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- CAT12.8.1 r1980: 1/1: ./condor/execute/dir_28549/ds/sub-04/sub-04_T1w.n
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- SANLM denoising (medium): 50s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 6s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 6s
- 38s
- Correct center-of-mass 3s
- Affine registration 9s
- SPM preprocessing 1 (estimate 1 - TPM registration): 65s
- SPM preprocessing 1 (estimate 2): 51s
- SPM preprocessing 2 (write):
- Write Segmentation 16s
- Update Segmentation 18s
- Update Skull-Stripping 41s
- Update probability maps 8s
- 84s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 9s
- Fast Optimized Shooting registration 30s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.14) 15s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 24s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 25s
- 91s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 15s
- Blood vessel detection 10s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.14) 27s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 75s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 35s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- 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 | 0.0851 0.0000 0.0851 | 32.0000
- 2 | 2.50 | 0.0826 0.0011 0.0838 | 29.4886
- 3 | 2.50 | 0.0820 0.0017 0.0837 | 26.9772
- 4 | 2.50 | 0.0816 0.0019 0.0835 | 24.6107
- 5 | 2.50 | 0.0813 0.0020 0.0834 | 22.6548
- 6 | 2.50 | 0.0811 0.0021 0.0832 | 20.6989
- 7 | 2.50 | 0.0808 0.0022 0.0830 | 18.9688
- 8 | 2.50 | 0.0805 0.0023 0.0828 | 17.4455
- 9 | 2.50 | 0.0803 0.0024 0.0826 | 15.9223
- 10 | 2.50 | 0.0800 0.0025 0.0824 | 14.6627
- 11 | 2.50 | 0.0797 0.0025 0.0822 | 13.4764
- 12 | 2.50 | 0.0794 0.0026 0.0820 | 12.3015
- 13 | 2.50 | 0.0790 0.0027 0.0817 | 11.3776
- 14 | 2.50 | 0.0787 0.0028 0.0815 | 10.4537
- 15 | 2.25 | 0.0790 0.0028 0.0818 | 9.5920
- 16 | 2.25 | 0.0758 0.0043 0.0802 | 8.8725
- 17 | 2.25 | 0.0745 0.0049 0.0795 | 8.1530
- 29 | 2.00 | 0.0768 0.0023 0.0790 | 3.3283
- 30 | 2.00 | 0.0703 0.0050 0.0753 | 3.1221
- 31 | 2.00 | 0.0680 0.0061 0.0741 | 2.9160
- 43 | 1.75 | 0.0669 0.0035 0.0704 | 1.5785
- 44 | 1.75 | 0.0619 0.0061 0.0680 | 1.5194
- 45 | 1.75 | 0.0603 0.0070 0.0673 | 1.4626
- 57 | 1.50 | 0.0587 0.0051 0.0637 | 1.0900
- 58 | 1.50 | 0.0552 0.0073 0.0626 | 1.0730
- 59 | 1.50 | 0.0541 0.0080 0.0621 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 166s
- Prepare output 11s
- 176s
- Jacobian determinant (RMS): 0.011 0.039 0.062 0.089 0.114 | 0.122191
- Template Matching: 0.085 0.224 0.204 0.181 0.162 | 0.162318
- Write result maps: 26s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 33s
- CSF distance: 15s
- PBT2x thickness: 45s
- 100s
- Create initial surface 84s
- Topology correction: 91s
- Surface refinement: 70s
- Reduction of surface collisions with optimization: 73s
- Spherical mapping with areal smoothing 85s
- Spherical registration 299s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 41s
- CSF distance: 16s
- PBT2x thickness: 46s
- 109s
- Create initial surface 91s
- Topology correction: 96s
- Surface refinement: 91s
- Reduction of surface collisions with optimization: 71s
- Spherical mapping with areal smoothing 83s
- Spherical registration 299s
- Final surface processing results:
- Average thickness (FS): 2.5241 0.5962 mm
- Surface intensity / position RMSE: 0.0576 / 0.0577
- Euler number / defect number / defect size: 12.0 / 11.0 / 0.21%
- Display thickness: /var/lib/condor/execute/dir_28549/ds/sub-04/surf/lh.thickness.sub-04_T1w
- Display thickness: /var/lib/condor/execute/dir_28549/ds/sub-04/surf/rh.thickness.sub-04_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_28549/ds/sub-04/sub-04_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1741s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 33s
- ROI estimation of 'lpba40' atlas 10s
- ROI estimation of 'hammers' atlas 23s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 8s
- ROI estimation of 'aal3' atlas 14s
- ROI estimation of 'mori' atlas 20s
- ROI estimation of 'anatomy3' atlas 28s
- ROI estimation of 'julichbrain' atlas 36s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 14s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 26s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 57s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 88s
- Write results 89s
- 369s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_28549/ds/sub-04/report/catreport_sub-04_T1w.pdf
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- CAT preprocessing takes 49 minute(s) and 34 second(s).
- Image Quality Rating (IQR): 85.42% (B)
- GM volume (GMV): 43.28% (695.12 / 1606.04 ml)
- GM thickness (GMT): 2.52 0.60 mm
- Segmentations are saved in /var/lib/condor/execute/dir_28549/ds/sub-04/mri
- Reports are saved in /var/lib/condor/execute/dir_28549/ds/sub-04/report
- Labels are saved in /var/lib/condor/execute/dir_28549/ds/sub-04/label
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