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- CAT12.8.1 r2040: 1/1: ./sub-0025998/ses-5/sub-0025998_ses-5_run-1_T1w.n
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- SANLM denoising (medium): 28s
- APP: Rough bias correction:
- Initialize 4s
- Estimate background 3s
- Initial correction 3s
- Refine background 2s
- Final correction 3s
- Final scaling 3s
- 22s
- Correct center-of-mass 2s
- Affine registration 5s
- SPM preprocessing 1 (estimate 1 - TPM registration): 6s
- Use initial fine affine registration. 35s
- SPM preprocessing 1 (estimate 2): 33s
- SPM preprocessing 2 (write):
- Write Segmentation 10s
- Update Segmentation 12s
- Update Skull-Stripping 25s
- Update probability maps 6s
- 53s
- Global intensity correction: 10s
- SANLM denoising after intensity normalization (medium): 13s
- Fast Optimized Shooting registration 20s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 2s
- Prepare partitions 1s
- Prepare segments (LASmod = 1.13) 8s
- Estimate local tissue thresholds (WM) 10s
- Estimate local tissue thresholds (GM) 13s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 25s
- 62s
- ROI segmentation (partitioning):
- Atlas -> subject space 4s
- Major structures 2s
- Ventricle detection 5s
- Blood vessel detection 5s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.22) 10s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 3s
- 32s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 20s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 2s
- Level 1 cleanup (brain masking) 2s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 6s
- 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 | 0.0910 0.0000 0.0910 | 32.0000
- 2 | 2.50 | 0.0877 0.0014 0.0891 | 29.4886
- 3 | 2.50 | 0.0868 0.0021 0.0889 | 26.9772
- 4 | 2.50 | 0.0863 0.0024 0.0887 | 24.6107
- 5 | 2.50 | 0.0859 0.0025 0.0885 | 22.6548
- 6 | 2.50 | 0.0856 0.0026 0.0882 | 20.6989
- 7 | 2.50 | 0.0853 0.0028 0.0880 | 18.9688
- 8 | 2.50 | 0.0849 0.0029 0.0878 | 17.4455
- 9 | 2.50 | 0.0846 0.0030 0.0875 | 15.9223
- 10 | 2.50 | 0.0842 0.0031 0.0873 | 14.6627
- 11 | 2.50 | 0.0838 0.0032 0.0870 | 13.4764
- 12 | 2.50 | 0.0834 0.0033 0.0867 | 12.3015
- 13 | 2.50 | 0.0830 0.0034 0.0864 | 11.3776
- 14 | 2.50 | 0.0827 0.0035 0.0861 | 10.4537
- 15 | 2.25 | 0.0826 0.0036 0.0862 | 9.5920
- 16 | 2.25 | 0.0791 0.0053 0.0844 | 8.8725
- 17 | 2.25 | 0.0778 0.0059 0.0837 | 8.1530
- 18 | 2.25 | 0.0770 0.0061 0.0831 | 7.5234
- 19 | 2.25 | 0.0763 0.0062 0.0826 | 6.9630
- 20 | 2.25 | 0.0758 0.0062 0.0820 | 6.4027
- 21 | 2.25 | 0.0752 0.0063 0.0815 | 5.9447
- 22 | 2.25 | 0.0747 0.0063 0.0810 | 5.5083
- 29 | 2.00 | 0.0762 0.0040 0.0802 | 3.3283
- 30 | 2.00 | 0.0719 0.0060 0.0779 | 3.1221
- 31 | 2.00 | 0.0704 0.0067 0.0771 | 2.9160
- 43 | 1.75 | 0.0695 0.0038 0.0733 | 1.5785
- 44 | 1.75 | 0.0649 0.0063 0.0712 | 1.5194
- 45 | 1.75 | 0.0634 0.0071 0.0705 | 1.4626
- 57 | 1.50 | 0.0619 0.0052 0.0671 | 1.0900
- 58 | 1.50 | 0.0586 0.0074 0.0660 | 1.0730
- 59 | 1.50 | 0.0575 0.0081 0.0656 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 107s
- Prepare output 6s
- 113s
- Jacobian determinant (RMS): 0.011 0.040 0.066 0.090 0.116 | 0.123195
- Template Matching: 0.091 0.224 0.211 0.190 0.173 | 0.172510
- Write result maps: 20s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 23s
- CSF distance: 9s
- PBT2x thickness: 24s
- 59s
- Create initial surface 43s
- Topology correction: 45s
- Surface refinement: 40s
- Reduction of surface collisions with optimization: 32s
- Spherical mapping with areal smoothing 44s
- Spherical registration 168s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 15s
- CSF distance: 8s
- PBT2x thickness: 23s
- 49s
- Create initial surface 41s
- Topology correction: 44s
- Surface refinement: 51s
- Reduction of surface collisions with optimization: 32s
- Spherical mapping with areal smoothing 44s
- Spherical registration 160s
- Final surface processing results:
- Average thickness (FS): 2.3192 0.6311 mm
- Surface intensity / position RMSE: 0.0615 / 0.0636
- Euler number / defect number / defect size: 22.0 / 13.5 / 0.49%
- Display thickness: /var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-5/surf/lh.thickness.sub-0025998_ses-5_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-5/surf/rh.thickness.sub-0025998_ses-5_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-5/sub-0025998_ses-5_run-1_T1w.nii
- Surface ROI estimation: 5s
- Surface and thickness estimation takes: 905s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 6s
- ROI estimation of 'neuromorphometrics' atlas 20s
- ROI estimation of 'lpba40' atlas 6s
- ROI estimation of 'hammers' atlas 14s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 5s
- ROI estimation of 'aal3' atlas 8s
- ROI estimation of 'mori' atlas 11s
- ROI estimation of 'anatomy3' atlas 16s
- ROI estimation of 'julichbrain' atlas 21s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 8s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 15s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 34s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 51s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 4s
- Write results 5s
- 221s
- Quality check: 7s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-5/report/catreport_sub-0025998_ses-5_run-1_T1w.pdf
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- CAT preprocessing takes 27 minute(s) and 39 second(s).
- Image Quality Rating (IQR): 82.92% (B-)
- GM volume (GMV): 44.16% (589.34 / 1334.68 ml)
- GM thickness (GMT): 2.32 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-5/mri
- Reports are saved in /var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-5/report
- Labels are saved in /var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-5/label
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