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- CAT12.8.1 r1980: 1/1: ./sub-2525JK/sub-2525JK_acq-MPRAGE_run-01_T1w.n
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- SANLM denoising (medium): 43s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 8s
- Initial correction 7s
- Refine background 3s
- Final correction 5s
- Final scaling 6s
- 41s
- Correct center-of-mass 6s
- Affine registration 13s
- SPM preprocessing 1 (estimate 1 - TPM registration): 65s
- SPM preprocessing 1 (estimate 2): 70s
- SPM preprocessing 2 (write):
- Write Segmentation 17s
- Update Segmentation 20s
- Update Skull-Stripping 41s
- Update probability maps 8s
- 87s
- Global intensity correction: 15s
- SANLM denoising after intensity normalization (medium): 10s
- Fast Optimized Shooting registration 31s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.02) 15s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 26s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 24s
- 94s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 19s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.03) 28s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 4s
- 79s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 36s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.990.04]
- 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
- 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 | 0.0802 0.0000 0.0802 | 32.0000
- 2 | 2.50 | 0.0782 0.0010 0.0791 | 29.4886
- 3 | 2.50 | 0.0776 0.0015 0.0791 | 26.9772
- 4 | 2.50 | 0.0773 0.0016 0.0789 | 24.6107
- 5 | 2.50 | 0.0771 0.0018 0.0788 | 22.6548
- 6 | 2.50 | 0.0769 0.0018 0.0787 | 20.6989
- 7 | 2.50 | 0.0767 0.0019 0.0785 | 18.9688
- 8 | 2.50 | 0.0764 0.0020 0.0784 | 17.4455
- 9 | 2.50 | 0.0762 0.0020 0.0782 | 15.9223
- 10 | 2.50 | 0.0760 0.0021 0.0781 | 14.6627
- 11 | 2.50 | 0.0757 0.0022 0.0779 | 13.4764
- 12 | 2.50 | 0.0755 0.0022 0.0777 | 12.3015
- 13 | 2.50 | 0.0752 0.0023 0.0775 | 11.3776
- 14 | 2.50 | 0.0750 0.0023 0.0773 | 10.4537
- 15 | 2.25 | 0.0734 0.0024 0.0758 | 9.5920
- 16 | 2.25 | 0.0709 0.0036 0.0745 | 8.8725
- 29 | 2.00 | 0.0722 0.0016 0.0738 | 3.3283
- 30 | 2.00 | 0.0668 0.0038 0.0706 | 3.1221
- 31 | 2.00 | 0.0650 0.0047 0.0697 | 2.9160
- 43 | 1.75 | 0.0642 0.0027 0.0669 | 1.5785
- 44 | 1.75 | 0.0602 0.0048 0.0650 | 1.5194
- 45 | 1.75 | 0.0588 0.0056 0.0644 | 1.4626
- 57 | 1.50 | 0.0573 0.0041 0.0614 | 1.0900
- 58 | 1.50 | 0.0543 0.0060 0.0603 | 1.0730
- 59 | 1.50 | 0.0532 0.0066 0.0599 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 159s
- Prepare output 10s
- 169s
- Jacobian determinant (RMS): 0.010 0.036 0.053 0.076 0.098 | 0.104959
- Template Matching: 0.080 0.213 0.195 0.176 0.160 | 0.159731
- Write result maps: 22s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 38s
- CSF distance: 18s
- PBT2x thickness: 51s
- 113s
- Create initial surface 95s
- Topology correction: 108s
- Surface refinement: 102s
- Reduction of surface collisions with optimization: 88s
- Spherical mapping with areal smoothing 102s
- Spherical registration 298s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 34s
- CSF distance: 17s
- PBT2x thickness: 50s
- 108s
- Create initial surface 91s
- Topology correction: 99s
- Surface refinement: 124s
- Reduction of surface collisions with optimization: 84s
- Spherical mapping with areal smoothing 95s
- Spherical registration 304s
- Final surface processing results:
- Average thickness (FS): 2.6202 0.5993 mm
- Surface intensity / position RMSE: 0.0675 / 0.0721
- Euler number / defect number / defect size: 18.0 / 20.0 / 0.42%
- Display thickness: /var/lib/condor/execute/dir_7616/ds/sub-2525JK/surf/lh.thickness.sub-2525JK_acq-MPRAGE_run-01_T1w
- Display thickness: /var/lib/condor/execute/dir_7616/ds/sub-2525JK/surf/rh.thickness.sub-2525JK_acq-MPRAGE_run-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_7616/ds/sub-2525JK/sub-2525JK_acq-MPRAGE_run-01_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1908s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 8s
- ROI estimation of 'neuromorphometrics' atlas 27s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 19s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 11s
- ROI estimation of 'mori' atlas 16s
- ROI estimation of 'anatomy3' atlas 23s
- ROI estimation of 'julichbrain' atlas 31s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 13s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 22s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 51s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 75s
- Write results 76s
- 312s
- Quality check: 5s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_7616/ds/sub-2525JK/report/catreport_sub-2525JK_acq-MPRAGE_run-01_T1w.pdf
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- CAT preprocessing takes 51 minute(s) and 52 second(s).
- Image Quality Rating (IQR): 84.80% (B)
- GM volume (GMV): 48.60% (803.81 / 1654.04 ml)
- GM thickness (GMT): 2.62 0.60 mm
- Segmentations are saved in /var/lib/condor/execute/dir_7616/ds/sub-2525JK/mri
- Reports are saved in /var/lib/condor/execute/dir_7616/ds/sub-2525JK/report
- Labels are saved in /var/lib/condor/execute/dir_7616/ds/sub-2525JK/label
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