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- CAT12.8.1 r2040: 1/1: ./sub-0026004/ses-2/sub-0026004_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 47s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 5s
- Initial correction 5s
- Refine background 3s
- Final correction 5s
- Final scaling 4s
- 33s
- Correct center-of-mass 3s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 62s
- SPM preprocessing 1 (estimate 2): 53s
- SPM preprocessing 2 (write):
- Write Segmentation 14s
- Update Segmentation 17s
- Update Skull-Stripping 35s
- Update probability maps 7s
- 74s
- Global intensity correction: 14s
- SANLM denoising after intensity normalization (medium): 24s
- Fast Optimized Shooting registration 27s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.05) 13s
- Estimate local tissue thresholds (WM) 16s
- Estimate local tissue thresholds (GM) 23s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 42s
- 103s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 3s
- Ventricle detection 16s
- Blood vessel detection 9s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.05) 21s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 63s
- Blood vessel correction (BVCstr=0.50): 1s
- 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) 4s
- Level 1 cleanup (brain masking) 2s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 10s
- 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 | 0.0871 0.0000 0.0871 | 32.0000
- 2 | 2.50 | 0.0838 0.0014 0.0851 | 29.4886
- 3 | 2.50 | 0.0828 0.0021 0.0849 | 26.9772
- 4 | 2.50 | 0.0823 0.0024 0.0847 | 24.6107
- 5 | 2.50 | 0.0819 0.0026 0.0845 | 22.6548
- 6 | 2.50 | 0.0815 0.0027 0.0842 | 20.6989
- 7 | 2.50 | 0.0812 0.0028 0.0840 | 18.9688
- 8 | 2.50 | 0.0808 0.0029 0.0837 | 17.4455
- 9 | 2.50 | 0.0804 0.0030 0.0835 | 15.9223
- 10 | 2.50 | 0.0800 0.0031 0.0832 | 14.6627
- 11 | 2.50 | 0.0797 0.0032 0.0829 | 13.4764
- 12 | 2.50 | 0.0793 0.0033 0.0826 | 12.3015
- 13 | 2.50 | 0.0788 0.0034 0.0823 | 11.3776
- 14 | 2.50 | 0.0785 0.0035 0.0820 | 10.4537
- 15 | 2.25 | 0.0795 0.0036 0.0831 | 9.5920
- 16 | 2.25 | 0.0761 0.0053 0.0814 | 8.8725
- 17 | 2.25 | 0.0747 0.0059 0.0807 | 8.1530
- 29 | 2.00 | 0.0772 0.0027 0.0799 | 3.3283
- 30 | 2.00 | 0.0709 0.0054 0.0763 | 3.1221
- 31 | 2.00 | 0.0686 0.0065 0.0751 | 2.9160
- 43 | 1.75 | 0.0677 0.0037 0.0714 | 1.5785
- 44 | 1.75 | 0.0629 0.0063 0.0692 | 1.5194
- 45 | 1.75 | 0.0612 0.0072 0.0684 | 1.4626
- 57 | 1.50 | 0.0599 0.0053 0.0652 | 1.0900
- 58 | 1.50 | 0.0563 0.0077 0.0640 | 1.0730
- 59 | 1.50 | 0.0551 0.0084 0.0635 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 137s
- Prepare output 9s
- 146s
- Jacobian determinant (RMS): 0.011 0.040 0.061 0.087 0.131 | 0.122403
- Template Matching: 0.087 0.224 0.206 0.184 0.165 | 0.165292
- Write result maps: 29s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 38s
- CSF distance: 13s
- PBT2x thickness: 41s
- 98s
- Create initial surface 76s
- Topology correction: 88s
- Surface refinement: 82s
- Reduction of surface collisions with optimization: 70s
- Spherical mapping with areal smoothing 74s
- Spherical registration 252s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 54s
- CSF distance: 14s
- PBT2x thickness: 41s
- 114s
- Create initial surface 76s
- Topology correction: 90s
- Surface refinement: 93s
- Reduction of surface collisions with optimization: 71s
- Spherical mapping with areal smoothing 90s
- Spherical registration 256s
- Final surface processing results:
- Average thickness (FS): 2.4381 0.6339 mm
- Surface intensity / position RMSE: 0.0677 / 0.0781
- Euler number / defect number / defect size: 22.0 / 15.0 / 0.99%
- Display thickness: /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-2/surf/lh.thickness.sub-0026004_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-2/surf/rh.thickness.sub-0026004_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-2/sub-0026004_ses-2_run-1_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1616s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 24s
- ROI estimation of 'lpba40' atlas 7s
- ROI estimation of 'hammers' atlas 17s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 6s
- ROI estimation of 'aal3' atlas 10s
- ROI estimation of 'mori' atlas 15s
- ROI estimation of 'anatomy3' atlas 22s
- ROI estimation of 'julichbrain' atlas 29s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 47s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 69s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s
- Write results 7s
- 294s
- Quality check: 10s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-2/report/catreport_sub-0026004_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 45 minute(s) and 33 second(s).
- Image Quality Rating (IQR): 82.71% (B-)
- GM volume (GMV): 44.93% (753.99 / 1678.13 ml)
- GM thickness (GMT): 2.44 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-2/label
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