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- CAT12.8.1 r1980: 1/1: ./dir_12076/ds/sub-021/sub-021_ses-t0_T1w.n
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- SANLM denoising (medium): 11s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 7s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 6s
- 36s
- Correct center-of-mass 2s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 69s
- SPM preprocessing 1 (estimate 2): 60s
- SPM preprocessing 2 (write):
- Write Segmentation 15s
- Update Segmentation 18s
- Update Skull-Stripping 38s
- Update probability maps 8s
- 79s
- Global intensity correction: 14s
- SANLM denoising after intensity normalization (medium): 7s
- Fast Optimized Shooting registration 29s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.10) 15s
- Estimate local tissue thresholds (WM) 16s
- Estimate local tissue thresholds (GM) 22s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 16s
- 78s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 4s
- Ventricle detection 16s
- Blood vessel detection 10s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.19) 30s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 4s
- 76s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 34s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 5s
- 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 | 0.0854 0.0000 0.0854 | 32.0000
- 2 | 2.50 | 0.0828 0.0012 0.0839 | 29.4886
- 3 | 2.50 | 0.0819 0.0018 0.0838 | 26.9772
- 4 | 2.50 | 0.0815 0.0021 0.0836 | 24.6107
- 5 | 2.50 | 0.0812 0.0022 0.0834 | 22.6548
- 6 | 2.50 | 0.0809 0.0023 0.0832 | 20.6989
- 7 | 2.50 | 0.0806 0.0025 0.0831 | 18.9688
- 8 | 2.50 | 0.0803 0.0026 0.0829 | 17.4455
- 9 | 2.50 | 0.0800 0.0027 0.0826 | 15.9223
- 10 | 2.50 | 0.0796 0.0028 0.0824 | 14.6627
- 11 | 2.50 | 0.0793 0.0029 0.0822 | 13.4764
- 12 | 2.50 | 0.0789 0.0030 0.0819 | 12.3015
- 13 | 2.50 | 0.0786 0.0031 0.0817 | 11.3776
- 14 | 2.50 | 0.0782 0.0032 0.0814 | 10.4537
- 15 | 2.25 | 0.0776 0.0033 0.0809 | 9.5920
- 16 | 2.25 | 0.0744 0.0049 0.0793 | 8.8725
- 29 | 2.00 | 0.0753 0.0022 0.0775 | 3.3283
- 30 | 2.00 | 0.0682 0.0051 0.0733 | 3.1221
- 31 | 2.00 | 0.0658 0.0062 0.0721 | 2.9160
- 43 | 1.75 | 0.0644 0.0036 0.0680 | 1.5785
- 44 | 1.75 | 0.0599 0.0060 0.0659 | 1.5194
- 45 | 1.75 | 0.0585 0.0068 0.0653 | 1.4626
- 57 | 1.50 | 0.0566 0.0050 0.0616 | 1.0900
- 58 | 1.50 | 0.0536 0.0070 0.0606 | 1.0730
- 59 | 1.50 | 0.0526 0.0076 0.0602 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 148s
- Prepare output 10s
- 158s
- Jacobian determinant (RMS): 0.011 0.042 0.067 0.096 0.121 | 0.128554
- Template Matching: 0.085 0.223 0.197 0.175 0.158 | 0.157868
- Write result maps: 20s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 48s
- CSF distance: 15s
- PBT2x thickness: 43s
- 112s
- Create initial surface 85s
- Topology correction: 89s
- Surface refinement: 76s
- Reduction of surface collisions with optimization: 67s
- Spherical mapping with areal smoothing 74s
- Spherical registration 255s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 53s
- CSF distance: 15s
- PBT2x thickness: 45s
- 119s
- Create initial surface 87s
- Topology correction: 95s
- Surface refinement: 97s
- Reduction of surface collisions with optimization: 71s
- Spherical mapping with areal smoothing 77s
- Spherical registration 285s
- Final surface processing results:
- Average thickness (FS): 2.5564 0.6435 mm
- Surface intensity / position RMSE: 0.0600 / 0.0628
- Euler number / defect number / defect size: 18.0 / 12.5 / 0.59%
- Display thickness: /var/lib/condor/execute/dir_12076/ds/sub-021/surf/lh.thickness.sub-021_ses-t0_T1w
- Display thickness: /var/lib/condor/execute/dir_12076/ds/sub-021/surf/rh.thickness.sub-021_ses-t0_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_12076/ds/sub-021/sub-021_ses-t0_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1676s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 10s
- ROI estimation of 'neuromorphometrics' atlas 32s
- ROI estimation of 'lpba40' atlas 9s
- ROI estimation of 'hammers' atlas 20s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 14s
- ROI estimation of 'mori' atlas 21s
- ROI estimation of 'anatomy3' atlas 25s
- ROI estimation of 'julichbrain' atlas 32s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 13s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 22s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 46s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 64s
- Write results 64s
- 316s
- Quality check: 5s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_12076/ds/sub-021/report/catreport_sub-021_ses-t0_T1w.pdf
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- CAT preprocessing takes 46 minute(s) and 12 second(s).
- Image Quality Rating (IQR): 84.61% (B)
- GM volume (GMV): 41.62% (728.65 / 1750.87 ml)
- GM thickness (GMT): 2.56 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_12076/ds/sub-021/mri
- Reports are saved in /var/lib/condor/execute/dir_12076/ds/sub-021/report
- Labels are saved in /var/lib/condor/execute/dir_12076/ds/sub-021/label
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