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- CAT12.8.1 r1980: 1/1: ./dir_25536/ds/sub-0934/sub-0934_ses-01_T1w.n
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- SANLM denoising (medium): 151s
- APP: Rough bias correction:
- Initialize 11s
- Estimate background 13s
- Initial correction 25s
- Refine background 6s
- Final correction 12s
- Final scaling 9s
- 87s
- Correct center-of-mass 5s
- Affine registration 28s
- SPM preprocessing 1 (estimate 1 - TPM registration): 116s
- SPM preprocessing 1 (estimate 2): 95s
- SPM preprocessing 2 (write):
- Write Segmentation 30s
- Update Segmentation 30s
- Update Skull-Stripping 69s
- Update probability maps 15s
- 144s
- Global intensity correction: 27s
- SANLM denoising after intensity normalization (medium): 20s
- Fast Optimized Shooting registration 49s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 6s
- Prepare partitions 9s
- Prepare segments (LASmod = 1.19) 23s
- Estimate local tissue thresholds (WM) 34s
- Estimate local tissue thresholds (GM) 48s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 72s
- 199s
- ROI segmentation (partitioning):
- Atlas -> subject space 13s
- Major structures 5s
- Ventricle detection 22s
- Blood vessel detection 15s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 39s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 5s
- Final corrections 8s
- 110s
- Blood vessel correction (BVCstr=0.50): 3s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 46s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- 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
- 17s
- 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 | 0.0848 0.0000 0.0848 | 32.0000
- 2 | 2.50 | 0.0824 0.0011 0.0835 | 29.4886
- 3 | 2.50 | 0.0817 0.0016 0.0833 | 26.9772
- 4 | 2.50 | 0.0814 0.0018 0.0832 | 24.6107
- 5 | 2.50 | 0.0811 0.0019 0.0830 | 22.6548
- 6 | 2.50 | 0.0809 0.0020 0.0829 | 20.6989
- 7 | 2.50 | 0.0806 0.0021 0.0827 | 18.9688
- 8 | 2.50 | 0.0804 0.0022 0.0826 | 17.4455
- 9 | 2.50 | 0.0801 0.0022 0.0824 | 15.9223
- 10 | 2.50 | 0.0799 0.0023 0.0822 | 14.6627
- 11 | 2.50 | 0.0796 0.0024 0.0820 | 13.4764
- 12 | 2.50 | 0.0793 0.0024 0.0818 | 12.3015
- 13 | 2.50 | 0.0791 0.0025 0.0816 | 11.3776
- 14 | 2.50 | 0.0788 0.0026 0.0813 | 10.4537
- 15 | 2.25 | 0.0781 0.0026 0.0807 | 9.5920
- 16 | 2.25 | 0.0754 0.0039 0.0793 | 8.8725
- 17 | 2.25 | 0.0744 0.0044 0.0787 | 8.1530
- 29 | 2.00 | 0.0761 0.0020 0.0781 | 3.3283
- 30 | 2.00 | 0.0708 0.0042 0.0750 | 3.1221
- 31 | 2.00 | 0.0690 0.0051 0.0742 | 2.9160
- 43 | 1.75 | 0.0683 0.0029 0.0712 | 1.5785
- 44 | 1.75 | 0.0640 0.0052 0.0692 | 1.5194
- 45 | 1.75 | 0.0626 0.0060 0.0687 | 1.4626
- 57 | 1.50 | 0.0615 0.0043 0.0658 | 1.0900
- 58 | 1.50 | 0.0582 0.0065 0.0647 | 1.0730
- 59 | 1.50 | 0.0572 0.0072 0.0644 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 211s
- Prepare output 17s
- 228s
- Jacobian determinant (RMS): 0.010 0.036 0.055 0.080 0.106 | 0.113492
- Template Matching: 0.085 0.223 0.207 0.188 0.172 | 0.171623
- Write result maps: 74s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 40s
- CSF distance: 20s
- PBT2x thickness: 60s
- 127s
- Create initial surface 107s
- Topology correction: 117s
- Surface refinement: 105s
- Reduction of surface collisions with optimization: 77s
- Spherical mapping with areal smoothing 109s
- Spherical registration 344s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 40s
- CSF distance: 20s
- PBT2x thickness: 58s
- 125s
- Create initial surface 104s
- Topology correction: 121s
- Surface refinement: 125s
- Reduction of surface collisions with optimization: 79s
- Spherical mapping with areal smoothing 108s
- Spherical registration 343s
- Final surface processing results:
- Average thickness (FS): 2.4180 0.5988 mm
- Surface intensity / position RMSE: 0.0732 / 0.0767
- Euler number / defect number / defect size: 38.0 / 26.0 / 1.12%
- Display thickness: /var/lib/condor/execute/dir_25536/ds/sub-0934/surf/lh.thickness.sub-0934_ses-01_T1w
- Display thickness: /var/lib/condor/execute/dir_25536/ds/sub-0934/surf/rh.thickness.sub-0934_ses-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_25536/ds/sub-0934/sub-0934_ses-01_T1w.nii
- Surface ROI estimation: 11s
- Surface and thickness estimation takes: 2124s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 16s
- ROI estimation of 'neuromorphometrics' atlas 60s
- ROI estimation of 'lpba40' atlas 19s
- ROI estimation of 'hammers' atlas 44s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 14s
- ROI estimation of 'aal3' atlas 22s
- ROI estimation of 'mori' atlas 34s
- ROI estimation of 'anatomy3' atlas 49s
- ROI estimation of 'julichbrain' atlas 68s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 26s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 41s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 96s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 165s
- Write results 167s
- 659s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_25536/ds/sub-0934/report/catreport_sub-0934_ses-01_T1w.pdf
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- CAT preprocessing takes 72 minute(s) and 39 second(s).
- Image Quality Rating (IQR): 82.26% (B-)
- GM volume (GMV): 49.20% (672.60 / 1367.11 ml)
- GM thickness (GMT): 2.42 0.60 mm
- Segmentations are saved in /var/lib/condor/execute/dir_25536/ds/sub-0934/mri
- Reports are saved in /var/lib/condor/execute/dir_25536/ds/sub-0934/report
- Labels are saved in /var/lib/condor/execute/dir_25536/ds/sub-0934/label
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