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- CAT12.8.1 r1980: 1/1: ./condor/execute/dir_23851/ds/sub-50/sub-50_T1w.n
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- SANLM denoising (medium): 27s
- APP: Rough bias correction:
- Initialize 3s
- Estimate background 5s
- Initial correction 4s
- Refine background 2s
- Final correction 3s
- Final scaling 3s
- 24s
- Correct center-of-mass 3s
- Affine registration 6s
- SPM preprocessing 1 (estimate 1 - TPM registration): 8s
- Use initial fine affine registration. 53s
- SPM preprocessing 1 (estimate 2): 52s
- SPM preprocessing 2 (write):
- Write Segmentation 11s
- Update Segmentation 16s
- Update Skull-Stripping 25s
- Update probability maps 4s
- 56s
- Global intensity correction: 8s
- SANLM denoising after intensity normalization (medium): 8s
- Fast Optimized Shooting registration 34s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 1s
- Prepare segments (LASmod = 1.00) 14s
- Estimate local tissue thresholds (WM) 12s
- Estimate local tissue thresholds (GM) 18s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 12s
- 63s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 4s
- Ventricle detection 14s
- Blood vessel detection 9s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 24s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 2s
- 65s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 39s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.09,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 11s
- 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 | 0.0843 0.0000 0.0843 | 32.0000
- 2 | 2.50 | 0.0814 0.0013 0.0826 | 29.4886
- 3 | 2.50 | 0.0805 0.0019 0.0824 | 26.9772
- 4 | 2.50 | 0.0800 0.0022 0.0822 | 24.6107
- 5 | 2.50 | 0.0797 0.0023 0.0820 | 22.6548
- 6 | 2.50 | 0.0794 0.0024 0.0818 | 20.6989
- 7 | 2.50 | 0.0791 0.0025 0.0816 | 18.9688
- 8 | 2.50 | 0.0788 0.0026 0.0814 | 17.4455
- 9 | 2.50 | 0.0785 0.0027 0.0812 | 15.9223
- 10 | 2.50 | 0.0781 0.0028 0.0810 | 14.6627
- 11 | 2.50 | 0.0778 0.0029 0.0807 | 13.4764
- 12 | 2.50 | 0.0775 0.0030 0.0805 | 12.3015
- 13 | 2.50 | 0.0771 0.0031 0.0802 | 11.3776
- 14 | 2.50 | 0.0768 0.0032 0.0800 | 10.4537
- 15 | 2.25 | 0.0769 0.0032 0.0802 | 9.5920
- 16 | 2.25 | 0.0737 0.0050 0.0786 | 8.8725
- 29 | 2.00 | 0.0745 0.0022 0.0767 | 3.3283
- 30 | 2.00 | 0.0678 0.0049 0.0727 | 3.1221
- 31 | 2.00 | 0.0655 0.0060 0.0715 | 2.9160
- 43 | 1.75 | 0.0642 0.0035 0.0677 | 1.5785
- 44 | 1.75 | 0.0599 0.0058 0.0656 | 1.5194
- 45 | 1.75 | 0.0584 0.0066 0.0650 | 1.4626
- 57 | 1.50 | 0.0569 0.0048 0.0618 | 1.0900
- 58 | 1.50 | 0.0539 0.0068 0.0607 | 1.0730
- 59 | 1.50 | 0.0529 0.0074 0.0603 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 226s
- Prepare output 8s
- 234s
- Jacobian determinant (RMS): 0.011 0.042 0.066 0.094 0.121 | 0.130451
- Template Matching: 0.084 0.221 0.197 0.175 0.159 | 0.158827
- Write result maps: 19s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 37s
- CSF distance: 17s
- PBT2x thickness: 55s
- 116s
- Create initial surface 95s
- Topology correction: 90s
- Surface refinement: 91s
- Reduction of surface collisions with optimization: 77s
- Spherical mapping with areal smoothing 94s
- Spherical registration 274s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 40s
- CSF distance: 17s
- PBT2x thickness: 52s
- 116s
- Create initial surface 94s
- Topology correction: 90s
- Surface refinement: 119s
- Reduction of surface collisions with optimization: 77s
- Spherical mapping with areal smoothing 94s
- Spherical registration 277s
- Final surface processing results:
- Average thickness (FS): 2.4476 0.6059 mm
- Surface intensity / position RMSE: 0.0649 / 0.0672
- Euler number / defect number / defect size: 22.0 / 15.0 / 0.68%
- Display thickness: /var/lib/condor/execute/dir_23851/ds/sub-50/surf/lh.thickness.sub-50_T1w
- Display thickness: /var/lib/condor/execute/dir_23851/ds/sub-50/surf/rh.thickness.sub-50_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_23851/ds/sub-50/sub-50_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1795s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 24s
- ROI estimation of 'lpba40' atlas 7s
- ROI estimation of 'hammers' atlas 17s
- 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 21s
- ROI estimation of 'julichbrain' atlas 28s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 9s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 13s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 45s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 64s
- Write results 66s
- 268s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_23851/ds/sub-50/report/catreport_sub-50_T1w.pdf
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- CAT preprocessing takes 47 minute(s) and 55 second(s).
- Image Quality Rating (IQR): 82.45% (B-)
- GM volume (GMV): 46.89% (612.28 / 1305.84 ml)
- GM thickness (GMT): 2.45 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_23851/ds/sub-50/mri
- Reports are saved in /var/lib/condor/execute/dir_23851/ds/sub-50/report
- Labels are saved in /var/lib/condor/execute/dir_23851/ds/sub-50/label
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