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- CAT12.8.1 r1980: 1/1: ./execute/dir_15375/ds/sub-145/sub-145_T1w.n
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- SANLM denoising (medium): 56s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 7s
- Initial correction 7s
- Refine background 4s
- Final correction 6s
- Final scaling 7s
- 43s
- Correct center-of-mass 5s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 6s
- Use initial fine affine registration. 59s
- SPM preprocessing 1 (estimate 2): 57s
- SPM preprocessing 2 (write):
- Write Segmentation 15s
- Update Segmentation 16s
- Update Skull-Stripping 36s
- Update probability maps 8s
- 75s
- Global intensity correction: 15s
- SANLM denoising after intensity normalization (medium): 10s
- Fast Optimized Shooting registration 33s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.16) 11s
- Estimate local tissue thresholds (WM) 19s
- Estimate local tissue thresholds (GM) 25s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 20s
- 84s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 10s
- Blood vessel detection 7s
- WMH detection (WMHCstr=0.48 > WMHCstr'=0.07) 20s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 55s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 28s
- AMAP peaks: [CSF,GM,WM] = [0.360.07,0.680.07,0.980.05]
- Final cleanup (gcutstr=0.24):
- Level 1 cleanup (ROI estimation) 3s
- 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 | 0.0893 0.0000 0.0893 | 32.0000
- 2 | 2.50 | 0.0855 0.0015 0.0870 | 29.4886
- 3 | 2.50 | 0.0843 0.0024 0.0867 | 26.9772
- 4 | 2.50 | 0.0838 0.0027 0.0864 | 24.6107
- 5 | 2.50 | 0.0833 0.0029 0.0862 | 22.6548
- 6 | 2.50 | 0.0829 0.0030 0.0859 | 20.6989
- 7 | 2.50 | 0.0826 0.0031 0.0857 | 18.9688
- 8 | 2.50 | 0.0821 0.0033 0.0854 | 17.4455
- 9 | 2.50 | 0.0817 0.0034 0.0851 | 15.9223
- 10 | 2.50 | 0.0813 0.0035 0.0848 | 14.6627
- 11 | 2.50 | 0.0809 0.0036 0.0845 | 13.4764
- 12 | 2.50 | 0.0804 0.0037 0.0841 | 12.3015
- 13 | 2.50 | 0.0799 0.0038 0.0838 | 11.3776
- 14 | 2.50 | 0.0795 0.0039 0.0834 | 10.4537
- 15 | 2.25 | 0.0798 0.0040 0.0839 | 9.5920
- 16 | 2.25 | 0.0762 0.0058 0.0820 | 8.8725
- 17 | 2.25 | 0.0748 0.0064 0.0812 | 8.1530
- 29 | 2.00 | 0.0764 0.0029 0.0794 | 3.3283
- 30 | 2.00 | 0.0701 0.0056 0.0757 | 3.1221
- 31 | 2.00 | 0.0678 0.0067 0.0745 | 2.9160
- 43 | 1.75 | 0.0666 0.0039 0.0705 | 1.5785
- 44 | 1.75 | 0.0622 0.0062 0.0684 | 1.5194
- 45 | 1.75 | 0.0607 0.0070 0.0677 | 1.4626
- 57 | 1.50 | 0.0594 0.0052 0.0645 | 1.0900
- 58 | 1.50 | 0.0562 0.0073 0.0635 | 1.0730
- 59 | 1.50 | 0.0552 0.0078 0.0630 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 161s
- Prepare output 9s
- 170s
- Jacobian determinant (RMS): 0.013 0.047 0.071 0.096 0.129 | 0.126807
- Template Matching: 0.089 0.224 0.204 0.182 0.166 | 0.165506
- Write result maps: 22s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 29s
- CSF distance: 13s
- PBT2x thickness: 39s
- 87s
- Create initial surface 74s
- Topology correction: 71s
- Surface refinement: 59s
- Reduction of surface collisions with optimization: 55s
- Spherical mapping with areal smoothing 72s
- Spherical registration 305s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 31s
- CSF distance: 13s
- PBT2x thickness: 38s
- 87s
- Create initial surface 70s
- Topology correction: 70s
- Surface refinement: 66s
- Reduction of surface collisions with optimization: 55s
- Spherical mapping with areal smoothing 72s
- Spherical registration 276s
- Final surface processing results:
- Average thickness (FS): 2.4670 0.5838 mm
- Surface intensity / position RMSE: 0.0635 / 0.0634
- Euler number / defect number / defect size: 6.0 / 7.0 / 0.21%
- Display thickness: /var/lib/condor/execute/dir_15375/ds/sub-145/surf/lh.thickness.sub-145_T1w
- Display thickness: /var/lib/condor/execute/dir_15375/ds/sub-145/surf/rh.thickness.sub-145_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_15375/ds/sub-145/sub-145_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1497s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 26s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 18s
- ROI estimation of 'thalamus' atlas 1s
- 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 30s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 22s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 49s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 71s
- Write results 71s
- 303s
- Quality check: 4s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_15375/ds/sub-145/report/catreport_sub-145_T1w.pdf
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- CAT preprocessing takes 43 minute(s) and 30 second(s).
- Image Quality Rating (IQR): 82.21% (B-)
- GM volume (GMV): 47.41% (597.55 / 1260.38 ml)
- GM thickness (GMT): 2.47 0.58 mm
- Segmentations are saved in /var/lib/condor/execute/dir_15375/ds/sub-145/mri
- Reports are saved in /var/lib/condor/execute/dir_15375/ds/sub-145/report
- Labels are saved in /var/lib/condor/execute/dir_15375/ds/sub-145/label
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