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- CAT12.8.1 r1980: 1/1: ./sub-047EPKL013053/sub-047EPKL013053_ses-1_T1w.n
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- SANLM denoising (medium): 48s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 5s
- Initial correction 5s
- Refine background 2s
- Final correction 5s
- Final scaling 6s
- 32s
- Correct center-of-mass 4s
- Affine registration 11s
- SPM preprocessing 1 (estimate 1 - TPM registration): 6s
- Use initial fine affine registration. 4s
- Use previous fine affine registration. 58s
- SPM preprocessing 1 (estimate 2): 45s
- SPM preprocessing 2 (write):
- Write Segmentation 13s
- Update Segmentation 16s
- Update Skull-Stripping 32s
- Update probability maps 6s
- 69s
- Global intensity correction: 12s
- SANLM denoising after intensity normalization (medium): 15s
- Fast Optimized Shooting registration 28s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 13s
- Estimate local tissue thresholds (WM) 16s
- Estimate local tissue thresholds (GM) 22s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 27s
- 85s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 3s
- Ventricle detection 12s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 27s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 3s
- 66s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 32s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 3s
- 11s
- 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 | 0.0799 0.0000 0.0799 | 32.0000
- 2 | 2.50 | 0.0779 0.0010 0.0789 | 29.4886
- 3 | 2.50 | 0.0773 0.0015 0.0788 | 26.9772
- 4 | 2.50 | 0.0771 0.0016 0.0787 | 24.6107
- 5 | 2.50 | 0.0768 0.0017 0.0786 | 22.6548
- 6 | 2.50 | 0.0767 0.0018 0.0784 | 20.6989
- 7 | 2.50 | 0.0765 0.0018 0.0783 | 18.9688
- 8 | 2.50 | 0.0763 0.0019 0.0782 | 17.4455
- 9 | 2.50 | 0.0761 0.0020 0.0780 | 15.9223
- 10 | 2.50 | 0.0759 0.0020 0.0779 | 14.6627
- 11 | 2.50 | 0.0757 0.0021 0.0777 | 13.4764
- 12 | 2.50 | 0.0755 0.0021 0.0776 | 12.3015
- 13 | 2.50 | 0.0752 0.0022 0.0774 | 11.3776
- 14 | 2.50 | 0.0750 0.0022 0.0772 | 10.4537
- 15 | 2.25 | 0.0745 0.0022 0.0767 | 9.5920
- 16 | 2.25 | 0.0718 0.0036 0.0753 | 8.8725
- 29 | 2.00 | 0.0741 0.0016 0.0757 | 3.3283
- 30 | 2.00 | 0.0681 0.0041 0.0721 | 3.1221
- 31 | 2.00 | 0.0661 0.0049 0.0711 | 2.9160
- 43 | 1.75 | 0.0657 0.0028 0.0685 | 1.5785
- 44 | 1.75 | 0.0610 0.0053 0.0663 | 1.5194
- 45 | 1.75 | 0.0595 0.0061 0.0656 | 1.4626
- 57 | 1.50 | 0.0584 0.0044 0.0627 | 1.0900
- 58 | 1.50 | 0.0550 0.0066 0.0616 | 1.0730
- 59 | 1.50 | 0.0539 0.0072 0.0611 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 160s
- Prepare output 9s
- 169s
- Jacobian determinant (RMS): 0.008 0.027 0.046 0.076 0.106 | 0.113757
- Template Matching: 0.080 0.215 0.198 0.179 0.162 | 0.161707
- Write result maps: 19s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 23s
- CSF distance: 15s
- PBT2x thickness: 44s
- 87s
- Create initial surface 79s
- Topology correction: 96s
- Surface refinement: 70s
- Reduction of surface collisions with optimization: 78s
- Spherical mapping with areal smoothing 82s
- Spherical registration 333s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 28s
- CSF distance: 15s
- PBT2x thickness: 44s
- 92s
- Create initial surface 79s
- Topology correction: 96s
- Surface refinement: 86s
- Reduction of surface collisions with optimization: 85s
- Spherical mapping with areal smoothing 90s
- Spherical registration 296s
- Final surface processing results:
- Average thickness (FS): 2.7921 0.6826 mm
- Surface intensity / position RMSE: 0.0846 / 0.0916
- Euler number / defect number / defect size: 58.0 / 28.5 / 1.96%
- Display thickness: /var/lib/condor/execute/dir_7857/ds/sub-047EPKL013053/surf/lh.thickness.sub-047EPKL013053_ses-1_T1w
- Display thickness: /var/lib/condor/execute/dir_7857/ds/sub-047EPKL013053/surf/rh.thickness.sub-047EPKL013053_ses-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_7857/ds/sub-047EPKL013053/sub-047EPKL013053_ses-1_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1738s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 6s
- ROI estimation of 'neuromorphometrics' atlas 23s
- ROI estimation of 'lpba40' atlas 7s
- ROI estimation of 'hammers' atlas 17s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 6s
- ROI estimation of 'aal3' atlas 10s
- ROI estimation of 'mori' atlas 14s
- ROI estimation of 'anatomy3' atlas 20s
- ROI estimation of 'julichbrain' atlas 27s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 20s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 43s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 63s
- Write results 64s
- 270s
- Quality check: 5s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_7857/ds/sub-047EPKL013053/report/catreport_sub-047EPKL013053_ses-1_T1w.pdf
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- CAT preprocessing takes 47 minute(s) and 6 second(s).
- Image Quality Rating (IQR): 83.55% (B)
- GM volume (GMV): 58.14% (823.59 / 1416.54 ml)
- GM thickness (GMT): 2.79 0.68 mm
- Segmentations are saved in /var/lib/condor/execute/dir_7857/ds/sub-047EPKL013053/mri
- Reports are saved in /var/lib/condor/execute/dir_7857/ds/sub-047EPKL013053/report
- Labels are saved in /var/lib/condor/execute/dir_7857/ds/sub-047EPKL013053/label
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