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- CAT12.8.1 r1980: 1/1: ./condor/execute/dir_11583/ds/sub-04/sub-04_T1w.n
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- SANLM denoising (medium): 9s
- APP: Rough bias correction:
- Initialize 2s
- Estimate background 4s
- Initial correction 3s
- Refine background 1s
- Final correction 3s
- Final scaling 2s
- 17s
- Correct center-of-mass 2s
- Affine registration 4s
- SPM preprocessing 1 (estimate 1 - TPM registration): 42s
- SPM preprocessing 1 (estimate 2): 25s
- SPM preprocessing 2 (write):
- Write Segmentation 8s
- Update Segmentation 12s
- Update Skull-Stripping 19s
- Update probability maps 3s
- 43s
- Global intensity correction: 6s
- SANLM denoising after intensity normalization (medium): 13s
- Fast Optimized Shooting registration 25s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 1s
- Prepare segments (LASmod = 1.00) 11s
- Estimate local tissue thresholds (WM) 11s
- Estimate local tissue thresholds (GM) 18s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 15s
- 60s
- ROI segmentation (partitioning):
- Atlas -> subject space 5s
- Major structures 3s
- Ventricle detection 14s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.01) 23s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 2s
- 59s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 29s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 2s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 9s
- 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 | 0.0845 0.0000 0.0845 | 32.0000
- 2 | 2.50 | 0.0814 0.0013 0.0828 | 29.4886
- 3 | 2.50 | 0.0805 0.0020 0.0825 | 26.9772
- 4 | 2.50 | 0.0801 0.0022 0.0823 | 24.6107
- 5 | 2.50 | 0.0798 0.0024 0.0822 | 22.6548
- 6 | 2.50 | 0.0795 0.0025 0.0820 | 20.6989
- 7 | 2.50 | 0.0792 0.0026 0.0818 | 18.9688
- 8 | 2.50 | 0.0789 0.0027 0.0816 | 17.4455
- 9 | 2.50 | 0.0786 0.0028 0.0814 | 15.9223
- 10 | 2.50 | 0.0782 0.0029 0.0811 | 14.6627
- 11 | 2.50 | 0.0779 0.0030 0.0809 | 13.4764
- 12 | 2.50 | 0.0776 0.0030 0.0806 | 12.3015
- 13 | 2.50 | 0.0773 0.0031 0.0804 | 11.3776
- 14 | 2.50 | 0.0770 0.0032 0.0801 | 10.4537
- 15 | 2.25 | 0.0766 0.0032 0.0799 | 9.5920
- 16 | 2.25 | 0.0734 0.0049 0.0783 | 8.8725
- 29 | 2.00 | 0.0745 0.0022 0.0767 | 3.3283
- 30 | 2.00 | 0.0681 0.0048 0.0729 | 3.1221
- 31 | 2.00 | 0.0661 0.0057 0.0718 | 2.9160
- 43 | 1.75 | 0.0650 0.0033 0.0683 | 1.5785
- 44 | 1.75 | 0.0607 0.0056 0.0663 | 1.5194
- 45 | 1.75 | 0.0593 0.0064 0.0657 | 1.4626
- 57 | 1.50 | 0.0580 0.0046 0.0626 | 1.0900
- 58 | 1.50 | 0.0549 0.0067 0.0616 | 1.0730
- 59 | 1.50 | 0.0539 0.0073 0.0612 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 161s
- Prepare output 8s
- 169s
- Jacobian determinant (RMS): 0.011 0.040 0.061 0.089 0.116 | 0.123606
- Template Matching: 0.085 0.220 0.198 0.178 0.162 | 0.161608
- Write result maps: 11s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 28s
- CSF distance: 15s
- PBT2x thickness: 42s
- 90s
- Create initial surface 80s
- Topology correction: 90s
- Surface refinement: 102s
- Reduction of surface collisions with optimization: 69s
- Spherical mapping with areal smoothing 83s
- Spherical registration 290s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 28s
- CSF distance: 14s
- PBT2x thickness: 40s
- 87s
- Create initial surface 76s
- Topology correction: 87s
- Surface refinement: 85s
- Reduction of surface collisions with optimization: 71s
- Spherical mapping with areal smoothing 84s
- Spherical registration 299s
- Final surface processing results:
- Average thickness (FS): 2.5519 0.6444 mm
- Surface intensity / position RMSE: 0.0797 / 0.1082
- Euler number / defect number / defect size: 20.0 / 11.5 / 1.45%
- Display thickness: /var/lib/condor/execute/dir_11583/ds/sub-04/surf/lh.thickness.sub-04_T1w
- Display thickness: /var/lib/condor/execute/dir_11583/ds/sub-04/surf/rh.thickness.sub-04_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_11583/ds/sub-04/sub-04_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1664s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 3s
- ROI estimation of 'neuromorphometrics' atlas 11s
- ROI estimation of 'lpba40' atlas 3s
- ROI estimation of 'hammers' atlas 8s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 3s
- ROI estimation of 'aal3' atlas 4s
- ROI estimation of 'mori' atlas 6s
- ROI estimation of 'anatomy3' atlas 9s
- ROI estimation of 'julichbrain' atlas 12s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 5s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 9s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 19s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 29s
- Write results 30s
- 125s
- Quality check: 4s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_11583/ds/sub-04/report/catreport_sub-04_T1w.pdf
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- CAT preprocessing takes 39 minute(s) and 51 second(s).
- Image Quality Rating (IQR): 83.81% (B)
- GM volume (GMV): 50.65% (697.49 / 1377.15 ml)
- GM thickness (GMT): 2.55 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_11583/ds/sub-04/mri
- Reports are saved in /var/lib/condor/execute/dir_11583/ds/sub-04/report
- Labels are saved in /var/lib/condor/execute/dir_11583/ds/sub-04/label
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