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- CAT12.8.1 r1980: 1/1: ./sub-season133_ses-1_acq-MPrageHiRes_T1w.n
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- SANLM denoising (medium): 67s
- APP: Rough bias correction:
- Initialize 11s
- Estimate background 11s
- Initial correction 22s
- Refine background 6s
- Final correction 16s
- Final scaling 13s
- 90s
- Correct center-of-mass 4s
- Affine registration 16s
- SPM preprocessing 1 (estimate 1 - TPM registration): 123s
- SPM preprocessing 1 (estimate 2): 111s
- SPM preprocessing 2 (write):
- Write Segmentation 27s
- Update Segmentation 32s
- Update Skull-Stripping 72s
- Update probability maps 14s
- 146s
- Global intensity correction: 28s
- SANLM denoising after intensity normalization (medium): 12s
- Fast Optimized Shooting registration 49s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 8s
- Prepare partitions 4s
- Prepare segments (LASmod = 1.00) 26s
- Estimate local tissue thresholds (WM) 30s
- Estimate local tissue thresholds (GM) 39s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 34s
- 147s
- ROI segmentation (partitioning):
- Atlas -> subject space 15s
- Major structures 6s
- Ventricle detection 22s
- Blood vessel detection 16s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 45s
- Manual stroke lesion detection 0s
- Closing of deep structures 3s
- Side alignment 6s
- Final corrections 8s
- 121s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 63s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 7s
- Level 1 cleanup (brain masking) 5s
- Level 2 cleanup (CSF correction) 3s
- Level 3 cleanup (CSF/WM PVE) 5s
- 20s
- 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 | 0.0806 0.0000 0.0806 | 32.0000
- 2 | 2.50 | 0.0781 0.0011 0.0793 | 29.4886
- 3 | 2.50 | 0.0774 0.0017 0.0791 | 26.9772
- 4 | 2.50 | 0.0770 0.0019 0.0790 | 24.6107
- 5 | 2.50 | 0.0767 0.0021 0.0788 | 22.6548
- 6 | 2.50 | 0.0765 0.0022 0.0787 | 20.6989
- 7 | 2.50 | 0.0762 0.0023 0.0785 | 18.9688
- 8 | 2.50 | 0.0759 0.0024 0.0783 | 17.4455
- 9 | 2.50 | 0.0757 0.0024 0.0781 | 15.9223
- 10 | 2.50 | 0.0754 0.0025 0.0779 | 14.6627
- 11 | 2.50 | 0.0751 0.0026 0.0777 | 13.4764
- 12 | 2.50 | 0.0748 0.0027 0.0774 | 12.3015
- 13 | 2.50 | 0.0745 0.0028 0.0772 | 11.3776
- 14 | 2.50 | 0.0742 0.0028 0.0770 | 10.4537
- 15 | 2.25 | 0.0728 0.0029 0.0756 | 9.5920
- 16 | 2.25 | 0.0698 0.0043 0.0741 | 8.8725
- 29 | 2.00 | 0.0704 0.0020 0.0724 | 3.3283
- 30 | 2.00 | 0.0644 0.0043 0.0687 | 3.1221
- 31 | 2.00 | 0.0623 0.0053 0.0676 | 2.9160
- 43 | 1.75 | 0.0610 0.0031 0.0641 | 1.5785
- 44 | 1.75 | 0.0569 0.0052 0.0621 | 1.5194
- 45 | 1.75 | 0.0555 0.0059 0.0614 | 1.4626
- 57 | 1.50 | 0.0537 0.0043 0.0580 | 1.0900
- 58 | 1.50 | 0.0509 0.0062 0.0570 | 1.0730
- 59 | 1.50 | 0.0499 0.0067 0.0567 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 230s
- Prepare output 14s
- 244s
- Jacobian determinant (RMS): 0.011 0.041 0.060 0.084 0.108 | 0.115521
- Template Matching: 0.081 0.209 0.187 0.166 0.150 | 0.149764
- Write result maps: 46s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 42s
- CSF distance: 18s
- PBT2x thickness: 56s
- 123s
- Create initial surface 96s
- Topology correction: 109s
- Surface refinement: 88s
- Reduction of surface collisions with optimization: 84s
- Spherical mapping with areal smoothing 97s
- Spherical registration 272s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 52s
- CSF distance: 19s
- PBT2x thickness: 56s
- 135s
- Create initial surface 96s
- Topology correction: 116s
- Surface refinement: 88s
- Reduction of surface collisions with optimization: 90s
- Spherical mapping with areal smoothing 100s
- Spherical registration 269s
- Final surface processing results:
- Average thickness (FS): 2.6714 0.5931 mm
- Surface intensity / position RMSE: 0.0670 / 0.0663
- Euler number / defect number / defect size: 12.0 / 13.0 / 0.35%
- Display thickness: /var/lib/condor/execute/dir_2524/ds/sub-season133/surf/lh.thickness.sub-season133_ses-1_acq-MPrageHiRes_T1w
- Display thickness: /var/lib/condor/execute/dir_2524/ds/sub-season133/surf/rh.thickness.sub-season133_ses-1_acq-MPrageHiRes_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2524/ds/sub-season133/sub-season133_ses-1_acq-MPrageHiRes_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1880s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 19s
- ROI estimation of 'neuromorphometrics' atlas 66s
- 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 27s
- ROI estimation of 'mori' atlas 40s
- ROI estimation of 'anatomy3' atlas 57s
- ROI estimation of 'julichbrain' atlas 76s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 28s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 36s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 123s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 180s
- Write results 181s
- 739s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2524/ds/sub-season133/report/catreport_sub-season133_ses-1_acq-MPrageHiRes_T1w.pdf
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- CAT preprocessing takes 68 minute(s) and 7 second(s).
- Image Quality Rating (IQR): 87.06% (B+)
- GM volume (GMV): 49.51% (702.34 / 1418.51 ml)
- GM thickness (GMT): 2.67 0.59 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2524/ds/sub-season133/mri
- Reports are saved in /var/lib/condor/execute/dir_2524/ds/sub-season133/report
- Labels are saved in /var/lib/condor/execute/dir_2524/ds/sub-season133/label
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