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- CAT12.8.1 r1980: 1/1: ./dir_3568911/ds/sub-049/sub-049_ses-t1_T1w.n
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- SANLM denoising (medium): 13s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 6s
- Initial correction 8s
- Refine background 4s
- Final correction 7s
- Final scaling 7s
- 46s
- Correct center-of-mass 10s
- Affine registration 11s
- SPM preprocessing 1 (estimate 1 - TPM registration): 84s
- SPM preprocessing 1 (estimate 2): 90s
- SPM preprocessing 2 (write):
- Write Segmentation 19s
- Update Segmentation 21s
- Update Skull-Stripping 49s
- Update probability maps 10s
- 99s
- Global intensity correction: 17s
- SANLM denoising after intensity normalization (medium): 7s
- Fast Optimized Shooting registration 43s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.10) 15s
- Estimate local tissue thresholds (WM) 19s
- Estimate local tissue thresholds (GM) 24s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 17s
- 86s
- ROI segmentation (partitioning):
- Atlas -> subject space 10s
- Major structures 4s
- Ventricle detection 15s
- Blood vessel detection 10s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.06) 27s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 76s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 33s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- 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 | 0.0901 0.0000 0.0901 | 32.0000
- 2 | 2.50 | 0.0862 0.0016 0.0877 | 29.4886
- 3 | 2.50 | 0.0850 0.0024 0.0874 | 26.9772
- 4 | 2.50 | 0.0844 0.0028 0.0871 | 24.6107
- 5 | 2.50 | 0.0839 0.0030 0.0869 | 22.6548
- 6 | 2.50 | 0.0835 0.0031 0.0866 | 20.6989
- 7 | 2.50 | 0.0831 0.0032 0.0864 | 18.9688
- 8 | 2.50 | 0.0827 0.0034 0.0861 | 17.4455
- 9 | 2.50 | 0.0823 0.0035 0.0857 | 15.9223
- 10 | 2.50 | 0.0818 0.0036 0.0854 | 14.6627
- 11 | 2.50 | 0.0813 0.0037 0.0851 | 13.4764
- 12 | 2.50 | 0.0809 0.0038 0.0847 | 12.3015
- 13 | 2.50 | 0.0804 0.0040 0.0844 | 11.3776
- 14 | 2.50 | 0.0799 0.0041 0.0840 | 10.4537
- 15 | 2.25 | 0.0802 0.0042 0.0844 | 9.5920
- 16 | 2.25 | 0.0763 0.0061 0.0824 | 8.8725
- 17 | 2.25 | 0.0747 0.0068 0.0815 | 8.1530
- 29 | 2.00 | 0.0759 0.0031 0.0790 | 3.3283
- 30 | 2.00 | 0.0694 0.0059 0.0753 | 3.1221
- 31 | 2.00 | 0.0672 0.0069 0.0741 | 2.9160
- 43 | 1.75 | 0.0660 0.0040 0.0700 | 1.5785
- 44 | 1.75 | 0.0617 0.0062 0.0679 | 1.5194
- 45 | 1.75 | 0.0603 0.0070 0.0673 | 1.4626
- 57 | 1.50 | 0.0588 0.0052 0.0639 | 1.0900
- 58 | 1.50 | 0.0557 0.0071 0.0628 | 1.0730
- 59 | 1.50 | 0.0547 0.0078 0.0624 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 213s
- Prepare output 11s
- 224s
- Jacobian determinant (RMS): 0.012 0.049 0.076 0.103 0.126 | 0.133633
- Template Matching: 0.090 0.224 0.202 0.181 0.164 | 0.164048
- Write result maps: 30s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 50s
- CSF distance: 18s
- PBT2x thickness: 51s
- 125s
- Create initial surface 81s
- Topology correction: 103s
- Surface refinement: 81s
- Reduction of surface collisions with optimization: 58s
- Spherical mapping with areal smoothing 132s
- Spherical registration 277s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 43s
- CSF distance: 17s
- PBT2x thickness: 51s
- 118s
- Create initial surface 83s
- Topology correction: 96s
- Surface refinement: 80s
- Reduction of surface collisions with optimization: 60s
- Spherical mapping with areal smoothing 88s
- Spherical registration 286s
- Final surface processing results:
- Average thickness (FS): 2.5045 0.6198 mm
- Surface intensity / position RMSE: 0.0655 / 0.0689
- Euler number / defect number / defect size: 28.0 / 14.5 / 1.27%
- Display thickness: /var/lib/condor/execute/dir_3568911/ds/sub-049/surf/lh.thickness.sub-049_ses-t1_T1w
- Display thickness: /var/lib/condor/execute/dir_3568911/ds/sub-049/surf/rh.thickness.sub-049_ses-t1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3568911/ds/sub-049/sub-049_ses-t1_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1769s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 15s
- ROI estimation of 'neuromorphometrics' atlas 54s
- ROI estimation of 'lpba40' atlas 15s
- ROI estimation of 'hammers' atlas 38s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 13s
- ROI estimation of 'aal3' atlas 21s
- ROI estimation of 'mori' atlas 31s
- ROI estimation of 'anatomy3' atlas 45s
- ROI estimation of 'julichbrain' atlas 60s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 22s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 28s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 95s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 142s
- Write results 142s
- 581s
- Quality check: 5s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3568911/ds/sub-049/report/catreport_sub-049_ses-t1_T1w.pdf
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- CAT preprocessing takes 55 minute(s) and 33 second(s).
- Image Quality Rating (IQR): 83.71% (B)
- GM volume (GMV): 46.80% (657.89 / 1405.86 ml)
- GM thickness (GMT): 2.50 0.62 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3568911/ds/sub-049/mri
- Reports are saved in /var/lib/condor/execute/dir_3568911/ds/sub-049/report
- Labels are saved in /var/lib/condor/execute/dir_3568911/ds/sub-049/label
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