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- CAT12.8.1 r1980: 1/1: ./condor/execute/dir_24135/ds/sub-12/sub-12_T1w.n
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- SANLM denoising (medium): 59s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 6s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 36s
- Correct center-of-mass 5s
- Affine registration 9s
- SPM preprocessing 1 (estimate 1 - TPM registration): 72s
- SPM preprocessing 1 (estimate 2): 51s
- SPM preprocessing 2 (write):
- Write Segmentation 16s
- Update Segmentation 18s
- Update Skull-Stripping 41s
- Update probability maps 8s
- 82s
- Global intensity correction: 15s
- SANLM denoising after intensity normalization (medium): 9s
- Fast Optimized Shooting registration 29s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.04) 14s
- Estimate local tissue thresholds (WM) 16s
- Estimate local tissue thresholds (GM) 23s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 24s
- 86s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 13s
- Blood vessel detection 9s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.11) 26s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 3s
- Final corrections 4s
- 67s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 32s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 2s
- 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 | 0.0861 0.0000 0.0861 | 32.0000
- 2 | 2.50 | 0.0834 0.0012 0.0846 | 29.4886
- 3 | 2.50 | 0.0827 0.0018 0.0845 | 26.9772
- 4 | 2.50 | 0.0823 0.0020 0.0843 | 24.6107
- 5 | 2.50 | 0.0820 0.0022 0.0841 | 22.6548
- 6 | 2.50 | 0.0817 0.0023 0.0839 | 20.6989
- 7 | 2.50 | 0.0814 0.0024 0.0838 | 18.9688
- 8 | 2.50 | 0.0811 0.0025 0.0836 | 17.4455
- 9 | 2.50 | 0.0808 0.0025 0.0834 | 15.9223
- 10 | 2.50 | 0.0805 0.0026 0.0831 | 14.6627
- 11 | 2.50 | 0.0802 0.0027 0.0829 | 13.4764
- 12 | 2.50 | 0.0799 0.0028 0.0827 | 12.3015
- 13 | 2.50 | 0.0796 0.0029 0.0824 | 11.3776
- 14 | 2.50 | 0.0793 0.0029 0.0822 | 10.4537
- 15 | 2.25 | 0.0783 0.0030 0.0813 | 9.5920
- 16 | 2.25 | 0.0756 0.0043 0.0799 | 8.8725
- 17 | 2.25 | 0.0745 0.0048 0.0793 | 8.1530
- 29 | 2.00 | 0.0761 0.0022 0.0783 | 3.3283
- 30 | 2.00 | 0.0707 0.0044 0.0752 | 3.1221
- 31 | 2.00 | 0.0689 0.0053 0.0742 | 2.9160
- 43 | 1.75 | 0.0679 0.0030 0.0709 | 1.5785
- 44 | 1.75 | 0.0637 0.0053 0.0689 | 1.5194
- 45 | 1.75 | 0.0622 0.0061 0.0682 | 1.4626
- 57 | 1.50 | 0.0607 0.0044 0.0651 | 1.0900
- 58 | 1.50 | 0.0576 0.0065 0.0640 | 1.0730
- 59 | 1.50 | 0.0565 0.0071 0.0636 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 162s
- Prepare output 10s
- 172s
- Jacobian determinant (RMS): 0.011 0.040 0.058 0.080 0.103 | 0.109188
- Template Matching: 0.086 0.223 0.207 0.187 0.170 | 0.169615
- Write result maps: 26s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 32s
- CSF distance: 16s
- PBT2x thickness: 47s
- 101s
- Create initial surface 90s
- Topology correction: 96s
- Surface refinement: 76s
- Reduction of surface collisions with optimization: 74s
- Spherical mapping with areal smoothing 85s
- Spherical registration 308s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 31s
- CSF distance: 16s
- PBT2x thickness: 45s
- 98s
- Create initial surface 83s
- Topology correction: 90s
- Surface refinement: 80s
- Reduction of surface collisions with optimization: 67s
- Spherical mapping with areal smoothing 73s
- Spherical registration 262s
- Final surface processing results:
- Average thickness (FS): 2.4391 0.5865 mm
- Surface intensity / position RMSE: 0.0645 / 0.0598
- Euler number / defect number / defect size: 8.0 / 9.5 / 0.19%
- Display thickness: /var/lib/condor/execute/dir_24135/ds/sub-12/surf/lh.thickness.sub-12_T1w
- Display thickness: /var/lib/condor/execute/dir_24135/ds/sub-12/surf/rh.thickness.sub-12_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_24135/ds/sub-12/sub-12_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1679s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 26s
- ROI estimation of 'lpba40' atlas 7s
- ROI estimation of 'hammers' atlas 18s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 6s
- ROI estimation of 'aal3' atlas 11s
- ROI estimation of 'mori' atlas 16s
- ROI estimation of 'anatomy3' atlas 23s
- ROI estimation of 'julichbrain' atlas 30s
- 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 47s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 71s
- Write results 71s
- 298s
- Quality check: 4s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_24135/ds/sub-12/report/catreport_sub-12_T1w.pdf
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- CAT preprocessing takes 46 minute(s) and 54 second(s).
- Image Quality Rating (IQR): 80.71% (B-)
- GM volume (GMV): 46.06% (711.90 / 1545.72 ml)
- GM thickness (GMT): 2.44 0.59 mm
- Segmentations are saved in /var/lib/condor/execute/dir_24135/ds/sub-12/mri
- Reports are saved in /var/lib/condor/execute/dir_24135/ds/sub-12/report
- Labels are saved in /var/lib/condor/execute/dir_24135/ds/sub-12/label
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