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- CAT12.8.1 r2040: 1/1: ./sub-0025996/ses-1/sub-0025996_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 44s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 5s
- Initial correction 5s
- Refine background 2s
- Final correction 4s
- Final scaling 4s
- 31s
- Correct center-of-mass 3s
- Affine registration 8s
- SPM preprocessing 1 (estimate 1 - TPM registration): 64s
- SPM preprocessing 1 (estimate 2): 46s
- SPM preprocessing 2 (write):
- Write Segmentation 14s
- Update Segmentation 16s
- Update Skull-Stripping 34s
- Update probability maps 7s
- 70s
- Global intensity correction: 13s
- SANLM denoising after intensity normalization (medium): 20s
- Fast Optimized Shooting registration 26s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.12) 12s
- Estimate local tissue thresholds (WM) 14s
- Estimate local tissue thresholds (GM) 19s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 35s
- 89s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 3s
- Ventricle detection 10s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.32) 19s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 53s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 28s
- 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
- 9s
- 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 | 0.0899 0.0000 0.0899 | 32.0000
- 2 | 2.50 | 0.0878 0.0011 0.0889 | 29.4886
- 3 | 2.50 | 0.0871 0.0016 0.0887 | 26.9772
- 4 | 2.50 | 0.0868 0.0018 0.0886 | 24.6107
- 5 | 2.50 | 0.0865 0.0020 0.0885 | 22.6548
- 6 | 2.50 | 0.0863 0.0021 0.0883 | 20.6989
- 7 | 2.50 | 0.0860 0.0021 0.0882 | 18.9688
- 8 | 2.50 | 0.0858 0.0022 0.0880 | 17.4455
- 9 | 2.50 | 0.0855 0.0023 0.0878 | 15.9223
- 10 | 2.50 | 0.0852 0.0024 0.0876 | 14.6627
- 11 | 2.50 | 0.0849 0.0025 0.0874 | 13.4764
- 12 | 2.50 | 0.0847 0.0026 0.0872 | 12.3015
- 13 | 2.50 | 0.0843 0.0027 0.0870 | 11.3776
- 14 | 2.50 | 0.0841 0.0027 0.0868 | 10.4537
- 15 | 2.25 | 0.0841 0.0028 0.0869 | 9.5920
- 16 | 2.25 | 0.0812 0.0042 0.0854 | 8.8725
- 17 | 2.25 | 0.0801 0.0047 0.0848 | 8.1530
- 18 | 2.25 | 0.0794 0.0049 0.0843 | 7.5234
- 19 | 2.25 | 0.0788 0.0051 0.0839 | 6.9630
- 20 | 2.25 | 0.0783 0.0051 0.0834 | 6.4027
- 21 | 2.25 | 0.0778 0.0051 0.0830 | 5.9447
- 22 | 2.25 | 0.0774 0.0052 0.0825 | 5.5083
- 23 | 2.25 | 0.0769 0.0051 0.0821 | 5.0803
- 24 | 2.25 | 0.0765 0.0052 0.0817 | 4.7404
- 25 | 2.25 | 0.0761 0.0052 0.0813 | 4.4005
- 26 | 2.25 | 0.0757 0.0052 0.0809 | 4.0868
- 27 | 2.25 | 0.0753 0.0052 0.0805 | 3.8221
- 28 | 2.25 | 0.0749 0.0052 0.0801 | 3.5574
- 29 | 2.00 | 0.0766 0.0049 0.0816 | 3.3283
- 30 | 2.00 | 0.0742 0.0059 0.0801 | 3.1221
- 43 | 1.75 | 0.0734 0.0031 0.0765 | 1.5785
- 44 | 1.75 | 0.0681 0.0059 0.0740 | 1.5194
- 45 | 1.75 | 0.0665 0.0068 0.0733 | 1.4626
- 57 | 1.50 | 0.0650 0.0049 0.0699 | 1.0900
- 58 | 1.50 | 0.0613 0.0073 0.0687 | 1.0730
- 59 | 1.50 | 0.0602 0.0081 0.0683 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 154s
- Prepare output 8s
- 163s
- Jacobian determinant (RMS): 0.010 0.038 0.068 0.088 0.115 | 0.123135
- Template Matching: 0.090 0.225 0.223 0.199 0.181 | 0.180572
- Write result maps: 27s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 35s
- CSF distance: 13s
- PBT2x thickness: 36s
- 89s
- Create initial surface 72s
- Topology correction: 78s
- Surface refinement: 66s
- Reduction of surface collisions with optimization: 53s
- Spherical mapping with areal smoothing 63s
- Spherical registration 248s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 36s
- CSF distance: 12s
- PBT2x thickness: 35s
- 88s
- Create initial surface 71s
- Topology correction: 77s
- Surface refinement: 63s
- Reduction of surface collisions with optimization: 53s
- Spherical mapping with areal smoothing 63s
- Spherical registration 248s
- Final surface processing results:
- Average thickness (FS): 2.1703 0.5885 mm
- Surface intensity / position RMSE: 0.0561 / 0.0589
- Euler number / defect number / defect size: 16.0 / 13.5 / 0.47%
- Display thickness: /var/lib/condor/execute/dir_1039462/ds/XHCUMS/sub-0025996/ses-1/surf/lh.thickness.sub-0025996_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1039462/ds/XHCUMS/sub-0025996/ses-1/surf/rh.thickness.sub-0025996_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1039462/ds/XHCUMS/sub-0025996/ses-1/sub-0025996_ses-1_run-1_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1409s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 25s
- ROI estimation of 'lpba40' atlas 7s
- ROI estimation of 'hammers' atlas 18s
- 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 21s
- ROI estimation of 'julichbrain' atlas 28s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 20s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 45s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 67s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s
- Write results 7s
- 289s
- Quality check: 10s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1039462/ds/XHCUMS/sub-0025996/ses-1/report/catreport_sub-0025996_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 41 minute(s) and 8 second(s).
- Image Quality Rating (IQR): 82.47% (B-)
- GM volume (GMV): 40.18% (601.04 / 1495.95 ml)
- GM thickness (GMT): 2.17 0.59 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1039462/ds/XHCUMS/sub-0025996/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_1039462/ds/XHCUMS/sub-0025996/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_1039462/ds/XHCUMS/sub-0025996/ses-1/label
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