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- CAT12.8.1 r2040: 1/1: ./sub-0026005/ses-4/sub-0026005_ses-4_run-1_T1w.n
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- SANLM denoising (medium): 58s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 5s
- Initial correction 6s
- Refine background 3s
- Final correction 6s
- Final scaling 5s
- 38s
- Correct center-of-mass 3s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 74s
- SPM preprocessing 1 (estimate 2): 62s
- SPM preprocessing 2 (write):
- Write Segmentation 17s
- Update Segmentation 21s
- Update Skull-Stripping 42s
- Update probability maps 9s
- 89s
- Global intensity correction: 17s
- SANLM denoising after intensity normalization (medium): 30s
- Fast Optimized Shooting registration 37s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.23) 15s
- Estimate local tissue thresholds (WM) 19s
- Estimate local tissue thresholds (GM) 27s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 48s
- 121s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 4s
- Ventricle detection 16s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.19) 28s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 79s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 31s
- 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 | 0.0882 0.0000 0.0882 | 32.0000
- 2 | 2.50 | 0.0854 0.0013 0.0866 | 29.4886
- 3 | 2.50 | 0.0845 0.0019 0.0864 | 26.9772
- 4 | 2.50 | 0.0841 0.0021 0.0863 | 24.6107
- 5 | 2.50 | 0.0838 0.0023 0.0861 | 22.6548
- 6 | 2.50 | 0.0835 0.0024 0.0859 | 20.6989
- 7 | 2.50 | 0.0832 0.0025 0.0857 | 18.9688
- 8 | 2.50 | 0.0829 0.0026 0.0855 | 17.4455
- 9 | 2.50 | 0.0825 0.0027 0.0852 | 15.9223
- 10 | 2.50 | 0.0822 0.0028 0.0850 | 14.6627
- 11 | 2.50 | 0.0819 0.0029 0.0847 | 13.4764
- 12 | 2.50 | 0.0815 0.0029 0.0845 | 12.3015
- 13 | 2.50 | 0.0812 0.0030 0.0842 | 11.3776
- 14 | 2.50 | 0.0808 0.0031 0.0839 | 10.4537
- 15 | 2.25 | 0.0812 0.0032 0.0844 | 9.5920
- 16 | 2.25 | 0.0779 0.0048 0.0827 | 8.8725
- 17 | 2.25 | 0.0766 0.0054 0.0820 | 8.1530
- 18 | 2.25 | 0.0758 0.0056 0.0814 | 7.5234
- 19 | 2.25 | 0.0752 0.0057 0.0809 | 6.9630
- 20 | 2.25 | 0.0746 0.0057 0.0804 | 6.4027
- 29 | 2.00 | 0.0766 0.0032 0.0798 | 3.3283
- 30 | 2.00 | 0.0714 0.0055 0.0770 | 3.1221
- 31 | 2.00 | 0.0697 0.0064 0.0761 | 2.9160
- 43 | 1.75 | 0.0689 0.0036 0.0725 | 1.5785
- 44 | 1.75 | 0.0641 0.0062 0.0703 | 1.5194
- 45 | 1.75 | 0.0627 0.0070 0.0697 | 1.4626
- 57 | 1.50 | 0.0612 0.0051 0.0663 | 1.0900
- 58 | 1.50 | 0.0577 0.0074 0.0651 | 1.0730
- 59 | 1.50 | 0.0566 0.0081 0.0646 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 200s
- Prepare output 11s
- 210s
- Jacobian determinant (RMS): 0.011 0.039 0.064 0.089 0.115 | 0.122016
- Template Matching: 0.088 0.224 0.209 0.188 0.170 | 0.169764
- Write result maps: 43s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 67s
- CSF distance: 19s
- PBT2x thickness: 56s
- 150s
- Create initial surface 97s
- Topology correction: 109s
- Surface refinement: 85s
- Reduction of surface collisions with optimization: 76s
- Spherical mapping with areal smoothing 100s
- Spherical registration 249s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 54s
- CSF distance: 19s
- PBT2x thickness: 56s
- 137s
- Create initial surface 95s
- Topology correction: 108s
- Surface refinement: 100s
- Reduction of surface collisions with optimization: 76s
- Spherical mapping with areal smoothing 94s
- Spherical registration 244s
- Final surface processing results:
- Average thickness (FS): 2.3170 0.6401 mm
- Surface intensity / position RMSE: 0.0654 / 0.0796
- Euler number / defect number / defect size: 34.0 / 18.0 / 1.30%
- Display thickness: /var/lib/condor/execute/dir_2737909/ds/XHCUMS/sub-0026005/ses-4/surf/lh.thickness.sub-0026005_ses-4_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2737909/ds/XHCUMS/sub-0026005/ses-4/surf/rh.thickness.sub-0026005_ses-4_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2737909/ds/XHCUMS/sub-0026005/ses-4/sub-0026005_ses-4_run-1_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1828s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 14s
- ROI estimation of 'neuromorphometrics' atlas 51s
- ROI estimation of 'lpba40' atlas 15s
- ROI estimation of 'hammers' atlas 36s
- 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 59s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 22s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 29s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 95s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 142s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 10s
- Write results 11s
- 584s
- Quality check: 13s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2737909/ds/XHCUMS/sub-0026005/ses-4/report/catreport_sub-0026005_ses-4_run-1_T1w.pdf
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- CAT preprocessing takes 57 minute(s) and 34 second(s).
- Image Quality Rating (IQR): 84.10% (B)
- GM volume (GMV): 41.66% (737.81 / 1771.05 ml)
- GM thickness (GMT): 2.32 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2737909/ds/XHCUMS/sub-0026005/ses-4/mri
- Reports are saved in /var/lib/condor/execute/dir_2737909/ds/XHCUMS/sub-0026005/ses-4/report
- Labels are saved in /var/lib/condor/execute/dir_2737909/ds/XHCUMS/sub-0026005/ses-4/label
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