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- CAT12.8.1 r1980: 1/1: ./execute/dir_9598/ds/sub-sc002/sub-sc002_T1w.n
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- SANLM denoising (medium): 34s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 9s
- Initial correction 7s
- Refine background 4s
- Final correction 7s
- Final scaling 7s
- 50s
- Correct center-of-mass 6s
- Affine registration 13s
- SPM preprocessing 1 (estimate 1 - TPM registration): 103s
- SPM preprocessing 1 (estimate 2): 87s
- SPM preprocessing 2 (write):
- Write Segmentation 23s
- Update Segmentation 26s
- Update Skull-Stripping 55s
- Update probability maps 11s
- 114s
- Global intensity correction: 21s
- SANLM denoising after intensity normalization (medium): 21s
- Fast Optimized Shooting registration 49s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 6s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.18) 21s
- Estimate local tissue thresholds (WM) 23s
- Estimate local tissue thresholds (GM) 28s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 24s
- 109s
- ROI segmentation (partitioning):
- Atlas -> subject space 11s
- Major structures 5s
- Ventricle detection 17s
- Blood vessel detection 12s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.04) 34s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 5s
- Final corrections 6s
- 93s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 55s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 6s
- Level 1 cleanup (brain masking) 4s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 4s
- 16s
- 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 | 0.0844 0.0000 0.0844 | 32.0000
- 2 | 2.50 | 0.0819 0.0012 0.0831 | 29.4886
- 3 | 2.50 | 0.0812 0.0017 0.0830 | 26.9772
- 4 | 2.50 | 0.0809 0.0020 0.0828 | 24.6107
- 5 | 2.50 | 0.0806 0.0021 0.0827 | 22.6548
- 6 | 2.50 | 0.0803 0.0022 0.0825 | 20.6989
- 7 | 2.50 | 0.0800 0.0023 0.0823 | 18.9688
- 8 | 2.50 | 0.0798 0.0024 0.0822 | 17.4455
- 9 | 2.50 | 0.0795 0.0025 0.0820 | 15.9223
- 10 | 2.50 | 0.0792 0.0026 0.0818 | 14.6627
- 11 | 2.50 | 0.0789 0.0027 0.0816 | 13.4764
- 12 | 2.50 | 0.0785 0.0028 0.0813 | 12.3015
- 13 | 2.50 | 0.0782 0.0029 0.0811 | 11.3776
- 14 | 2.50 | 0.0779 0.0030 0.0808 | 10.4537
- 15 | 2.25 | 0.0777 0.0030 0.0807 | 9.5920
- 16 | 2.25 | 0.0746 0.0046 0.0791 | 8.8725
- 29 | 2.00 | 0.0757 0.0021 0.0778 | 3.3283
- 30 | 2.00 | 0.0688 0.0048 0.0736 | 3.1221
- 31 | 2.00 | 0.0664 0.0060 0.0724 | 2.9160
- 43 | 1.75 | 0.0651 0.0035 0.0686 | 1.5785
- 44 | 1.75 | 0.0606 0.0059 0.0664 | 1.5194
- 45 | 1.75 | 0.0590 0.0067 0.0657 | 1.4626
- 57 | 1.50 | 0.0574 0.0049 0.0623 | 1.0900
- 58 | 1.50 | 0.0543 0.0070 0.0612 | 1.0730
- 59 | 1.50 | 0.0532 0.0076 0.0608 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 259s
- Prepare output 13s
- 272s
- Jacobian determinant (RMS): 0.012 0.044 0.067 0.096 0.121 | 0.127490
- Template Matching: 0.084 0.224 0.199 0.177 0.160 | 0.159632
- Write result maps: 46s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 50s
- CSF distance: 21s
- PBT2x thickness: 63s
- 143s
- Create initial surface 113s
- Topology correction: 125s
- Surface refinement: 123s
- Reduction of surface collisions with optimization: 104s
- Spherical mapping with areal smoothing 115s
- Spherical registration 287s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 49s
- CSF distance: 21s
- PBT2x thickness: 64s
- 143s
- Create initial surface 112s
- Topology correction: 158s
- Surface refinement: 154s
- Reduction of surface collisions with optimization: 102s
- Spherical mapping with areal smoothing 116s
- Spherical registration 314s
- Final surface processing results:
- Average thickness (FS): 2.5170 0.5973 mm
- Surface intensity / position RMSE: 0.0581 / 0.0580
- Euler number / defect number / defect size: 8.0 / 7.5 / 0.19%
- Display thickness: /var/lib/condor/execute/dir_9598/ds/sub-sc002/surf/lh.thickness.sub-sc002_T1w
- Display thickness: /var/lib/condor/execute/dir_9598/ds/sub-sc002/surf/rh.thickness.sub-sc002_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_9598/ds/sub-sc002/sub-sc002_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 2235s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 14s
- ROI estimation of 'neuromorphometrics' atlas 53s
- ROI estimation of 'lpba40' atlas 15s
- ROI estimation of 'hammers' atlas 37s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 13s
- ROI estimation of 'aal3' atlas 22s
- ROI estimation of 'mori' atlas 32s
- ROI estimation of 'anatomy3' atlas 47s
- ROI estimation of 'julichbrain' atlas 62s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 24s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 30s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 100s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 149s
- Write results 151s
- 606s
- Quality check: 7s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_9598/ds/sub-sc002/report/catreport_sub-sc002_T1w.pdf
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- CAT preprocessing takes 67 minute(s) and 33 second(s).
- Image Quality Rating (IQR): 85.40% (B)
- GM volume (GMV): 44.51% (664.93 / 1494.03 ml)
- GM thickness (GMT): 2.52 0.60 mm
- Segmentations are saved in /var/lib/condor/execute/dir_9598/ds/sub-sc002/mri
- Reports are saved in /var/lib/condor/execute/dir_9598/ds/sub-sc002/report
- Labels are saved in /var/lib/condor/execute/dir_9598/ds/sub-sc002/label
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