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- CAT12.8.1 r1980: 1/1: ./dir_15247/ds/sub-31/sub-31_acq-highres_T1w.n
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- SANLM denoising (medium): 42s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 7s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 4s
- 36s
- Correct center-of-mass 2s
- Affine registration 8s
- SPM preprocessing 1 (estimate 1 - TPM registration): 64s
- SPM preprocessing 1 (estimate 2): 52s
- SPM preprocessing 2 (write):
- Write Segmentation 15s
- Update Segmentation 17s
- Update Skull-Stripping 40s
- Update probability maps 8s
- 80s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 7s
- Fast Optimized Shooting registration 30s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 4s
- Prepare segments (LASmod = 1.00) 14s
- Estimate local tissue thresholds (WM) 19s
- Estimate local tissue thresholds (GM) 25s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 33s
- 102s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 19s
- Blood vessel detection 9s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.03) 28s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 3s
- Final corrections 4s
- 77s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 34s
- 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 | 0.0838 0.0000 0.0838 | 32.0000
- 2 | 2.50 | 0.0810 0.0012 0.0822 | 29.4886
- 3 | 2.50 | 0.0802 0.0018 0.0820 | 26.9772
- 4 | 2.50 | 0.0797 0.0021 0.0818 | 24.6107
- 5 | 2.50 | 0.0794 0.0022 0.0816 | 22.6548
- 6 | 2.50 | 0.0791 0.0023 0.0814 | 20.6989
- 7 | 2.50 | 0.0789 0.0024 0.0813 | 18.9688
- 8 | 2.50 | 0.0786 0.0025 0.0810 | 17.4455
- 9 | 2.50 | 0.0783 0.0026 0.0808 | 15.9223
- 10 | 2.50 | 0.0779 0.0027 0.0806 | 14.6627
- 11 | 2.50 | 0.0776 0.0027 0.0803 | 13.4764
- 12 | 2.50 | 0.0773 0.0028 0.0801 | 12.3015
- 13 | 2.50 | 0.0769 0.0029 0.0798 | 11.3776
- 14 | 2.50 | 0.0766 0.0029 0.0796 | 10.4537
- 15 | 2.25 | 0.0761 0.0030 0.0791 | 9.5920
- 16 | 2.25 | 0.0732 0.0044 0.0776 | 8.8725
- 29 | 2.00 | 0.0743 0.0020 0.0763 | 3.3283
- 30 | 2.00 | 0.0687 0.0043 0.0730 | 3.1221
- 31 | 2.00 | 0.0667 0.0052 0.0720 | 2.9160
- 43 | 1.75 | 0.0657 0.0030 0.0687 | 1.5785
- 44 | 1.75 | 0.0615 0.0052 0.0667 | 1.5194
- 45 | 1.75 | 0.0601 0.0060 0.0661 | 1.4626
- 57 | 1.50 | 0.0588 0.0044 0.0632 | 1.0900
- 58 | 1.50 | 0.0556 0.0064 0.0621 | 1.0730
- 59 | 1.50 | 0.0546 0.0070 0.0616 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 157s
- Prepare output 10s
- 168s
- Jacobian determinant (RMS): 0.011 0.039 0.057 0.080 0.102 | 0.108814
- Template Matching: 0.084 0.220 0.200 0.180 0.164 | 0.163785
- Write result maps: 25s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 41s
- CSF distance: 15s
- PBT2x thickness: 45s
- 108s
- Create initial surface 82s
- Topology correction: 95s
- Surface refinement: 106s
- Reduction of surface collisions with optimization: 75s
- Spherical mapping with areal smoothing 90s
- Spherical registration 286s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 40s
- CSF distance: 15s
- PBT2x thickness: 46s
- 107s
- Create initial surface 84s
- Topology correction: 96s
- Surface refinement: 103s
- Reduction of surface collisions with optimization: 74s
- Spherical mapping with areal smoothing 87s
- Spherical registration 288s
- Final surface processing results:
- Average thickness (FS): 2.5231 0.6184 mm
- Surface intensity / position RMSE: 0.0681 / 0.0705
- Euler number / defect number / defect size: 24.0 / 15.0 / 0.60%
- Display thickness: /var/lib/condor/execute/dir_15247/ds/sub-31/surf/lh.thickness.sub-31_acq-highres_T1w
- Display thickness: /var/lib/condor/execute/dir_15247/ds/sub-31/surf/rh.thickness.sub-31_acq-highres_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_15247/ds/sub-31/sub-31_acq-highres_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1777s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 32s
- ROI estimation of 'lpba40' atlas 9s
- ROI estimation of 'hammers' atlas 22s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 8s
- ROI estimation of 'aal3' atlas 13s
- ROI estimation of 'mori' atlas 19s
- ROI estimation of 'anatomy3' atlas 27s
- ROI estimation of 'julichbrain' atlas 36s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 26s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 64s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 93s
- Write results 94s
- 375s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_15247/ds/sub-31/report/catreport_sub-31_acq-highres_T1w.pdf
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- CAT preprocessing takes 50 minute(s) and 42 second(s).
- Image Quality Rating (IQR): 85.12% (B)
- GM volume (GMV): 48.80% (763.45 / 1564.42 ml)
- GM thickness (GMT): 2.52 0.62 mm
- Segmentations are saved in /var/lib/condor/execute/dir_15247/ds/sub-31/mri
- Reports are saved in /var/lib/condor/execute/dir_15247/ds/sub-31/report
- Labels are saved in /var/lib/condor/execute/dir_15247/ds/sub-31/label
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