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- CAT12.8.1 r1980: 1/1: ./dir_9764/ds/sub-0279/sub-0279_ses-01_T1w.n
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- SANLM denoising (medium): 146s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 9s
- Initial correction 15s
- Refine background 4s
- Final correction 9s
- Final scaling 7s
- 61s
- Correct center-of-mass 5s
- Affine registration 16s
- SPM preprocessing 1 (estimate 1 - TPM registration): 3s
- Use initial fine affine registration. 70s
- SPM preprocessing 1 (estimate 2): 75s
- SPM preprocessing 2 (write):
- Write Segmentation 22s
- Update Segmentation 22s
- Update Skull-Stripping 53s
- Update probability maps 12s
- 108s
- Global intensity correction: 22s
- SANLM denoising after intensity normalization (medium): 25s
- Fast Optimized Shooting registration 36s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 6s
- Prepare segments (LASmod = 1.19) 15s
- Estimate local tissue thresholds (WM) 23s
- Estimate local tissue thresholds (GM) 32s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 51s
- 135s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 4s
- Ventricle detection 13s
- Blood vessel detection 10s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 26s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 6s
- 71s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 34s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- 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
- 12s
- 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 | 0.0826 0.0000 0.0826 | 32.0000
- 2 | 2.50 | 0.0801 0.0011 0.0812 | 29.4886
- 3 | 2.50 | 0.0794 0.0017 0.0811 | 26.9772
- 4 | 2.50 | 0.0791 0.0019 0.0809 | 24.6107
- 5 | 2.50 | 0.0788 0.0020 0.0808 | 22.6548
- 6 | 2.50 | 0.0785 0.0021 0.0806 | 20.6989
- 7 | 2.50 | 0.0783 0.0022 0.0805 | 18.9688
- 8 | 2.50 | 0.0780 0.0022 0.0803 | 17.4455
- 9 | 2.50 | 0.0778 0.0023 0.0801 | 15.9223
- 10 | 2.50 | 0.0775 0.0024 0.0799 | 14.6627
- 11 | 2.50 | 0.0772 0.0025 0.0797 | 13.4764
- 12 | 2.50 | 0.0769 0.0025 0.0794 | 12.3015
- 13 | 2.50 | 0.0766 0.0026 0.0792 | 11.3776
- 14 | 2.50 | 0.0763 0.0026 0.0790 | 10.4537
- 15 | 2.25 | 0.0747 0.0027 0.0774 | 9.5920
- 16 | 2.25 | 0.0721 0.0040 0.0761 | 8.8725
- 29 | 2.00 | 0.0731 0.0018 0.0749 | 3.3283
- 30 | 2.00 | 0.0674 0.0041 0.0715 | 3.1221
- 31 | 2.00 | 0.0655 0.0050 0.0705 | 2.9160
- 43 | 1.75 | 0.0644 0.0029 0.0672 | 1.5785
- 44 | 1.75 | 0.0603 0.0050 0.0653 | 1.5194
- 45 | 1.75 | 0.0590 0.0058 0.0647 | 1.4626
- 57 | 1.50 | 0.0575 0.0042 0.0617 | 1.0900
- 58 | 1.50 | 0.0546 0.0061 0.0607 | 1.0730
- Shooting registration with 2.50:-0.25:1.50 mm takes: 131s
- Prepare output 11s
- 142s
- Jacobian determinant (RMS): 0.010 0.035 0.053 0.080 0.106 | 0.112023
- Template Matching: 0.083 0.216 0.196 0.177 0.164 | 0.163758
- Write result maps: 32s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 30s
- CSF distance: 13s
- PBT2x thickness: 39s
- 88s
- Create initial surface 71s
- Topology correction: 76s
- Surface refinement: 85s
- Reduction of surface collisions with optimization: 52s
- Spherical mapping with areal smoothing 65s
- Spherical registration 283s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 25s
- CSF distance: 13s
- PBT2x thickness: 38s
- 82s
- Create initial surface 71s
- Topology correction: 70s
- Surface refinement: 72s
- Reduction of surface collisions with optimization: 55s
- Spherical mapping with areal smoothing 66s
- Spherical registration 291s
- Final surface processing results:
- Average thickness (FS): 2.5813 0.6754 mm
- Surface intensity / position RMSE: 0.0793 / 0.0949
- Euler number / defect number / defect size: 60.0 / 21.0 / 2.29%
- Display thickness: /var/lib/condor/execute/dir_9764/ds/sub-0279/surf/lh.thickness.sub-0279_ses-01_T1w
- Display thickness: /var/lib/condor/execute/dir_9764/ds/sub-0279/surf/rh.thickness.sub-0279_ses-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_9764/ds/sub-0279/sub-0279_ses-01_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1521s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 11s
- ROI estimation of 'neuromorphometrics' atlas 40s
- ROI estimation of 'lpba40' atlas 12s
- ROI estimation of 'hammers' atlas 28s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 10s
- ROI estimation of 'aal3' atlas 16s
- ROI estimation of 'mori' atlas 24s
- ROI estimation of 'anatomy3' atlas 34s
- ROI estimation of 'julichbrain' atlas 45s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 18s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 32s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 73s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 110s
- Write results 111s
- 457s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_9764/ds/sub-0279/report/catreport_sub-0279_ses-01_T1w.pdf
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- CAT preprocessing takes 51 minute(s) and 17 second(s).
- Image Quality Rating (IQR): 82.66% (B-)
- GM volume (GMV): 50.76% (633.44 / 1247.79 ml)
- GM thickness (GMT): 2.58 0.68 mm
- Segmentations are saved in /var/lib/condor/execute/dir_9764/ds/sub-0279/mri
- Reports are saved in /var/lib/condor/execute/dir_9764/ds/sub-0279/report
- Labels are saved in /var/lib/condor/execute/dir_9764/ds/sub-0279/label
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