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- CAT12.8.1 r1980: 1/1: ./execute/dir_2771311/ds/sub-26/sub-26_T1w.n
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- SANLM denoising (medium): 81s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 14s
- Initial correction 10s
- Refine background 5s
- Final correction 7s
- Final scaling 8s
- 58s
- Correct center-of-mass 6s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 74s
- SPM preprocessing 1 (estimate 2): 66s
- SPM preprocessing 2 (write):
- Write Segmentation 20s
- Update Segmentation 21s
- Update Skull-Stripping 47s
- Update probability maps 10s
- 99s
- Global intensity correction: 18s
- SANLM denoising after intensity normalization (medium): 11s
- Fast Optimized Shooting registration 41s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.02) 16s
- Estimate local tissue thresholds (WM) 26s
- Estimate local tissue thresholds (GM) 37s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 42s
- 132s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 16s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.48 > WMHCstr'=0.01) 28s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 78s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 37s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.07,0.990.05]
- Final cleanup (gcutstr=0.24):
- 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
- 13s
- 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 | 0.0840 0.0000 0.0840 | 32.0000
- 2 | 2.50 | 0.0811 0.0012 0.0824 | 29.4886
- 3 | 2.50 | 0.0803 0.0019 0.0822 | 26.9772
- 4 | 2.50 | 0.0799 0.0021 0.0820 | 24.6107
- 5 | 2.50 | 0.0795 0.0022 0.0818 | 22.6548
- 6 | 2.50 | 0.0793 0.0023 0.0816 | 20.6989
- 7 | 2.50 | 0.0790 0.0024 0.0814 | 18.9688
- 8 | 2.50 | 0.0786 0.0025 0.0812 | 17.4455
- 9 | 2.50 | 0.0783 0.0026 0.0809 | 15.9223
- 10 | 2.50 | 0.0780 0.0027 0.0807 | 14.6627
- 11 | 2.50 | 0.0777 0.0028 0.0804 | 13.4764
- 12 | 2.50 | 0.0773 0.0028 0.0802 | 12.3015
- 13 | 2.50 | 0.0770 0.0029 0.0799 | 11.3776
- 14 | 2.50 | 0.0766 0.0030 0.0796 | 10.4537
- 15 | 2.25 | 0.0756 0.0031 0.0787 | 9.5920
- 16 | 2.25 | 0.0727 0.0045 0.0771 | 8.8725
- 29 | 2.00 | 0.0739 0.0020 0.0759 | 3.3283
- 30 | 2.00 | 0.0677 0.0045 0.0722 | 3.1221
- 31 | 2.00 | 0.0655 0.0055 0.0710 | 2.9160
- 43 | 1.75 | 0.0645 0.0032 0.0676 | 1.5785
- 44 | 1.75 | 0.0602 0.0054 0.0656 | 1.5194
- 45 | 1.75 | 0.0588 0.0061 0.0650 | 1.4626
- 57 | 1.50 | 0.0573 0.0045 0.0618 | 1.0900
- 58 | 1.50 | 0.0543 0.0064 0.0607 | 1.0730
- 59 | 1.50 | 0.0533 0.0070 0.0603 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 200s
- Prepare output 13s
- 213s
- Jacobian determinant (RMS): 0.011 0.041 0.060 0.083 0.105 | 0.112455
- Template Matching: 0.084 0.218 0.197 0.176 0.160 | 0.160014
- Write result maps: 29s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 35s
- CSF distance: 19s
- PBT2x thickness: 58s
- 119s
- Create initial surface 103s
- Topology correction: 112s
- Surface refinement: 82s
- Reduction of surface collisions with optimization: 78s
- Spherical mapping with areal smoothing 99s
- Spherical registration 339s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 32s
- CSF distance: 17s
- PBT2x thickness: 53s
- 110s
- Create initial surface 95s
- Topology correction: 105s
- Surface refinement: 89s
- Reduction of surface collisions with optimization: 75s
- Spherical mapping with areal smoothing 96s
- Spherical registration 318s
- Final surface processing results:
- Average thickness (FS): 2.5766 0.6175 mm
- Surface intensity / position RMSE: 0.0657 / 0.0651
- Euler number / defect number / defect size: 12.0 / 14.0 / 0.30%
- Display thickness: /var/lib/condor/execute/dir_2771311/ds/sub-26/surf/lh.thickness.sub-26_T1w
- Display thickness: /var/lib/condor/execute/dir_2771311/ds/sub-26/surf/rh.thickness.sub-26_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2771311/ds/sub-26/sub-26_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1926s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 32s
- ROI estimation of 'lpba40' atlas 9s
- ROI estimation of 'hammers' atlas 22s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 8s
- ROI estimation of 'aal3' atlas 13s
- ROI estimation of 'mori' atlas 20s
- ROI estimation of 'anatomy3' atlas 28s
- ROI estimation of 'julichbrain' atlas 37s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 26s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 60s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 80s
- Write results 81s
- 362s
- Quality check: 5s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2771311/ds/sub-26/report/catreport_sub-26_T1w.pdf
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- CAT preprocessing takes 55 minute(s) and 55 second(s).
- Image Quality Rating (IQR): 84.43% (B)
- GM volume (GMV): 49.47% (701.70 / 1418.51 ml)
- GM thickness (GMT): 2.58 0.62 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2771311/ds/sub-26/mri
- Reports are saved in /var/lib/condor/execute/dir_2771311/ds/sub-26/report
- Labels are saved in /var/lib/condor/execute/dir_2771311/ds/sub-26/label
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