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- CAT12.8.1 r2040: 1/1: ./sub-0025945/ses-2/sub-0025945_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 54s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 6s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 37s
- Correct center-of-mass 4s
- Affine registration 9s
- SPM preprocessing 1 (estimate 1 - TPM registration): 79s
- SPM preprocessing 1 (estimate 2): 68s
- SPM preprocessing 2 (write):
- Write Segmentation 17s
- Update Segmentation 19s
- Update Skull-Stripping 42s
- Update probability maps 9s
- 87s
- Global intensity correction: 17s
- SANLM denoising after intensity normalization (medium): 30s
- Fast Optimized Shooting registration 32s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 15s
- Estimate local tissue thresholds (WM) 19s
- Estimate local tissue thresholds (GM) 27s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 40s
- 111s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 19s
- Blood vessel detection 9s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 25s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 4s
- 74s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 35s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.07,0.990.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 3s
- 12s
- 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 | 0.0792 0.0000 0.0792 | 32.0000
- 2 | 2.50 | 0.0772 0.0010 0.0782 | 29.4886
- 3 | 2.50 | 0.0766 0.0014 0.0781 | 26.9772
- 4 | 2.50 | 0.0764 0.0016 0.0780 | 24.6107
- 5 | 2.50 | 0.0762 0.0017 0.0779 | 22.6548
- 6 | 2.50 | 0.0760 0.0018 0.0777 | 20.6989
- 7 | 2.50 | 0.0758 0.0018 0.0776 | 18.9688
- 8 | 2.50 | 0.0756 0.0019 0.0775 | 17.4455
- 9 | 2.50 | 0.0754 0.0020 0.0773 | 15.9223
- 10 | 2.50 | 0.0751 0.0020 0.0772 | 14.6627
- 11 | 2.50 | 0.0749 0.0021 0.0770 | 13.4764
- 12 | 2.50 | 0.0747 0.0021 0.0768 | 12.3015
- 13 | 2.50 | 0.0745 0.0022 0.0767 | 11.3776
- 14 | 2.50 | 0.0742 0.0023 0.0765 | 10.4537
- 15 | 2.25 | 0.0723 0.0023 0.0746 | 9.5920
- 16 | 2.25 | 0.0699 0.0035 0.0734 | 8.8725
- 29 | 2.00 | 0.0716 0.0016 0.0732 | 3.3283
- 30 | 2.00 | 0.0664 0.0037 0.0700 | 3.1221
- 31 | 2.00 | 0.0646 0.0045 0.0691 | 2.9160
- 43 | 1.75 | 0.0640 0.0026 0.0665 | 1.5785
- 44 | 1.75 | 0.0598 0.0047 0.0646 | 1.5194
- 45 | 1.75 | 0.0585 0.0055 0.0640 | 1.4626
- 57 | 1.50 | 0.0570 0.0039 0.0610 | 1.0900
- 58 | 1.50 | 0.0540 0.0059 0.0599 | 1.0730
- 59 | 1.50 | 0.0529 0.0066 0.0595 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 168s
- Prepare output 11s
- 179s
- Jacobian determinant (RMS): 0.010 0.034 0.050 0.071 0.093 | 0.099121
- Template Matching: 0.079 0.210 0.194 0.175 0.159 | 0.158829
- Write result maps: 34s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 29s
- CSF distance: 17s
- PBT2x thickness: 48s
- 101s
- Create initial surface 95s
- Topology correction: 105s
- Surface refinement: 96s
- Reduction of surface collisions with optimization: 88s
- Spherical mapping with areal smoothing 92s
- Spherical registration 296s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 28s
- CSF distance: 16s
- PBT2x thickness: 48s
- 98s
- Create initial surface 93s
- Topology correction: 106s
- Surface refinement: 92s
- Reduction of surface collisions with optimization: 89s
- Spherical mapping with areal smoothing 100s
- Spherical registration 315s
- Final surface processing results:
- Average thickness (FS): 2.6215 0.5879 mm
- Surface intensity / position RMSE: 0.0656 / 0.0638
- Euler number / defect number / defect size: 14.0 / 13.5 / 0.48%
- Display thickness: /var/lib/condor/execute/dir_2999354/ds/BNU_2/sub-0025945/ses-2/surf/lh.thickness.sub-0025945_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2999354/ds/BNU_2/sub-0025945/ses-2/surf/rh.thickness.sub-0025945_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2999354/ds/BNU_2/sub-0025945/ses-2/sub-0025945_ses-2_run-1_T1w.nii
- Surface ROI estimation: 11s
- Surface and thickness estimation takes: 1874s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 11s
- ROI estimation of 'neuromorphometrics' atlas 41s
- ROI estimation of 'lpba40' atlas 11s
- ROI estimation of 'hammers' atlas 29s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 10s
- ROI estimation of 'aal3' atlas 14s
- ROI estimation of 'mori' atlas 20s
- ROI estimation of 'anatomy3' atlas 32s
- ROI estimation of 'julichbrain' atlas 40s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 33s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 67s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 101s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s
- Write results 9s
- 439s
- Quality check: 12s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2999354/ds/BNU_2/sub-0025945/ses-2/report/catreport_sub-0025945_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 54 minute(s) and 37 second(s).
- Image Quality Rating (IQR): 82.52% (B-)
- GM volume (GMV): 50.51% (777.86 / 1540.08 ml)
- GM thickness (GMT): 2.62 0.59 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2999354/ds/BNU_2/sub-0025945/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_2999354/ds/BNU_2/sub-0025945/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_2999354/ds/BNU_2/sub-0025945/ses-2/label
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