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- CAT12.8.1 r1980: 1/1: ./condor/execute/dir_10502/ds/sub-11/sub-11_T1w.n
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- SANLM denoising (medium): 87s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 7s
- Initial correction 7s
- Refine background 3s
- Final correction 5s
- Final scaling 6s
- 40s
- Correct center-of-mass 2s
- Affine registration 9s
- SPM preprocessing 1 (estimate 1 - TPM registration): 80s
- SPM preprocessing 1 (estimate 2): 60s
- SPM preprocessing 2 (write):
- Write Segmentation 17s
- Update Segmentation 19s
- Update Skull-Stripping 46s
- Update probability maps 9s
- 91s
- Global intensity correction: 17s
- SANLM denoising after intensity normalization (medium): 24s
- Fast Optimized Shooting registration 33s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.23) 16s
- Estimate local tissue thresholds (WM) 20s
- Estimate local tissue thresholds (GM) 28s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 37s
- 111s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 19s
- Blood vessel detection 10s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.04) 29s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 81s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 36s
- 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 | 0.0863 0.0000 0.0863 | 32.0000
- 2 | 2.50 | 0.0831 0.0013 0.0844 | 29.4886
- 3 | 2.50 | 0.0823 0.0020 0.0842 | 26.9772
- 4 | 2.50 | 0.0818 0.0022 0.0840 | 24.6107
- 5 | 2.50 | 0.0815 0.0023 0.0838 | 22.6548
- 6 | 2.50 | 0.0812 0.0024 0.0836 | 20.6989
- 7 | 2.50 | 0.0809 0.0025 0.0834 | 18.9688
- 8 | 2.50 | 0.0806 0.0026 0.0832 | 17.4455
- 9 | 2.50 | 0.0803 0.0027 0.0830 | 15.9223
- 10 | 2.50 | 0.0800 0.0028 0.0827 | 14.6627
- 11 | 2.50 | 0.0797 0.0028 0.0825 | 13.4764
- 12 | 2.50 | 0.0793 0.0029 0.0822 | 12.3015
- 13 | 2.50 | 0.0790 0.0030 0.0820 | 11.3776
- 14 | 2.50 | 0.0787 0.0030 0.0817 | 10.4537
- 15 | 2.25 | 0.0788 0.0031 0.0818 | 9.5920
- 16 | 2.25 | 0.0756 0.0046 0.0802 | 8.8725
- 17 | 2.25 | 0.0744 0.0051 0.0795 | 8.1530
- 29 | 2.00 | 0.0766 0.0023 0.0789 | 3.3283
- 30 | 2.00 | 0.0706 0.0049 0.0755 | 3.1221
- 31 | 2.00 | 0.0686 0.0058 0.0744 | 2.9160
- 43 | 1.75 | 0.0678 0.0033 0.0711 | 1.5785
- 44 | 1.75 | 0.0631 0.0058 0.0689 | 1.5194
- 45 | 1.75 | 0.0616 0.0066 0.0682 | 1.4626
- 57 | 1.50 | 0.0603 0.0048 0.0651 | 1.0900
- 58 | 1.50 | 0.0569 0.0071 0.0639 | 1.0730
- 59 | 1.50 | 0.0558 0.0077 0.0635 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 164s
- Prepare output 11s
- 174s
- Jacobian determinant (RMS): 0.009 0.033 0.052 0.076 0.103 | 0.108474
- Template Matching: 0.086 0.223 0.206 0.185 0.167 | 0.167254
- Write result maps: 24s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 46s
- CSF distance: 16s
- PBT2x thickness: 49s
- 118s
- Create initial surface 96s
- Topology correction: 108s
- Surface refinement: 96s
- Reduction of surface collisions with optimization: 84s
- Spherical mapping with areal smoothing 88s
- Spherical registration 282s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 46s
- CSF distance: 17s
- PBT2x thickness: 50s
- 120s
- Create initial surface 93s
- Topology correction: 105s
- Surface refinement: 121s
- Reduction of surface collisions with optimization: 94s
- Spherical mapping with areal smoothing 102s
- Spherical registration 321s
- Final surface processing results:
- Average thickness (FS): 2.5982 0.6290 mm
- Surface intensity / position RMSE: 0.0721 / 0.0767
- Euler number / defect number / defect size: 42.0 / 17.5 / 1.34%
- Display thickness: /var/lib/condor/execute/dir_10502/ds/sub-11/surf/lh.thickness.sub-11_T1w
- Display thickness: /var/lib/condor/execute/dir_10502/ds/sub-11/surf/rh.thickness.sub-11_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_10502/ds/sub-11/sub-11_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1929s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 10s
- ROI estimation of 'neuromorphometrics' atlas 35s
- ROI estimation of 'lpba40' atlas 11s
- ROI estimation of 'hammers' atlas 24s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 8s
- ROI estimation of 'aal3' atlas 14s
- ROI estimation of 'mori' atlas 19s
- 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 56s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 85s
- Write results 86s
- 370s
- Quality check: 5s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_10502/ds/sub-11/report/catreport_sub-11_T1w.pdf
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- CAT preprocessing takes 54 minute(s) and 30 second(s).
- Image Quality Rating (IQR): 83.68% (B)
- GM volume (GMV): 48.32% (807.54 / 1671.10 ml)
- GM thickness (GMT): 2.60 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_10502/ds/sub-11/mri
- Reports are saved in /var/lib/condor/execute/dir_10502/ds/sub-11/report
- Labels are saved in /var/lib/condor/execute/dir_10502/ds/sub-11/label
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