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- CAT12.8.1 r1980: 1/1: ./sub-season102_ses-1_acq-MPrageHiRes_T1w.n
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- SANLM denoising (medium): 28s
- APP: Rough bias correction:
- Initialize 10s
- Estimate background 12s
- Initial correction 24s
- Refine background 5s
- Final correction 18s
- Final scaling 11s
- 90s
- Correct center-of-mass 3s
- Affine registration 15s
- SPM preprocessing 1 (estimate 1 - TPM registration): 139s
- SPM preprocessing 1 (estimate 2): 122s
- SPM preprocessing 2 (write):
- Write Segmentation 27s
- Update Segmentation 34s
- Update Skull-Stripping 69s
- Update probability maps 13s
- 144s
- Global intensity correction: 26s
- SANLM denoising after intensity normalization (medium): 14s
- Fast Optimized Shooting registration 47s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 9s
- Prepare partitions 4s
- Prepare segments (LASmod = 1.00) 29s
- Estimate local tissue thresholds (WM) 29s
- Estimate local tissue thresholds (GM) 40s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 34s
- 151s
- ROI segmentation (partitioning):
- Atlas -> subject space 15s
- Major structures 7s
- Ventricle detection 28s
- Blood vessel detection 18s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.03) 54s
- Manual stroke lesion detection 0s
- Closing of deep structures 3s
- Side alignment 8s
- Final corrections 8s
- 142s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 68s
- 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
- 21s
- 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 | 0.0816 0.0000 0.0816 | 32.0000
- 2 | 2.50 | 0.0793 0.0011 0.0803 | 29.4886
- 3 | 2.50 | 0.0786 0.0016 0.0802 | 26.9772
- 4 | 2.50 | 0.0783 0.0018 0.0801 | 24.6107
- 5 | 2.50 | 0.0780 0.0019 0.0799 | 22.6548
- 6 | 2.50 | 0.0778 0.0020 0.0798 | 20.6989
- 7 | 2.50 | 0.0775 0.0021 0.0796 | 18.9688
- 8 | 2.50 | 0.0773 0.0022 0.0795 | 17.4455
- 9 | 2.50 | 0.0770 0.0022 0.0793 | 15.9223
- 10 | 2.50 | 0.0767 0.0023 0.0791 | 14.6627
- 11 | 2.50 | 0.0765 0.0024 0.0789 | 13.4764
- 12 | 2.50 | 0.0762 0.0025 0.0787 | 12.3015
- 13 | 2.50 | 0.0759 0.0025 0.0785 | 11.3776
- 14 | 2.50 | 0.0757 0.0026 0.0783 | 10.4537
- 15 | 2.25 | 0.0743 0.0027 0.0769 | 9.5920
- 16 | 2.25 | 0.0717 0.0039 0.0756 | 8.8725
- 29 | 2.00 | 0.0730 0.0018 0.0748 | 3.3283
- 30 | 2.00 | 0.0674 0.0040 0.0714 | 3.1221
- 31 | 2.00 | 0.0654 0.0050 0.0704 | 2.9160
- 43 | 1.75 | 0.0646 0.0029 0.0674 | 1.5785
- 44 | 1.75 | 0.0602 0.0051 0.0653 | 1.5194
- 45 | 1.75 | 0.0588 0.0059 0.0647 | 1.4626
- 57 | 1.50 | 0.0571 0.0043 0.0613 | 1.0900
- 58 | 1.50 | 0.0539 0.0063 0.0603 | 1.0730
- 59 | 1.50 | 0.0529 0.0070 0.0599 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 225s
- Prepare output 14s
- 239s
- Jacobian determinant (RMS): 0.011 0.037 0.054 0.076 0.099 | 0.106667
- Template Matching: 0.082 0.215 0.196 0.176 0.159 | 0.158677
- Write result maps: 43s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 51s
- CSF distance: 25s
- PBT2x thickness: 65s
- 150s
- Create initial surface 111s
- Topology correction: 126s
- Surface refinement: 113s
- Reduction of surface collisions with optimization: 112s
- Spherical mapping with areal smoothing 112s
- Spherical registration 264s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 43s
- CSF distance: 21s
- PBT2x thickness: 63s
- 137s
- Create initial surface 111s
- Topology correction: 126s
- Surface refinement: 122s
- Reduction of surface collisions with optimization: 110s
- Spherical mapping with areal smoothing 109s
- Spherical registration 258s
- Final surface processing results:
- Average thickness (FS): 2.5653 0.5902 mm
- Surface intensity / position RMSE: 0.0618 / 0.0592
- Euler number / defect number / defect size: 6.0 / 7.0 / 0.09%
- Display thickness: /var/lib/condor/execute/dir_11856/ds/sub-season102/surf/lh.thickness.sub-season102_ses-1_acq-MPrageHiRes_T1w
- Display thickness: /var/lib/condor/execute/dir_11856/ds/sub-season102/surf/rh.thickness.sub-season102_ses-1_acq-MPrageHiRes_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_11856/ds/sub-season102/sub-season102_ses-1_acq-MPrageHiRes_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 2086s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 17s
- ROI estimation of 'neuromorphometrics' atlas 65s
- ROI estimation of 'lpba40' atlas 19s
- ROI estimation of 'hammers' atlas 46s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 16s
- ROI estimation of 'aal3' atlas 26s
- ROI estimation of 'mori' atlas 39s
- ROI estimation of 'anatomy3' atlas 56s
- ROI estimation of 'julichbrain' atlas 76s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 34s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 43s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 148s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 220s
- Write results 222s
- 812s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_11856/ds/sub-season102/report/catreport_sub-season102_ses-1_acq-MPrageHiRes_T1w.pdf
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- CAT preprocessing takes 72 minute(s) and 38 second(s).
- Image Quality Rating (IQR): 87.09% (B+)
- GM volume (GMV): 47.60% (793.41 / 1666.80 ml)
- GM thickness (GMT): 2.57 0.59 mm
- Segmentations are saved in /var/lib/condor/execute/dir_11856/ds/sub-season102/mri
- Reports are saved in /var/lib/condor/execute/dir_11856/ds/sub-season102/report
- Labels are saved in /var/lib/condor/execute/dir_11856/ds/sub-season102/label
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