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- CAT12.8.1 r1980: 1/1: ./condor/execute/dir_2241/ds/sub-58/sub-58_T1w.n
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- SANLM denoising (medium): 85s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 8s
- Initial correction 7s
- Refine background 4s
- Final correction 6s
- Final scaling 7s
- 44s
- Correct center-of-mass 3s
- Affine registration 8s
- SPM preprocessing 1 (estimate 1 - TPM registration): 63s
- SPM preprocessing 1 (estimate 2): 49s
- SPM preprocessing 2 (write):
- Write Segmentation 16s
- Update Segmentation 18s
- Update Skull-Stripping 39s
- Update probability maps 9s
- 81s
- Global intensity correction: 15s
- SANLM denoising after intensity normalization (medium): 17s
- Fast Optimized Shooting registration 33s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.01) 13s
- Estimate local tissue thresholds (WM) 20s
- Estimate local tissue thresholds (GM) 24s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 21s
- 86s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 14s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.48 > WMHCstr'=0.00) 23s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 65s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 31s
- AMAP peaks: [CSF,GM,WM] = [0.360.07,0.680.07,0.980.05]
- Final cleanup (gcutstr=0.24):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 3s
- 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 | 0.0873 0.0000 0.0873 | 32.0000
- 2 | 2.50 | 0.0836 0.0015 0.0851 | 29.4886
- 3 | 2.50 | 0.0826 0.0022 0.0848 | 26.9772
- 4 | 2.50 | 0.0820 0.0025 0.0846 | 24.6107
- 5 | 2.50 | 0.0816 0.0027 0.0843 | 22.6548
- 6 | 2.50 | 0.0813 0.0028 0.0841 | 20.6989
- 7 | 2.50 | 0.0809 0.0029 0.0838 | 18.9688
- 8 | 2.50 | 0.0805 0.0031 0.0836 | 17.4455
- 9 | 2.50 | 0.0801 0.0032 0.0833 | 15.9223
- 10 | 2.50 | 0.0797 0.0033 0.0830 | 14.6627
- 11 | 2.50 | 0.0793 0.0034 0.0827 | 13.4764
- 12 | 2.50 | 0.0789 0.0034 0.0824 | 12.3015
- 13 | 2.50 | 0.0785 0.0036 0.0821 | 11.3776
- 14 | 2.50 | 0.0781 0.0036 0.0817 | 10.4537
- 15 | 2.25 | 0.0774 0.0037 0.0811 | 9.5920
- 16 | 2.25 | 0.0742 0.0053 0.0795 | 8.8725
- 29 | 2.00 | 0.0752 0.0024 0.0776 | 3.3283
- 30 | 2.00 | 0.0690 0.0049 0.0739 | 3.1221
- 31 | 2.00 | 0.0669 0.0059 0.0728 | 2.9160
- 43 | 1.75 | 0.0659 0.0034 0.0694 | 1.5785
- 44 | 1.75 | 0.0617 0.0056 0.0674 | 1.5194
- 45 | 1.75 | 0.0603 0.0064 0.0667 | 1.4626
- 57 | 1.50 | 0.0589 0.0047 0.0636 | 1.0900
- 58 | 1.50 | 0.0558 0.0067 0.0625 | 1.0730
- 59 | 1.50 | 0.0547 0.0074 0.0621 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 158s
- Prepare output 10s
- 168s
- Jacobian determinant (RMS): 0.012 0.046 0.068 0.096 0.122 | 0.129681
- Template Matching: 0.087 0.223 0.201 0.181 0.164 | 0.164250
- Write result maps: 22s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 30s
- CSF distance: 15s
- PBT2x thickness: 44s
- 95s
- Create initial surface 81s
- Topology correction: 92s
- Surface refinement: 75s
- Reduction of surface collisions with optimization: 71s
- Spherical mapping with areal smoothing 126s
- Spherical registration 264s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 29s
- CSF distance: 14s
- PBT2x thickness: 40s
- 88s
- Create initial surface 72s
- Topology correction: 86s
- Surface refinement: 98s
- Reduction of surface collisions with optimization: 67s
- Spherical mapping with areal smoothing 72s
- Spherical registration 247s
- Final surface processing results:
- Average thickness (FS): 2.6075 0.6162 mm
- Surface intensity / position RMSE: 0.0688 / 0.0656
- Euler number / defect number / defect size: 16.0 / 15.5 / 0.30%
- Display thickness: /var/lib/condor/execute/dir_2241/ds/sub-58/surf/lh.thickness.sub-58_T1w
- Display thickness: /var/lib/condor/execute/dir_2241/ds/sub-58/surf/rh.thickness.sub-58_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2241/ds/sub-58/sub-58_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1617s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 25s
- 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 22s
- ROI estimation of 'julichbrain' atlas 29s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 47s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 70s
- Write results 71s
- 290s
- Quality check: 4s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2241/ds/sub-58/report/catreport_sub-58_T1w.pdf
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- CAT preprocessing takes 46 minute(s) and 10 second(s).
- Image Quality Rating (IQR): 81.28% (B-)
- GM volume (GMV): 50.99% (749.06 / 1468.96 ml)
- GM thickness (GMT): 2.61 0.62 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2241/ds/sub-58/mri
- Reports are saved in /var/lib/condor/execute/dir_2241/ds/sub-58/report
- Labels are saved in /var/lib/condor/execute/dir_2241/ds/sub-58/label
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