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- CAT12.8.1 r2040: 1/1: ./sub-0025254/ses-3/sub-0025254_ses-3_run-1_T1w.n
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- SANLM denoising (medium): 56s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 6s
- Initial correction 7s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 40s
- Correct center-of-mass 4s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 93s
- SPM preprocessing 1 (estimate 2): 98s
- SPM preprocessing 2 (write):
- Write Segmentation 19s
- Update Segmentation 20s
- Update Skull-Stripping 42s
- Update probability maps 8s
- 89s
- Global intensity correction: 15s
- SANLM denoising after intensity normalization (medium): 28s
- Fast Optimized Shooting registration 37s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 15s
- Estimate local tissue thresholds (WM) 20s
- Estimate local tissue thresholds (GM) 30s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 41s
- 115s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 16s
- Blood vessel detection 10s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 25s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 71s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 33s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- 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 | 0.0847 0.0000 0.0847 | 32.0000
- 2 | 2.50 | 0.0814 0.0014 0.0828 | 29.4886
- 3 | 2.50 | 0.0804 0.0021 0.0825 | 26.9772
- 4 | 2.50 | 0.0799 0.0024 0.0823 | 24.6107
- 5 | 2.50 | 0.0795 0.0026 0.0821 | 22.6548
- 6 | 2.50 | 0.0792 0.0027 0.0819 | 20.6989
- 7 | 2.50 | 0.0788 0.0029 0.0817 | 18.9688
- 8 | 2.50 | 0.0785 0.0030 0.0814 | 17.4455
- 9 | 2.50 | 0.0781 0.0031 0.0812 | 15.9223
- 10 | 2.50 | 0.0777 0.0032 0.0809 | 14.6627
- 11 | 2.50 | 0.0773 0.0033 0.0806 | 13.4764
- 12 | 2.50 | 0.0769 0.0034 0.0803 | 12.3015
- 13 | 2.50 | 0.0765 0.0035 0.0800 | 11.3776
- 14 | 2.50 | 0.0761 0.0036 0.0797 | 10.4537
- 15 | 2.25 | 0.0760 0.0037 0.0797 | 9.5920
- 16 | 2.25 | 0.0724 0.0055 0.0779 | 8.8725
- 29 | 2.00 | 0.0729 0.0025 0.0754 | 3.3283
- 30 | 2.00 | 0.0663 0.0051 0.0714 | 3.1221
- 31 | 2.00 | 0.0640 0.0062 0.0702 | 2.9160
- 43 | 1.75 | 0.0627 0.0036 0.0663 | 1.5785
- 44 | 1.75 | 0.0585 0.0058 0.0643 | 1.5194
- 45 | 1.75 | 0.0571 0.0066 0.0637 | 1.4626
- 57 | 1.50 | 0.0555 0.0049 0.0604 | 1.0900
- 58 | 1.50 | 0.0526 0.0068 0.0594 | 1.0730
- 59 | 1.50 | 0.0516 0.0074 0.0590 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 185s
- Prepare output 12s
- 197s
- Jacobian determinant (RMS): 0.013 0.046 0.069 0.095 0.117 | 0.124704
- Template Matching: 0.085 0.217 0.192 0.171 0.155 | 0.154900
- Write result maps: 32s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 41s
- CSF distance: 16s
- PBT2x thickness: 49s
- 112s
- Create initial surface 88s
- Topology correction: 83s
- Surface refinement: 100s
- Reduction of surface collisions with optimization: 63s
- Spherical mapping with areal smoothing 89s
- Spherical registration 331s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 31s
- CSF distance: 16s
- PBT2x thickness: 49s
- 102s
- Create initial surface 86s
- Topology correction: 84s
- Surface refinement: 75s
- Reduction of surface collisions with optimization: 62s
- Spherical mapping with areal smoothing 89s
- Spherical registration 336s
- Final surface processing results:
- Average thickness (FS): 2.5700 0.6220 mm
- Surface intensity / position RMSE: 0.0681 / 0.0649
- Euler number / defect number / defect size: 6.0 / 6.5 / 0.06%
- Display thickness: /var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-3/surf/lh.thickness.sub-0025254_ses-3_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-3/surf/rh.thickness.sub-0025254_ses-3_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-3/sub-0025254_ses-3_run-1_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1797s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 27s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 19s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 11s
- ROI estimation of 'mori' atlas 16s
- ROI estimation of 'anatomy3' atlas 23s
- ROI estimation of 'julichbrain' atlas 31s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 49s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 74s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s
- Write results 8s
- 315s
- Quality check: 12s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-3/report/catreport_sub-0025254_ses-3_run-1_T1w.pdf
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- CAT preprocessing takes 52 minute(s) and 18 second(s).
- Image Quality Rating (IQR): 81.40% (B-)
- GM volume (GMV): 49.71% (648.28 / 1304.13 ml)
- GM thickness (GMT): 2.57 0.62 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-3/mri
- Reports are saved in /var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-3/report
- Labels are saved in /var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-3/label
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