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- CAT12.8.1 r1980: 1/1: ./dir_14141/ds/sub-027/sub-027_ses-t2_T1w.n
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- SANLM denoising (medium): 11s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 8s
- Initial correction 7s
- Refine background 4s
- Final correction 5s
- Final scaling 7s
- 44s
- Correct center-of-mass 10s
- Affine registration 15s
- SPM preprocessing 1 (estimate 1 - TPM registration): 115s
- SPM preprocessing 1 (estimate 2): 86s
- SPM preprocessing 2 (write):
- Write Segmentation 17s
- Update Segmentation 20s
- Update Skull-Stripping 42s
- Update probability maps 8s
- 87s
- Global intensity correction: 17s
- SANLM denoising after intensity normalization (medium): 6s
- Fast Optimized Shooting registration 40s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.01) 15s
- Estimate local tissue thresholds (WM) 17s
- Estimate local tissue thresholds (GM) 22s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 15s
- 80s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 4s
- Ventricle detection 13s
- Blood vessel detection 9s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.16) 24s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 4s
- 69s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 41s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- 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
- 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 | 0.0913 0.0000 0.0913 | 32.0000
- 2 | 2.50 | 0.0873 0.0016 0.0888 | 29.4886
- 3 | 2.50 | 0.0860 0.0024 0.0884 | 26.9772
- 4 | 2.50 | 0.0854 0.0028 0.0882 | 24.6107
- 5 | 2.50 | 0.0849 0.0030 0.0879 | 22.6548
- 6 | 2.50 | 0.0845 0.0031 0.0876 | 20.6989
- 7 | 2.50 | 0.0840 0.0033 0.0873 | 18.9688
- 8 | 2.50 | 0.0836 0.0035 0.0870 | 17.4455
- 9 | 2.50 | 0.0831 0.0036 0.0867 | 15.9223
- 10 | 2.50 | 0.0826 0.0037 0.0863 | 14.6627
- 11 | 2.50 | 0.0821 0.0039 0.0860 | 13.4764
- 12 | 2.50 | 0.0816 0.0040 0.0856 | 12.3015
- 13 | 2.50 | 0.0811 0.0041 0.0852 | 11.3776
- 14 | 2.50 | 0.0806 0.0043 0.0848 | 10.4537
- 15 | 2.25 | 0.0829 0.0044 0.0873 | 9.5920
- 16 | 2.25 | 0.0788 0.0064 0.0852 | 8.8725
- 17 | 2.25 | 0.0770 0.0073 0.0842 | 8.1530
- 18 | 2.25 | 0.0757 0.0077 0.0834 | 7.5234
- 19 | 2.25 | 0.0748 0.0079 0.0827 | 6.9630
- 29 | 2.00 | 0.0770 0.0041 0.0811 | 3.3283
- 30 | 2.00 | 0.0707 0.0069 0.0776 | 3.1221
- 31 | 2.00 | 0.0683 0.0081 0.0763 | 2.9160
- 43 | 1.75 | 0.0670 0.0047 0.0716 | 1.5785
- 44 | 1.75 | 0.0619 0.0073 0.0693 | 1.5194
- 45 | 1.75 | 0.0602 0.0083 0.0684 | 1.4626
- 57 | 1.50 | 0.0587 0.0061 0.0649 | 1.0900
- 58 | 1.50 | 0.0552 0.0084 0.0636 | 1.0730
- 59 | 1.50 | 0.0540 0.0092 0.0632 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 211s
- Prepare output 10s
- 220s
- Jacobian determinant (RMS): 0.013 0.049 0.081 0.112 0.140 | 0.149200
- Template Matching: 0.091 0.224 0.205 0.181 0.162 | 0.161913
- Write result maps: 26s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 67s
- CSF distance: 15s
- PBT2x thickness: 46s
- 136s
- Create initial surface 82s
- Topology correction: 81s
- Surface refinement: 68s
- Reduction of surface collisions with optimization: 64s
- Spherical mapping with areal smoothing 78s
- Spherical registration 230s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 98s
- CSF distance: 16s
- PBT2x thickness: 46s
- 166s
- Create initial surface 80s
- Topology correction: 85s
- Surface refinement: 98s
- Reduction of surface collisions with optimization: 67s
- Spherical mapping with areal smoothing 79s
- Spherical registration 236s
- Final surface processing results:
- Average thickness (FS): 2.3556 0.6217 mm
- Surface intensity / position RMSE: 0.0640 / 0.0702
- Euler number / defect number / defect size: 28.0 / 15.5 / 1.16%
- Display thickness: /var/lib/condor/execute/dir_14141/ds/sub-027/surf/lh.thickness.sub-027_ses-t2_T1w
- Display thickness: /var/lib/condor/execute/dir_14141/ds/sub-027/surf/rh.thickness.sub-027_ses-t2_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_14141/ds/sub-027/sub-027_ses-t2_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1634s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 12s
- ROI estimation of 'neuromorphometrics' atlas 43s
- ROI estimation of 'lpba40' atlas 12s
- ROI estimation of 'hammers' atlas 30s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 11s
- ROI estimation of 'aal3' atlas 18s
- ROI estimation of 'mori' atlas 26s
- ROI estimation of 'anatomy3' atlas 37s
- ROI estimation of 'julichbrain' atlas 49s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 18s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 23s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 79s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 119s
- Write results 120s
- 480s
- Quality check: 5s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_14141/ds/sub-027/report/catreport_sub-027_ses-t2_T1w.pdf
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- CAT preprocessing takes 51 minute(s) and 24 second(s).
- Image Quality Rating (IQR): 83.60% (B)
- GM volume (GMV): 41.80% (597.59 / 1429.74 ml)
- GM thickness (GMT): 2.36 0.62 mm
- Segmentations are saved in /var/lib/condor/execute/dir_14141/ds/sub-027/mri
- Reports are saved in /var/lib/condor/execute/dir_14141/ds/sub-027/report
- Labels are saved in /var/lib/condor/execute/dir_14141/ds/sub-027/label
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