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- CAT12.8.1 r1980: 1/1: ./dir_15333/ds/sub-0406/sub-0406_ses-01_T1w.n
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- SANLM denoising (medium): 168s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 9s
- Initial correction 17s
- Refine background 5s
- Final correction 9s
- Final scaling 7s
- 62s
- Correct center-of-mass 5s
- Affine registration 20s
- SPM preprocessing 1 (estimate 1 - TPM registration): 93s
- SPM preprocessing 1 (estimate 2): 78s
- SPM preprocessing 2 (write):
- Write Segmentation 21s
- Update Segmentation 23s
- Update Skull-Stripping 52s
- Update probability maps 11s
- 107s
- Global intensity correction: 22s
- SANLM denoising after intensity normalization (medium): 25s
- Fast Optimized Shooting registration 36s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.13) 17s
- Estimate local tissue thresholds (WM) 22s
- Estimate local tissue thresholds (GM) 32s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 57s
- 141s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 4s
- Ventricle detection 18s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 34s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 88s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 36s
- 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) 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 | 0.0888 0.0000 0.0888 | 32.0000
- 2 | 2.50 | 0.0855 0.0014 0.0869 | 29.4886
- 3 | 2.50 | 0.0845 0.0021 0.0866 | 26.9772
- 4 | 2.50 | 0.0840 0.0024 0.0864 | 24.6107
- 5 | 2.50 | 0.0837 0.0026 0.0862 | 22.6548
- 6 | 2.50 | 0.0833 0.0027 0.0860 | 20.6989
- 7 | 2.50 | 0.0830 0.0028 0.0858 | 18.9688
- 8 | 2.50 | 0.0826 0.0029 0.0855 | 17.4455
- 9 | 2.50 | 0.0823 0.0030 0.0853 | 15.9223
- 10 | 2.50 | 0.0819 0.0031 0.0850 | 14.6627
- 11 | 2.50 | 0.0815 0.0032 0.0847 | 13.4764
- 12 | 2.50 | 0.0811 0.0033 0.0844 | 12.3015
- 13 | 2.50 | 0.0807 0.0034 0.0841 | 11.3776
- 14 | 2.50 | 0.0803 0.0035 0.0838 | 10.4537
- 15 | 2.25 | 0.0813 0.0036 0.0848 | 9.5920
- 16 | 2.25 | 0.0779 0.0053 0.0831 | 8.8725
- 17 | 2.25 | 0.0766 0.0058 0.0824 | 8.1530
- 18 | 2.25 | 0.0757 0.0061 0.0818 | 7.5234
- 19 | 2.25 | 0.0750 0.0062 0.0812 | 6.9630
- 20 | 2.25 | 0.0745 0.0062 0.0806 | 6.4027
- 29 | 2.00 | 0.0763 0.0034 0.0797 | 3.3283
- 30 | 2.00 | 0.0714 0.0056 0.0770 | 3.1221
- 31 | 2.00 | 0.0697 0.0065 0.0761 | 2.9160
- 43 | 1.75 | 0.0689 0.0037 0.0726 | 1.5785
- 44 | 1.75 | 0.0644 0.0061 0.0705 | 1.5194
- 45 | 1.75 | 0.0630 0.0069 0.0699 | 1.4626
- 57 | 1.50 | 0.0619 0.0051 0.0670 | 1.0900
- 58 | 1.50 | 0.0585 0.0073 0.0658 | 1.0730
- 59 | 1.50 | 0.0574 0.0080 0.0655 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 173s
- Prepare output 12s
- 184s
- Jacobian determinant (RMS): 0.012 0.044 0.070 0.095 0.122 | 0.129826
- Template Matching: 0.089 0.223 0.209 0.189 0.172 | 0.172342
- Write result maps: 30s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 26s
- CSF distance: 14s
- PBT2x thickness: 42s
- 88s
- Create initial surface 78s
- Topology correction: 77s
- Surface refinement: 74s
- Reduction of surface collisions with optimization: 60s
- Spherical mapping with areal smoothing 77s
- Spherical registration 300s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 34s
- CSF distance: 15s
- PBT2x thickness: 41s
- 95s
- Create initial surface 77s
- Topology correction: 89s
- Surface refinement: 80s
- Reduction of surface collisions with optimization: 59s
- Spherical mapping with areal smoothing 77s
- Spherical registration 282s
- Final surface processing results:
- Average thickness (FS): 2.4585 0.6099 mm
- Surface intensity / position RMSE: 0.0764 / 0.0809
- Euler number / defect number / defect size: 36.0 / 22.0 / 1.29%
- Display thickness: /var/lib/condor/execute/dir_15333/ds/sub-0406/surf/lh.thickness.sub-0406_ses-01_T1w
- Display thickness: /var/lib/condor/execute/dir_15333/ds/sub-0406/surf/rh.thickness.sub-0406_ses-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_15333/ds/sub-0406/sub-0406_ses-01_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1613s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 12s
- ROI estimation of 'neuromorphometrics' atlas 40s
- ROI estimation of 'lpba40' atlas 12s
- ROI estimation of 'hammers' atlas 30s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 10s
- ROI estimation of 'aal3' atlas 16s
- ROI estimation of 'mori' atlas 26s
- ROI estimation of 'anatomy3' atlas 34s
- ROI estimation of 'julichbrain' atlas 46s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 18s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 31s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 72s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 109s
- Write results 109s
- 461s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_15333/ds/sub-0406/report/catreport_sub-0406_ses-01_T1w.pdf
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- CAT preprocessing takes 55 minute(s) and 19 second(s).
- Image Quality Rating (IQR): 80.86% (B-)
- GM volume (GMV): 47.89% (649.27 / 1355.75 ml)
- GM thickness (GMT): 2.46 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_15333/ds/sub-0406/mri
- Reports are saved in /var/lib/condor/execute/dir_15333/ds/sub-0406/report
- Labels are saved in /var/lib/condor/execute/dir_15333/ds/sub-0406/label
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