute/dir_1631/ds/sub-120/surf/lh.thickness.sub-120_T1w
- Display thickness: /var/lib/condor/execute/dir_1631/ds/sub-120/surf/rh.thickness.sub-120_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1631/ds/sub-120/sub-120_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1773s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 8s
- ROI estimation of 'neuromorphometrics' atlas 27s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 19s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 10s
- ROI estimation of 'mori' atlas 16s
- ROI estimation of 'anatomy3' atlas 22s
- ROI estimation of 'julichbrain' atlas 29s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 45s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 68s
- Write results 69s
- 294s
- Quality check: 5s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1631/ds/sub-120/report/catreport_sub-120_T1w.pdf
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- CAT preprocessing takes 47 minute(s) and 35 second(s).
- Image Quality Rating (IQR): 80.77% (B-)
- GM volume (GMV): 43.51% (749.44 / 1722.52 ml)
- GM thickness (GMT): 2.37 0.57 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1631/ds/sub-120/mri
- Reports are saved in /var/lib/condor/execute/dir_1631/ds/sub-120/report
- Labels are saved in /var/lib/condor/execute/dir_1631/ds/sub-120/label
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