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- CAT12.8.1 r1980: 1/1: ./sub-season131_ses-2_acq-MPrageHiRes_T1w.n
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- SANLM denoising (medium): 63s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 9s
- Initial correction 21s
- Refine background 4s
- Final correction 15s
- Final scaling 10s
- 74s
- Correct center-of-mass 4s
- Affine registration 13s
- SPM preprocessing 1 (estimate 1 - TPM registration): 104s
- SPM preprocessing 1 (estimate 2): 92s
- SPM preprocessing 2 (write):
- Write Segmentation 21s
- Update Segmentation 29s
- Update Skull-Stripping 56s
- Update probability maps 11s
- 118s
- Global intensity correction: 21s
- SANLM denoising after intensity normalization (medium): 30s
- Fast Optimized Shooting registration 35s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 7s
- Prepare partitions 7s
- Prepare segments (LASmod = 1.00) 23s
- Estimate local tissue thresholds (WM) 25s
- Estimate local tissue thresholds (GM) 35s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 46s
- 147s
- ROI segmentation (partitioning):
- Atlas -> subject space 11s
- Major structures 6s
- Ventricle detection 25s
- Blood vessel detection 16s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.06) 47s
- Manual stroke lesion detection 0s
- Closing of deep structures 3s
- Side alignment 6s
- Final corrections 5s
- 118s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 51s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 7s
- Level 1 cleanup (brain masking) 4s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 4s
- 17s
- 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 | 0.0839 0.0000 0.0839 | 32.0000
- 2 | 2.50 | 0.0811 0.0012 0.0824 | 29.4886
- 3 | 2.50 | 0.0802 0.0019 0.0822 | 26.9772
- 4 | 2.50 | 0.0798 0.0022 0.0820 | 24.6107
- 5 | 2.50 | 0.0795 0.0023 0.0818 | 22.6548
- 6 | 2.50 | 0.0792 0.0024 0.0816 | 20.6989
- 7 | 2.50 | 0.0788 0.0025 0.0814 | 18.9688
- 8 | 2.50 | 0.0785 0.0027 0.0812 | 17.4455
- 9 | 2.50 | 0.0782 0.0027 0.0809 | 15.9223
- 10 | 2.50 | 0.0778 0.0029 0.0807 | 14.6627
- 11 | 2.50 | 0.0775 0.0029 0.0804 | 13.4764
- 12 | 2.50 | 0.0772 0.0030 0.0802 | 12.3015
- 13 | 2.50 | 0.0768 0.0031 0.0799 | 11.3776
- 14 | 2.50 | 0.0764 0.0032 0.0796 | 10.4537
- 15 | 2.25 | 0.0751 0.0033 0.0784 | 9.5920
- 16 | 2.25 | 0.0721 0.0048 0.0768 | 8.8725
- 29 | 2.00 | 0.0726 0.0021 0.0748 | 3.3283
- 30 | 2.00 | 0.0665 0.0045 0.0711 | 3.1221
- 31 | 2.00 | 0.0644 0.0055 0.0700 | 2.9160
- 43 | 1.75 | 0.0632 0.0032 0.0664 | 1.5785
- 44 | 1.75 | 0.0591 0.0053 0.0644 | 1.5194
- 45 | 1.75 | 0.0577 0.0061 0.0638 | 1.4626
- 57 | 1.50 | 0.0560 0.0044 0.0604 | 1.0900
- 58 | 1.50 | 0.0531 0.0063 0.0594 | 1.0730
- 59 | 1.50 | 0.0522 0.0069 0.0591 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 152s
- Prepare output 12s
- 164s
- Jacobian determinant (RMS): 0.012 0.044 0.064 0.088 0.111 | 0.117760
- Template Matching: 0.084 0.216 0.193 0.173 0.156 | 0.156452
- Write result maps: 28s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 45s
- CSF distance: 17s
- PBT2x thickness: 47s
- 116s
- Create initial surface 88s
- Topology correction: 97s
- Surface refinement: 90s
- Reduction of surface collisions with optimization: 78s
- Spherical mapping with areal smoothing 89s
- Spherical registration 272s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 34s
- CSF distance: 16s
- PBT2x thickness: 46s
- 102s
- Create initial surface 85s
- Topology correction: 91s
- Surface refinement: 85s
- Reduction of surface collisions with optimization: 72s
- Spherical mapping with areal smoothing 97s
- Spherical registration 264s
- Final surface processing results:
- Average thickness (FS): 2.4875 0.6045 mm
- Surface intensity / position RMSE: 0.0617 / 0.0599
- Euler number / defect number / defect size: 14.0 / 13.0 / 0.22%
- Display thickness: /var/lib/condor/execute/dir_28757/ds/sub-season131/surf/lh.thickness.sub-season131_ses-2_acq-MPrageHiRes_T1w
- Display thickness: /var/lib/condor/execute/dir_28757/ds/sub-season131/surf/rh.thickness.sub-season131_ses-2_acq-MPrageHiRes_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_28757/ds/sub-season131/sub-season131_ses-2_acq-MPrageHiRes_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1723s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 8s
- ROI estimation of 'neuromorphometrics' atlas 30s
- ROI estimation of 'lpba40' atlas 9s
- ROI estimation of 'hammers' atlas 21s
- 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 28s
- 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 58s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 88s
- Write results 88s
- 362s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_28757/ds/sub-season131/report/catreport_sub-season131_ses-2_acq-MPrageHiRes_T1w.pdf
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- CAT preprocessing takes 54 minute(s) and 53 second(s).
- Image Quality Rating (IQR): 85.48% (B)
- GM volume (GMV): 44.32% (735.63 / 1659.80 ml)
- GM thickness (GMT): 2.49 0.60 mm
- Segmentations are saved in /var/lib/condor/execute/dir_28757/ds/sub-season131/mri
- Reports are saved in /var/lib/condor/execute/dir_28757/ds/sub-season131/report
- Labels are saved in /var/lib/condor/execute/dir_28757/ds/sub-season131/label
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