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- CAT12.8.1 r1980: 1/1: ./sub-season121_ses-1_acq-MPrageHiRes_T1w.n
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- SANLM denoising (medium): 51s
- APP: Rough bias correction:
- Initialize 9s
- Estimate background 9s
- Initial correction 16s
- Refine background 5s
- Final correction 13s
- Final scaling 13s
- 73s
- Correct center-of-mass 3s
- Affine registration 15s
- SPM preprocessing 1 (estimate 1 - TPM registration): 129s
- SPM preprocessing 1 (estimate 2): 151s
- SPM preprocessing 2 (write):
- Write Segmentation 24s
- Update Segmentation 30s
- Update Skull-Stripping 59s
- Update probability maps 12s
- 125s
- Global intensity correction: 22s
- SANLM denoising after intensity normalization (medium): 15s
- Fast Optimized Shooting registration 45s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 8s
- Prepare partitions 4s
- Prepare segments (LASmod = 1.08) 24s
- Estimate local tissue thresholds (WM) 28s
- Estimate local tissue thresholds (GM) 38s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 30s
- 135s
- ROI segmentation (partitioning):
- Atlas -> subject space 13s
- Major structures 7s
- Ventricle detection 20s
- Blood vessel detection 16s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 50s
- Manual stroke lesion detection 0s
- Closing of deep structures 3s
- Side alignment 7s
- Final corrections 6s
- 122s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 46s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.04]
- 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
- 18s
- 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 | 0.0825 0.0000 0.0825 | 32.0000
- 2 | 2.50 | 0.0795 0.0013 0.0808 | 29.4886
- 3 | 2.50 | 0.0787 0.0019 0.0806 | 26.9772
- 4 | 2.50 | 0.0782 0.0022 0.0804 | 24.6107
- 5 | 2.50 | 0.0779 0.0023 0.0802 | 22.6548
- 6 | 2.50 | 0.0776 0.0024 0.0800 | 20.6989
- 7 | 2.50 | 0.0773 0.0025 0.0798 | 18.9688
- 8 | 2.50 | 0.0770 0.0026 0.0796 | 17.4455
- 9 | 2.50 | 0.0767 0.0027 0.0794 | 15.9223
- 10 | 2.50 | 0.0763 0.0028 0.0791 | 14.6627
- 11 | 2.50 | 0.0760 0.0029 0.0789 | 13.4764
- 12 | 2.50 | 0.0756 0.0029 0.0786 | 12.3015
- 13 | 2.50 | 0.0753 0.0031 0.0783 | 11.3776
- 14 | 2.50 | 0.0750 0.0031 0.0781 | 10.4537
- 15 | 2.25 | 0.0749 0.0032 0.0781 | 9.5920
- 16 | 2.25 | 0.0717 0.0047 0.0765 | 8.8725
- 29 | 2.00 | 0.0736 0.0021 0.0758 | 3.3283
- 30 | 2.00 | 0.0675 0.0046 0.0721 | 3.1221
- 31 | 2.00 | 0.0654 0.0056 0.0710 | 2.9160
- 43 | 1.75 | 0.0647 0.0032 0.0680 | 1.5785
- 44 | 1.75 | 0.0603 0.0056 0.0659 | 1.5194
- 45 | 1.75 | 0.0587 0.0064 0.0652 | 1.4626
- 57 | 1.50 | 0.0575 0.0047 0.0622 | 1.0900
- 58 | 1.50 | 0.0542 0.0068 0.0611 | 1.0730
- 59 | 1.50 | 0.0531 0.0076 0.0607 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 212s
- Prepare output 13s
- 225s
- Jacobian determinant (RMS): 0.011 0.042 0.062 0.089 0.115 | 0.122553
- Template Matching: 0.083 0.215 0.196 0.176 0.159 | 0.159348
- Write result maps: 37s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 44s
- CSF distance: 20s
- PBT2x thickness: 58s
- 130s
- Create initial surface 99s
- Topology correction: 120s
- Surface refinement: 103s
- Reduction of surface collisions with optimization: 86s
- Spherical mapping with areal smoothing 110s
- Spherical registration 266s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 44s
- CSF distance: 20s
- PBT2x thickness: 59s
- 130s
- Create initial surface 101s
- Topology correction: 119s
- Surface refinement: 131s
- Reduction of surface collisions with optimization: 87s
- Spherical mapping with areal smoothing 110s
- Spherical registration 263s
- Final surface processing results:
- Average thickness (FS): 2.5236 0.6085 mm
- Surface intensity / position RMSE: 0.0753 / 0.0854
- Euler number / defect number / defect size: 98.0 / 31.5 / 2.31%
- Display thickness: /var/lib/condor/execute/dir_10496/ds/sub-season121/surf/lh.thickness.sub-season121_ses-1_acq-MPrageHiRes_T1w
- Display thickness: /var/lib/condor/execute/dir_10496/ds/sub-season121/surf/rh.thickness.sub-season121_ses-1_acq-MPrageHiRes_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_10496/ds/sub-season121/sub-season121_ses-1_acq-MPrageHiRes_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1975s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 18s
- ROI estimation of 'neuromorphometrics' atlas 65s
- ROI estimation of 'lpba40' atlas 19s
- ROI estimation of 'hammers' atlas 45s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 16s
- ROI estimation of 'aal3' atlas 26s
- ROI estimation of 'mori' atlas 38s
- ROI estimation of 'anatomy3' atlas 55s
- ROI estimation of 'julichbrain' atlas 73s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 27s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 34s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 116s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 174s
- Write results 174s
- 709s
- Quality check: 7s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_10496/ds/sub-season121/report/catreport_sub-season121_ses-1_acq-MPrageHiRes_T1w.pdf
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- CAT preprocessing takes 67 minute(s) and 37 second(s).
- Image Quality Rating (IQR): 86.88% (B+)
- GM volume (GMV): 51.06% (836.00 / 1637.33 ml)
- GM thickness (GMT): 2.52 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_10496/ds/sub-season121/mri
- Reports are saved in /var/lib/condor/execute/dir_10496/ds/sub-season121/report
- Labels are saved in /var/lib/condor/execute/dir_10496/ds/sub-season121/label
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