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- CAT12.8.1 r1980: 1/1: ./dir_26212/ds/sub-0261/sub-0261_ses-01_T1w.n
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- SANLM denoising (medium): 77s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 8s
- Initial correction 16s
- Refine background 4s
- Final correction 8s
- Final scaling 7s
- 60s
- Correct center-of-mass 4s
- Affine registration 21s
- SPM preprocessing 1 (estimate 1 - TPM registration): 90s
- SPM preprocessing 1 (estimate 2): 79s
- SPM preprocessing 2 (write):
- Write Segmentation 20s
- Update Segmentation 23s
- Update Skull-Stripping 50s
- Update probability maps 11s
- 104s
- Global intensity correction: 21s
- SANLM denoising after intensity normalization (medium): 13s
- Fast Optimized Shooting registration 34s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.00) 16s
- Estimate local tissue thresholds (WM) 22s
- Estimate local tissue thresholds (GM) 30s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 43s
- 123s
- 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) 33s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 86s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 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 | 0.0864 0.0000 0.0864 | 32.0000
- 2 | 2.50 | 0.0825 0.0015 0.0840 | 29.4886
- 3 | 2.50 | 0.0814 0.0023 0.0837 | 26.9772
- 4 | 2.50 | 0.0809 0.0026 0.0835 | 24.6107
- 5 | 2.50 | 0.0804 0.0028 0.0832 | 22.6548
- 6 | 2.50 | 0.0801 0.0029 0.0830 | 20.6989
- 7 | 2.50 | 0.0797 0.0030 0.0827 | 18.9688
- 8 | 2.50 | 0.0793 0.0031 0.0824 | 17.4455
- 9 | 2.50 | 0.0789 0.0032 0.0821 | 15.9223
- 10 | 2.50 | 0.0785 0.0033 0.0818 | 14.6627
- 11 | 2.50 | 0.0781 0.0034 0.0815 | 13.4764
- 12 | 2.50 | 0.0777 0.0035 0.0812 | 12.3015
- 13 | 2.50 | 0.0772 0.0036 0.0808 | 11.3776
- 14 | 2.50 | 0.0768 0.0037 0.0805 | 10.4537
- 15 | 2.25 | 0.0759 0.0038 0.0797 | 9.5920
- 16 | 2.25 | 0.0726 0.0054 0.0780 | 8.8725
- 29 | 2.00 | 0.0725 0.0024 0.0749 | 3.3283
- 30 | 2.00 | 0.0665 0.0048 0.0713 | 3.1221
- 31 | 2.00 | 0.0645 0.0058 0.0703 | 2.9160
- 43 | 1.75 | 0.0632 0.0033 0.0665 | 1.5785
- 44 | 1.75 | 0.0595 0.0053 0.0648 | 1.5194
- 45 | 1.75 | 0.0583 0.0059 0.0643 | 1.4626
- 57 | 1.50 | 0.0571 0.0043 0.0614 | 1.0900
- 58 | 1.50 | 0.0544 0.0061 0.0605 | 1.0730
- Shooting registration with 2.50:-0.25:1.50 mm takes: 135s
- Prepare output 11s
- 146s
- Jacobian determinant (RMS): 0.013 0.047 0.068 0.091 0.112 | 0.116510
- Template Matching: 0.086 0.218 0.194 0.175 0.163 | 0.163050
- Write result maps: 29s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 27s
- CSF distance: 14s
- PBT2x thickness: 42s
- 89s
- Create initial surface 78s
- Topology correction: 87s
- Surface refinement: 97s
- Reduction of surface collisions with optimization: 63s
- Spherical mapping with areal smoothing 85s
- Spherical registration 286s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 31s
- CSF distance: 14s
- PBT2x thickness: 41s
- 91s
- Create initial surface 78s
- Topology correction: 85s
- Surface refinement: 68s
- Reduction of surface collisions with optimization: 63s
- Spherical mapping with areal smoothing 75s
- Spherical registration 280s
- Final surface processing results:
- Average thickness (FS): 2.5382 0.6425 mm
- Surface intensity / position RMSE: 0.0762 / 0.0760
- Euler number / defect number / defect size: 38.0 / 21.0 / 0.97%
- Display thickness: /var/lib/condor/execute/dir_26212/ds/sub-0261/surf/lh.thickness.sub-0261_ses-01_T1w
- Display thickness: /var/lib/condor/execute/dir_26212/ds/sub-0261/surf/rh.thickness.sub-0261_ses-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_26212/ds/sub-0261/sub-0261_ses-01_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1619s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 10s
- ROI estimation of 'neuromorphometrics' atlas 37s
- ROI estimation of 'lpba40' atlas 11s
- ROI estimation of 'hammers' atlas 26s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 9s
- ROI estimation of 'aal3' atlas 15s
- ROI estimation of 'mori' atlas 23s
- ROI estimation of 'anatomy3' atlas 33s
- ROI estimation of 'julichbrain' atlas 43s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 31s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 70s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 105s
- Write results 106s
- 434s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_26212/ds/sub-0261/report/catreport_sub-0261_ses-01_T1w.pdf
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- CAT preprocessing takes 51 minute(s) and 53 second(s).
- Image Quality Rating (IQR): 82.79% (B-)
- GM volume (GMV): 49.40% (681.79 / 1380.19 ml)
- GM thickness (GMT): 2.54 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_26212/ds/sub-0261/mri
- Reports are saved in /var/lib/condor/execute/dir_26212/ds/sub-0261/report
- Labels are saved in /var/lib/condor/execute/dir_26212/ds/sub-0261/label
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