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- CAT12.8.1 r2040: 1/1: ./sub-0026002/ses-3/sub-0026002_ses-3_run-1_T1w.n
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- SANLM denoising (medium): 51s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 6s
- Initial correction 7s
- Refine background 4s
- Final correction 5s
- Final scaling 5s
- 41s
- Correct center-of-mass 4s
- Affine registration 12s
- SPM preprocessing 1 (estimate 1 - TPM registration): 76s
- SPM preprocessing 1 (estimate 2): 66s
- SPM preprocessing 2 (write):
- Write Segmentation 18s
- Update Segmentation 20s
- Update Skull-Stripping 42s
- Update probability maps 9s
- 89s
- Global intensity correction: 18s
- SANLM denoising after intensity normalization (medium): 24s
- Fast Optimized Shooting registration 40s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.14) 14s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 26s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 42s
- 111s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 4s
- Ventricle detection 12s
- Blood vessel detection 9s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.11) 24s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 68s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 30s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- 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
- 11s
- 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 | 0.0833 0.0000 0.0833 | 32.0000
- 2 | 2.50 | 0.0812 0.0011 0.0822 | 29.4886
- 3 | 2.50 | 0.0805 0.0016 0.0821 | 26.9772
- 4 | 2.50 | 0.0802 0.0018 0.0820 | 24.6107
- 5 | 2.50 | 0.0799 0.0019 0.0819 | 22.6548
- 6 | 2.50 | 0.0797 0.0020 0.0817 | 20.6989
- 7 | 2.50 | 0.0794 0.0021 0.0816 | 18.9688
- 8 | 2.50 | 0.0792 0.0022 0.0814 | 17.4455
- 9 | 2.50 | 0.0789 0.0023 0.0812 | 15.9223
- 10 | 2.50 | 0.0787 0.0024 0.0810 | 14.6627
- 11 | 2.50 | 0.0784 0.0024 0.0809 | 13.4764
- 12 | 2.50 | 0.0781 0.0025 0.0806 | 12.3015
- 13 | 2.50 | 0.0779 0.0026 0.0805 | 11.3776
- 14 | 2.50 | 0.0776 0.0027 0.0802 | 10.4537
- 15 | 2.25 | 0.0765 0.0027 0.0793 | 9.5920
- 16 | 2.25 | 0.0739 0.0040 0.0779 | 8.8725
- 29 | 2.00 | 0.0754 0.0018 0.0772 | 3.3283
- 30 | 2.00 | 0.0690 0.0043 0.0733 | 3.1221
- 31 | 2.00 | 0.0669 0.0054 0.0722 | 2.9160
- 43 | 1.75 | 0.0656 0.0031 0.0687 | 1.5785
- 44 | 1.75 | 0.0612 0.0054 0.0666 | 1.5194
- 45 | 1.75 | 0.0598 0.0062 0.0660 | 1.4626
- 57 | 1.50 | 0.0581 0.0045 0.0626 | 1.0900
- 58 | 1.50 | 0.0550 0.0065 0.0615 | 1.0730
- 59 | 1.50 | 0.0540 0.0071 0.0611 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 207s
- Prepare output 10s
- 218s
- Jacobian determinant (RMS): 0.011 0.038 0.055 0.078 0.100 | 0.106660
- Template Matching: 0.083 0.222 0.201 0.179 0.162 | 0.161927
- Write result maps: 46s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 56s
- CSF distance: 16s
- PBT2x thickness: 48s
- 127s
- Create initial surface 80s
- Topology correction: 90s
- Surface refinement: 98s
- Reduction of surface collisions with optimization: 57s
- Spherical mapping with areal smoothing 82s
- Spherical registration 250s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 37s
- CSF distance: 16s
- PBT2x thickness: 48s
- 107s
- Create initial surface 78s
- Topology correction: 89s
- Surface refinement: 79s
- Reduction of surface collisions with optimization: 58s
- Spherical mapping with areal smoothing 82s
- Spherical registration 244s
- Final surface processing results:
- Average thickness (FS): 2.4545 0.6273 mm
- Surface intensity / position RMSE: 0.0631 / 0.0663
- Euler number / defect number / defect size: 20.0 / 10.0 / 0.83%
- Display thickness: /var/lib/condor/execute/dir_2737911/ds/XHCUMS/sub-0026002/ses-3/surf/lh.thickness.sub-0026002_ses-3_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2737911/ds/XHCUMS/sub-0026002/ses-3/surf/rh.thickness.sub-0026002_ses-3_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2737911/ds/XHCUMS/sub-0026002/ses-3/sub-0026002_ses-3_run-1_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1620s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 14s
- ROI estimation of 'neuromorphometrics' atlas 52s
- ROI estimation of 'lpba40' atlas 15s
- ROI estimation of 'hammers' atlas 37s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 13s
- ROI estimation of 'aal3' atlas 22s
- ROI estimation of 'mori' atlas 32s
- ROI estimation of 'anatomy3' atlas 46s
- ROI estimation of 'julichbrain' atlas 61s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 23s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 30s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 101s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 152s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 10s
- Write results 12s
- 613s
- Quality check: 13s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2737911/ds/XHCUMS/sub-0026002/ses-3/report/catreport_sub-0026002_ses-3_run-1_T1w.pdf
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- CAT preprocessing takes 55 minute(s) and 10 second(s).
- Image Quality Rating (IQR): 82.61% (B-)
- GM volume (GMV): 44.95% (639.13 / 1421.83 ml)
- GM thickness (GMT): 2.45 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2737911/ds/XHCUMS/sub-0026002/ses-3/mri
- Reports are saved in /var/lib/condor/execute/dir_2737911/ds/XHCUMS/sub-0026002/ses-3/report
- Labels are saved in /var/lib/condor/execute/dir_2737911/ds/XHCUMS/sub-0026002/ses-3/label
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