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- CAT12.8.1 r2040: 1/1: ./sub-0027022/ses-1/sub-0027022_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 68s
- APP: Rough bias correction:
- Initialize 9s
- Estimate background 8s
- Initial correction 9s
- Refine background 4s
- Final correction 8s
- Final scaling 9s
- 56s
- Correct center-of-mass 6s
- Affine registration 12s
- SPM preprocessing 1 (estimate 1 - TPM registration): 111s
- SPM preprocessing 1 (estimate 2): 97s
- SPM preprocessing 2 (write):
- Write Segmentation 24s
- Update Segmentation 26s
- Update Skull-Stripping 57s
- Update probability maps 12s
- 119s
- Global intensity correction: 22s
- SANLM denoising after intensity normalization (medium): 40s
- Fast Optimized Shooting registration 43s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 5s
- Prepare segments (LASmod = 1.02) 19s
- Estimate local tissue thresholds (WM) 27s
- Estimate local tissue thresholds (GM) 41s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 68s
- 169s
- ROI segmentation (partitioning):
- Atlas -> subject space 10s
- Major structures 5s
- Ventricle detection 21s
- Blood vessel detection 14s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.03) 37s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 5s
- Final corrections 6s
- 100s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 43s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 6s
- Level 1 cleanup (brain masking) 4s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 4s
- 16s
- 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 | 0.0829 0.0000 0.0829 | 32.0000
- 2 | 2.50 | 0.0806 0.0011 0.0817 | 29.4886
- 3 | 2.50 | 0.0799 0.0017 0.0816 | 26.9772
- 4 | 2.50 | 0.0796 0.0019 0.0814 | 24.6107
- 5 | 2.50 | 0.0793 0.0020 0.0813 | 22.6548
- 6 | 2.50 | 0.0790 0.0021 0.0811 | 20.6989
- 7 | 2.50 | 0.0788 0.0022 0.0810 | 18.9688
- 8 | 2.50 | 0.0785 0.0023 0.0808 | 17.4455
- 9 | 2.50 | 0.0782 0.0024 0.0806 | 15.9223
- 10 | 2.50 | 0.0779 0.0025 0.0804 | 14.6627
- 11 | 2.50 | 0.0776 0.0026 0.0802 | 13.4764
- 12 | 2.50 | 0.0774 0.0027 0.0800 | 12.3015
- 13 | 2.50 | 0.0770 0.0028 0.0798 | 11.3776
- 14 | 2.50 | 0.0767 0.0028 0.0796 | 10.4537
- 15 | 2.25 | 0.0761 0.0029 0.0790 | 9.5920
- 16 | 2.25 | 0.0732 0.0043 0.0775 | 8.8725
- 29 | 2.00 | 0.0749 0.0019 0.0768 | 3.3283
- 30 | 2.00 | 0.0687 0.0044 0.0731 | 3.1221
- 31 | 2.00 | 0.0665 0.0054 0.0719 | 2.9160
- 43 | 1.75 | 0.0656 0.0031 0.0687 | 1.5785
- 44 | 1.75 | 0.0611 0.0055 0.0666 | 1.5194
- 45 | 1.75 | 0.0596 0.0063 0.0659 | 1.4626
- 57 | 1.50 | 0.0581 0.0046 0.0627 | 1.0900
- 58 | 1.50 | 0.0548 0.0067 0.0615 | 1.0730
- 59 | 1.50 | 0.0538 0.0073 0.0611 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 213s
- Prepare output 15s
- 228s
- Jacobian determinant (RMS): 0.011 0.040 0.059 0.084 0.108 | 0.114329
- Template Matching: 0.083 0.220 0.200 0.179 0.161 | 0.161367
- Write result maps: 54s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 71s
- CSF distance: 21s
- PBT2x thickness: 65s
- 166s
- Create initial surface 116s
- Topology correction: 120s
- Surface refinement: 107s
- Reduction of surface collisions with optimization: 95s
- Spherical mapping with areal smoothing 114s
- Spherical registration 349s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 42s
- CSF distance: 22s
- PBT2x thickness: 66s
- 138s
- Create initial surface 115s
- Topology correction: 122s
- Surface refinement: 104s
- Reduction of surface collisions with optimization: 90s
- Spherical mapping with areal smoothing 118s
- Spherical registration 333s
- Final surface processing results:
- Average thickness (FS): 2.7068 0.6851 mm
- Surface intensity / position RMSE: 0.0716 / 0.0724
- Euler number / defect number / defect size: 22.0 / 16.5 / 0.58%
- Display thickness: /var/lib/condor/execute/dir_3317999/ds/MRN/sub-0027022/ses-1/surf/lh.thickness.sub-0027022_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3317999/ds/MRN/sub-0027022/ses-1/surf/rh.thickness.sub-0027022_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3317999/ds/MRN/sub-0027022/ses-1/sub-0027022_ses-1_run-1_T1w.nii
- Surface ROI estimation: 12s
- Surface and thickness estimation takes: 2219s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 12s
- ROI estimation of 'neuromorphometrics' atlas 48s
- ROI estimation of 'lpba40' atlas 14s
- ROI estimation of 'hammers' atlas 31s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 13s
- ROI estimation of 'aal3' atlas 20s
- ROI estimation of 'mori' atlas 26s
- ROI estimation of 'anatomy3' atlas 47s
- ROI estimation of 'julichbrain' atlas 53s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 20s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 35s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 79s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 121s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 10s
- Write results 11s
- 533s
- Quality check: 17s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3317999/ds/MRN/sub-0027022/ses-1/report/catreport_sub-0027022_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 68 minute(s) and 2 second(s).
- Image Quality Rating (IQR): 79.91% (C+)
- GM volume (GMV): 49.83% (784.44 / 1574.09 ml)
- GM thickness (GMT): 2.71 0.69 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3317999/ds/MRN/sub-0027022/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_3317999/ds/MRN/sub-0027022/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_3317999/ds/MRN/sub-0027022/ses-1/label
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