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- CAT12.8.1 r2040: 1/1: ./sub-0025989/ses-5/sub-0025989_ses-5_run-1_T1w.n
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- SANLM denoising (medium): 44s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 5s
- Initial correction 5s
- Refine background 2s
- Final correction 4s
- Final scaling 4s
- 30s
- Correct center-of-mass 3s
- Affine registration 7s
- SPM preprocessing 1 (estimate 1 - TPM registration): 54s
- SPM preprocessing 1 (estimate 2): 46s
- SPM preprocessing 2 (write):
- Write Segmentation 14s
- Update Segmentation 15s
- Update Skull-Stripping 34s
- Update probability maps 7s
- 70s
- Global intensity correction: 14s
- SANLM denoising after intensity normalization (medium): 20s
- Fast Optimized Shooting registration 27s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.18) 11s
- Estimate local tissue thresholds (WM) 15s
- Estimate local tissue thresholds (GM) 21s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 38s
- 94s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 3s
- Ventricle detection 9s
- Blood vessel detection 7s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.10) 19s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 52s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 27s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 3s
- Level 1 cleanup (brain masking) 2s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 9s
- 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 | 0.0849 0.0000 0.0849 | 32.0000
- 2 | 2.50 | 0.0818 0.0013 0.0831 | 29.4886
- 3 | 2.50 | 0.0809 0.0020 0.0829 | 26.9772
- 4 | 2.50 | 0.0805 0.0023 0.0827 | 24.6107
- 5 | 2.50 | 0.0801 0.0024 0.0825 | 22.6548
- 6 | 2.50 | 0.0798 0.0025 0.0823 | 20.6989
- 7 | 2.50 | 0.0795 0.0026 0.0821 | 18.9688
- 8 | 2.50 | 0.0792 0.0027 0.0819 | 17.4455
- 9 | 2.50 | 0.0788 0.0028 0.0816 | 15.9223
- 10 | 2.50 | 0.0785 0.0029 0.0814 | 14.6627
- 11 | 2.50 | 0.0782 0.0030 0.0811 | 13.4764
- 12 | 2.50 | 0.0778 0.0030 0.0808 | 12.3015
- 13 | 2.50 | 0.0774 0.0031 0.0806 | 11.3776
- 14 | 2.50 | 0.0771 0.0032 0.0803 | 10.4537
- 15 | 2.25 | 0.0763 0.0033 0.0796 | 9.5920
- 16 | 2.25 | 0.0730 0.0049 0.0779 | 8.8725
- 29 | 2.00 | 0.0742 0.0022 0.0764 | 3.3283
- 30 | 2.00 | 0.0675 0.0049 0.0724 | 3.1221
- 31 | 2.00 | 0.0652 0.0060 0.0712 | 2.9160
- 43 | 1.75 | 0.0638 0.0035 0.0672 | 1.5785
- 44 | 1.75 | 0.0593 0.0058 0.0651 | 1.5194
- 45 | 1.75 | 0.0578 0.0066 0.0644 | 1.4626
- 57 | 1.50 | 0.0560 0.0048 0.0608 | 1.0900
- 58 | 1.50 | 0.0530 0.0068 0.0598 | 1.0730
- 59 | 1.50 | 0.0520 0.0074 0.0594 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 134s
- Prepare output 8s
- 142s
- Jacobian determinant (RMS): 0.012 0.042 0.063 0.089 0.112 | 0.118890
- Template Matching: 0.085 0.219 0.196 0.173 0.156 | 0.156049
- Write result maps: 28s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 34s
- CSF distance: 12s
- PBT2x thickness: 35s
- 86s
- Create initial surface 70s
- Topology correction: 76s
- Surface refinement: 83s
- Reduction of surface collisions with optimization: 54s
- Spherical mapping with areal smoothing 63s
- Spherical registration 251s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 29s
- CSF distance: 12s
- PBT2x thickness: 35s
- 81s
- Create initial surface 69s
- Topology correction: 76s
- Surface refinement: 62s
- Reduction of surface collisions with optimization: 54s
- Spherical mapping with areal smoothing 63s
- Spherical registration 262s
- Final surface processing results:
- Average thickness (FS): 2.3896 0.6195 mm
- Surface intensity / position RMSE: 0.0609 / 0.0623
- Euler number / defect number / defect size: 18.0 / 12.0 / 0.56%
- Display thickness: /var/lib/condor/execute/dir_912714/ds/XHCUMS/sub-0025989/ses-5/surf/lh.thickness.sub-0025989_ses-5_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_912714/ds/XHCUMS/sub-0025989/ses-5/surf/rh.thickness.sub-0025989_ses-5_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_912714/ds/XHCUMS/sub-0025989/ses-5/sub-0025989_ses-5_run-1_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1424s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 25s
- ROI estimation of 'lpba40' atlas 7s
- ROI estimation of 'hammers' atlas 18s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 6s
- ROI estimation of 'aal3' atlas 10s
- ROI estimation of 'mori' atlas 15s
- ROI estimation of 'anatomy3' atlas 22s
- ROI estimation of 'julichbrain' atlas 29s
- 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 47s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 69s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s
- Write results 7s
- 298s
- Quality check: 9s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_912714/ds/XHCUMS/sub-0025989/ses-5/report/catreport_sub-0025989_ses-5_run-1_T1w.pdf
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- CAT preprocessing takes 41 minute(s) and 24 second(s).
- Image Quality Rating (IQR): 82.75% (B-)
- GM volume (GMV): 42.43% (611.33 / 1440.95 ml)
- GM thickness (GMT): 2.39 0.62 mm
- Segmentations are saved in /var/lib/condor/execute/dir_912714/ds/XHCUMS/sub-0025989/ses-5/mri
- Reports are saved in /var/lib/condor/execute/dir_912714/ds/XHCUMS/sub-0025989/ses-5/report
- Labels are saved in /var/lib/condor/execute/dir_912714/ds/XHCUMS/sub-0025989/ses-5/label
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