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- CAT12.8.1 r1980: 1/1: ./dir_30963/ds/sub-0159/sub-0159_ses-01_T1w.n
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- SANLM denoising (medium): 192s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 9s
- Initial correction 16s
- Refine background 5s
- Final correction 9s
- Final scaling 7s
- 63s
- Correct center-of-mass 6s
- Affine registration 21s
- SPM preprocessing 1 (estimate 1 - TPM registration): 93s
- SPM preprocessing 1 (estimate 2): 68s
- SPM preprocessing 2 (write):
- Write Segmentation 22s
- Update Segmentation 24s
- Update Skull-Stripping 55s
- Update probability maps 12s
- 113s
- Global intensity correction: 22s
- SANLM denoising after intensity normalization (medium): 28s
- Fast Optimized Shooting registration 36s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 7s
- Prepare segments (LASmod = 1.03) 17s
- Estimate local tissue thresholds (WM) 24s
- Estimate local tissue thresholds (GM) 33s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 50s
- 141s
- ROI segmentation (partitioning):
- Atlas -> subject space 10s
- Major structures 4s
- Ventricle detection 17s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 34s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 6s
- 88s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 37s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- 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
- 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 | 0.0833 0.0000 0.0833 | 32.0000
- 2 | 2.50 | 0.0809 0.0011 0.0820 | 29.4886
- 3 | 2.50 | 0.0802 0.0016 0.0819 | 26.9772
- 4 | 2.50 | 0.0799 0.0018 0.0817 | 24.6107
- 5 | 2.50 | 0.0796 0.0020 0.0815 | 22.6548
- 6 | 2.50 | 0.0793 0.0020 0.0814 | 20.6989
- 7 | 2.50 | 0.0791 0.0021 0.0812 | 18.9688
- 8 | 2.50 | 0.0788 0.0022 0.0810 | 17.4455
- 9 | 2.50 | 0.0786 0.0022 0.0808 | 15.9223
- 10 | 2.50 | 0.0783 0.0023 0.0806 | 14.6627
- 11 | 2.50 | 0.0780 0.0024 0.0804 | 13.4764
- 12 | 2.50 | 0.0777 0.0024 0.0801 | 12.3015
- 13 | 2.50 | 0.0774 0.0025 0.0799 | 11.3776
- 14 | 2.50 | 0.0771 0.0026 0.0797 | 10.4537
- 15 | 2.25 | 0.0768 0.0027 0.0795 | 9.5920
- 16 | 2.25 | 0.0739 0.0040 0.0779 | 8.8725
- 29 | 2.00 | 0.0754 0.0018 0.0772 | 3.3283
- 30 | 2.00 | 0.0695 0.0042 0.0737 | 3.1221
- 31 | 2.00 | 0.0675 0.0051 0.0726 | 2.9160
- 43 | 1.75 | 0.0667 0.0030 0.0697 | 1.5785
- 44 | 1.75 | 0.0624 0.0052 0.0677 | 1.5194
- 45 | 1.75 | 0.0610 0.0060 0.0671 | 1.4626
- 57 | 1.50 | 0.0601 0.0044 0.0645 | 1.0900
- 58 | 1.50 | 0.0569 0.0065 0.0634 | 1.0730
- 59 | 1.50 | 0.0559 0.0072 0.0630 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 155s
- Prepare output 12s
- 167s
- Jacobian determinant (RMS): 0.009 0.034 0.054 0.082 0.111 | 0.118747
- Template Matching: 0.083 0.222 0.203 0.183 0.168 | 0.167586
- Write result maps: 33s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 30s
- CSF distance: 15s
- PBT2x thickness: 44s
- 95s
- Create initial surface 83s
- Topology correction: 101s
- Surface refinement: 93s
- Reduction of surface collisions with optimization: 77s
- Spherical mapping with areal smoothing 91s
- Spherical registration 295s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 34s
- CSF distance: 15s
- PBT2x thickness: 44s
- 99s
- Create initial surface 82s
- Topology correction: 98s
- Surface refinement: 82s
- Reduction of surface collisions with optimization: 75s
- Spherical mapping with areal smoothing 83s
- Spherical registration 275s
- Final surface processing results:
- Average thickness (FS): 2.4760 0.6539 mm
- Surface intensity / position RMSE: 0.0834 / 0.0971
- Euler number / defect number / defect size: 112.0 / 46.5 / 3.76%
- Display thickness: /var/lib/condor/execute/dir_30963/ds/sub-0159/surf/lh.thickness.sub-0159_ses-01_T1w
- Display thickness: /var/lib/condor/execute/dir_30963/ds/sub-0159/surf/rh.thickness.sub-0159_ses-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_30963/ds/sub-0159/sub-0159_ses-01_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1736s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 11s
- ROI estimation of 'neuromorphometrics' atlas 40s
- ROI estimation of 'lpba40' atlas 12s
- ROI estimation of 'hammers' atlas 29s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 10s
- ROI estimation of 'aal3' atlas 17s
- ROI estimation of 'mori' atlas 25s
- ROI estimation of 'anatomy3' atlas 35s
- ROI estimation of 'julichbrain' atlas 47s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 19s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 34s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 76s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 113s
- Write results 113s
- 473s
- Quality check: 5s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_30963/ds/sub-0159/report/catreport_sub-0159_ses-01_T1w.pdf
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- CAT preprocessing takes 57 minute(s) and 13 second(s).
- Image Quality Rating (IQR): 81.83% (B-)
- GM volume (GMV): 51.99% (720.07 / 1384.97 ml)
- GM thickness (GMT): 2.48 0.65 mm
- Segmentations are saved in /var/lib/condor/execute/dir_30963/ds/sub-0159/mri
- Reports are saved in /var/lib/condor/execute/dir_30963/ds/sub-0159/report
- Labels are saved in /var/lib/condor/execute/dir_30963/ds/sub-0159/label
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