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- CAT12.8.1 r1980: 1/1: ./dir_16358/ds/sub-203/sub-203_ses-20110727_T1w.n
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- SANLM denoising (medium): 26s
- Internal resampling (3.90x0.56x0.56mm > 1.00x1.00x1.00mm): 1s
- APP: Rough bias correction:
- Initialize 4s
- Estimate background 6s
- Initial correction 5s
- Refine background 2s
- Final correction 5s
- Final scaling 4s
- 31s
- Correct center-of-mass 4s
- Affine registration 8s
- SPM preprocessing 1 (estimate 1 - TPM registration): 66s
- SPM preprocessing 1 (estimate 2): 67s
- SPM preprocessing 2 (write):
- Write Segmentation 12s
- Update Segmentation 16s
- Update Skull-Stripping 30s
- Update probability maps 11s
- 70s
- Global intensity correction: 11s
- SANLM denoising after intensity normalization (medium): 12s
- Fast Optimized Shooting registration 27s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 1s
- Prepare segments (LASmod = 1.63) 12s
- Estimate local tissue thresholds (WM) 11s
- Estimate local tissue thresholds (GM) 13s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 21s
- 64s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 3s
- Ventricle detection 10s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.23) 20s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 3s
- 54s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 28s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.970.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 2s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 9s
- 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 | 0.0921 0.0000 0.0921 | 32.0000
- 2 | 2.50 | 0.0883 0.0015 0.0898 | 29.4886
- 3 | 2.50 | 0.0871 0.0024 0.0895 | 26.9772
- 4 | 2.50 | 0.0865 0.0027 0.0892 | 24.6107
- 5 | 2.50 | 0.0860 0.0029 0.0890 | 22.6548
- 6 | 2.50 | 0.0856 0.0031 0.0887 | 20.6989
- 7 | 2.50 | 0.0852 0.0032 0.0884 | 18.9688
- 8 | 2.50 | 0.0848 0.0034 0.0881 | 17.4455
- 9 | 2.50 | 0.0843 0.0035 0.0878 | 15.9223
- 10 | 2.50 | 0.0838 0.0036 0.0875 | 14.6627
- 11 | 2.50 | 0.0834 0.0038 0.0871 | 13.4764
- 12 | 2.50 | 0.0829 0.0039 0.0868 | 12.3015
- 13 | 2.50 | 0.0824 0.0040 0.0864 | 11.3776
- 14 | 2.50 | 0.0819 0.0041 0.0860 | 10.4537
- 15 | 2.25 | 0.0832 0.0043 0.0875 | 9.5920
- 16 | 2.25 | 0.0794 0.0062 0.0856 | 8.8725
- 17 | 2.25 | 0.0778 0.0069 0.0847 | 8.1530
- 18 | 2.25 | 0.0768 0.0072 0.0840 | 7.5234
- 19 | 2.25 | 0.0760 0.0074 0.0834 | 6.9630
- 20 | 2.25 | 0.0753 0.0074 0.0827 | 6.4027
- 21 | 2.25 | 0.0747 0.0074 0.0821 | 5.9447
- 29 | 2.00 | 0.0765 0.0044 0.0809 | 3.3283
- 30 | 2.00 | 0.0715 0.0067 0.0783 | 3.1221
- 31 | 2.00 | 0.0697 0.0076 0.0773 | 2.9160
- 43 | 1.75 | 0.0687 0.0043 0.0730 | 1.5785
- 44 | 1.75 | 0.0639 0.0069 0.0708 | 1.5194
- 45 | 1.75 | 0.0624 0.0078 0.0702 | 1.4626
- 57 | 1.50 | 0.0615 0.0057 0.0672 | 1.0900
- 58 | 1.50 | 0.0581 0.0080 0.0661 | 1.0730
- 59 | 1.50 | 0.0570 0.0087 0.0657 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 171s
- Prepare output 9s
- 180s
- Jacobian determinant (RMS): 0.013 0.052 0.084 0.111 0.139 | 0.147830
- Template Matching: 0.092 0.224 0.209 0.187 0.171 | 0.170990
- Write result maps: 52s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 27s
- CSF distance: 14s
- PBT2x thickness: 40s
- 87s
- Create initial surface 89s
- Topology correction: 98s
- Surface refinement: 97s
- Reduction of surface collisions with optimization: 62s
- Spherical mapping with areal smoothing 77s
- Spherical registration 300s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 30s
- CSF distance: 13s
- PBT2x thickness: 38s
- 87s
- Create initial surface 84s
- Topology correction: 95s
- Surface refinement: 83s
- Reduction of surface collisions with optimization: 61s
- Spherical mapping with areal smoothing 75s
- Spherical registration 309s
- Final surface processing results:
- Average thickness (FS): 2.0914 0.5996 mm
- Surface intensity / position RMSE: 0.0795 / 0.0929
- Euler number / defect number / defect size: 106.0 / 71.0 / 3.61%
- Display thickness: /var/lib/condor/execute/dir_16358/ds/sub-203/surf/lh.thickness.sub-203_ses-20110727_T1w
- Display thickness: /var/lib/condor/execute/dir_16358/ds/sub-203/surf/rh.thickness.sub-203_ses-20110727_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_16358/ds/sub-203/sub-203_ses-20110727_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1690s
- 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 15s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 5s
- ROI estimation of 'aal3' atlas 10s
- ROI estimation of 'mori' atlas 13s
- ROI estimation of 'anatomy3' atlas 18s
- ROI estimation of 'julichbrain' atlas 23s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 9s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 17s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 36s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 53s
- Write results 54s
- 238s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_16358/ds/sub-203/report/catreport_sub-203_ses-20110727_T1w.pdf
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- CAT preprocessing takes 45 minute(s) and 19 second(s).
- Image Quality Rating (IQR): 60.51% (D-)
- GM volume (GMV): 41.02% (589.68 / 1437.56 ml)
- GM thickness (GMT): 2.09 0.60 mm
- Segmentations are saved in /var/lib/condor/execute/dir_16358/ds/sub-203/mri
- Reports are saved in /var/lib/condor/execute/dir_16358/ds/sub-203/report
- Labels are saved in /var/lib/condor/execute/dir_16358/ds/sub-203/label
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