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- CAT12.8.1 r1980: 1/1: ./sub-season117_ses-3_acq-MPrageHiRes_T1w.n
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- SANLM denoising (medium): 31s
- APP: Rough bias correction:
- Initialize 9s
- Estimate background 11s
- Initial correction 32s
- Refine background 5s
- Final correction 21s
- Final scaling 12s
- 99s
- Correct center-of-mass 2s
- Affine registration 18s
- SPM preprocessing 1 (estimate 1 - TPM registration): 125s
- SPM preprocessing 1 (estimate 2): 111s
- SPM preprocessing 2 (write):
- Write Segmentation 26s
- Update Segmentation 33s
- Update Skull-Stripping 67s
- Update probability maps 13s
- 139s
- Global intensity correction: 24s
- SANLM denoising after intensity normalization (medium): 15s
- Fast Optimized Shooting registration 43s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 7s
- Prepare partitions 4s
- Prepare segments (LASmod = 1.06) 27s
- Estimate local tissue thresholds (WM) 35s
- Estimate local tissue thresholds (GM) 49s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 39s
- 167s
- ROI segmentation (partitioning):
- Atlas -> subject space 13s
- Major structures 7s
- Ventricle detection 24s
- Blood vessel detection 20s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 56s
- Manual stroke lesion detection 0s
- Closing of deep structures 3s
- Side alignment 6s
- Final corrections 7s
- 136s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 52s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 8s
- Level 1 cleanup (brain masking) 5s
- Level 2 cleanup (CSF correction) 3s
- Level 3 cleanup (CSF/WM PVE) 5s
- 22s
- 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 | 0.0824 0.0000 0.0824 | 32.0000
- 2 | 2.50 | 0.0798 0.0012 0.0810 | 29.4886
- 3 | 2.50 | 0.0791 0.0017 0.0808 | 26.9772
- 4 | 2.50 | 0.0787 0.0020 0.0806 | 24.6107
- 5 | 2.50 | 0.0784 0.0021 0.0805 | 22.6548
- 6 | 2.50 | 0.0781 0.0022 0.0803 | 20.6989
- 7 | 2.50 | 0.0779 0.0023 0.0801 | 18.9688
- 8 | 2.50 | 0.0776 0.0024 0.0799 | 17.4455
- 9 | 2.50 | 0.0773 0.0024 0.0797 | 15.9223
- 10 | 2.50 | 0.0770 0.0025 0.0795 | 14.6627
- 11 | 2.50 | 0.0767 0.0026 0.0793 | 13.4764
- 12 | 2.50 | 0.0764 0.0027 0.0790 | 12.3015
- 13 | 2.50 | 0.0761 0.0028 0.0788 | 11.3776
- 14 | 2.50 | 0.0757 0.0028 0.0786 | 10.4537
- 15 | 2.25 | 0.0753 0.0029 0.0782 | 9.5920
- 16 | 2.25 | 0.0725 0.0042 0.0767 | 8.8725
- 29 | 2.00 | 0.0737 0.0019 0.0757 | 3.3283
- 30 | 2.00 | 0.0677 0.0043 0.0721 | 3.1221
- 31 | 2.00 | 0.0656 0.0054 0.0710 | 2.9160
- 43 | 1.75 | 0.0646 0.0031 0.0677 | 1.5785
- 44 | 1.75 | 0.0603 0.0054 0.0656 | 1.5194
- 45 | 1.75 | 0.0588 0.0062 0.0650 | 1.4626
- 57 | 1.50 | 0.0574 0.0045 0.0619 | 1.0900
- 58 | 1.50 | 0.0541 0.0066 0.0607 | 1.0730
- 59 | 1.50 | 0.0531 0.0073 0.0604 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 185s
- Prepare output 16s
- 201s
- Jacobian determinant (RMS): 0.011 0.039 0.059 0.084 0.109 | 0.117670
- Template Matching: 0.082 0.217 0.197 0.176 0.159 | 0.159185
- Write result maps: 40s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 47s
- CSF distance: 21s
- PBT2x thickness: 60s
- 136s
- Create initial surface 109s
- Topology correction: 121s
- Surface refinement: 89s
- Reduction of surface collisions with optimization: 86s
- Spherical mapping with areal smoothing 98s
- Spherical registration 294s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 47s
- CSF distance: 17s
- PBT2x thickness: 51s
- 121s
- Create initial surface 90s
- Topology correction: 105s
- Surface refinement: 81s
- Reduction of surface collisions with optimization: 75s
- Spherical mapping with areal smoothing 93s
- Spherical registration 282s
- Final surface processing results:
- Average thickness (FS): 2.5296 0.6254 mm
- Surface intensity / position RMSE: 0.0660 / 0.0708
- Euler number / defect number / defect size: 20.0 / 13.5 / 0.42%
- Display thickness: /var/lib/condor/execute/dir_57709/ds/sub-season117/surf/lh.thickness.sub-season117_ses-3_acq-MPrageHiRes_T1w
- Display thickness: /var/lib/condor/execute/dir_57709/ds/sub-season117/surf/rh.thickness.sub-season117_ses-3_acq-MPrageHiRes_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_57709/ds/sub-season117/sub-season117_ses-3_acq-MPrageHiRes_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1896s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 10s
- ROI estimation of 'neuromorphometrics' atlas 35s
- ROI estimation of 'lpba40' atlas 10s
- ROI estimation of 'hammers' atlas 24s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 9s
- ROI estimation of 'aal3' atlas 14s
- ROI estimation of 'mori' atlas 21s
- ROI estimation of 'anatomy3' atlas 30s
- ROI estimation of 'julichbrain' atlas 39s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 16s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 28s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 63s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 94s
- Write results 95s
- 395s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_57709/ds/sub-season117/report/catreport_sub-season117_ses-3_acq-MPrageHiRes_T1w.pdf
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- CAT preprocessing takes 60 minute(s) and 51 second(s).
- Image Quality Rating (IQR): 87.19% (B+)
- GM volume (GMV): 47.22% (773.16 / 1637.48 ml)
- GM thickness (GMT): 2.53 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_57709/ds/sub-season117/mri
- Reports are saved in /var/lib/condor/execute/dir_57709/ds/sub-season117/report
- Labels are saved in /var/lib/condor/execute/dir_57709/ds/sub-season117/label
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