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- CAT12.8.1 r2040: 1/1: ./sub-0027229/ses-1/sub-0027229_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 44s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 7s
- Initial correction 7s
- Refine background 4s
- Final correction 5s
- Final scaling 5s
- 41s
- Correct center-of-mass 4s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 86s
- SPM preprocessing 1 (estimate 2): 81s
- SPM preprocessing 2 (write):
- Write Segmentation 20s
- Update Segmentation 21s
- Update Skull-Stripping 51s
- Update probability maps 10s
- 103s
- Global intensity correction: 20s
- SANLM denoising after intensity normalization (medium): 30s
- Fast Optimized Shooting registration 43s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 17s
- Estimate local tissue thresholds (WM) 22s
- Estimate local tissue thresholds (GM) 33s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 51s
- 133s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 15s
- Blood vessel detection 13s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.28) 24s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 77s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 40s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.670.08,0.990.05]
- 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
- 13s
- 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 | 0.0914 0.0000 0.0914 | 32.0000
- 2 | 2.50 | 0.0877 0.0015 0.0892 | 29.4886
- 3 | 2.50 | 0.0865 0.0023 0.0888 | 26.9772
- 4 | 2.50 | 0.0859 0.0027 0.0886 | 24.6107
- 5 | 2.50 | 0.0855 0.0029 0.0884 | 22.6548
- 6 | 2.50 | 0.0851 0.0030 0.0881 | 20.6989
- 7 | 2.50 | 0.0846 0.0032 0.0878 | 18.9688
- 8 | 2.50 | 0.0842 0.0034 0.0875 | 17.4455
- 9 | 2.50 | 0.0837 0.0035 0.0872 | 15.9223
- 10 | 2.50 | 0.0832 0.0037 0.0869 | 14.6627
- 11 | 2.50 | 0.0827 0.0038 0.0866 | 13.4764
- 12 | 2.50 | 0.0822 0.0039 0.0862 | 12.3015
- 13 | 2.50 | 0.0817 0.0041 0.0858 | 11.3776
- 14 | 2.50 | 0.0812 0.0043 0.0854 | 10.4537
- 15 | 2.25 | 0.0848 0.0044 0.0892 | 9.5920
- 16 | 2.25 | 0.0807 0.0065 0.0872 | 8.8725
- 17 | 2.25 | 0.0788 0.0074 0.0861 | 8.1530
- 18 | 2.25 | 0.0775 0.0078 0.0853 | 7.5234
- 19 | 2.25 | 0.0765 0.0081 0.0845 | 6.9630
- 20 | 2.25 | 0.0756 0.0081 0.0837 | 6.4027
- 21 | 2.25 | 0.0747 0.0083 0.0830 | 5.9447
- 29 | 2.00 | 0.0767 0.0050 0.0817 | 3.3283
- 30 | 2.00 | 0.0712 0.0075 0.0787 | 3.1221
- 31 | 2.00 | 0.0689 0.0085 0.0774 | 2.9160
- 43 | 1.75 | 0.0675 0.0049 0.0724 | 1.5785
- 44 | 1.75 | 0.0625 0.0076 0.0701 | 1.5194
- 45 | 1.75 | 0.0607 0.0085 0.0692 | 1.4626
- 57 | 1.50 | 0.0595 0.0063 0.0658 | 1.0900
- 58 | 1.50 | 0.0560 0.0086 0.0646 | 1.0730
- 59 | 1.50 | 0.0548 0.0093 0.0641 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 224s
- Prepare output 14s
- 238s
- Jacobian determinant (RMS): 0.014 0.054 0.091 0.119 0.146 | 0.154569
- Template Matching: 0.091 0.224 0.207 0.182 0.165 | 0.164536
- Write result maps: 46s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 55s
- CSF distance: 19s
- PBT2x thickness: 52s
- 132s
- Create initial surface 89s
- Topology correction: 80s
- Surface refinement: 89s
- Reduction of surface collisions with optimization: 57s
- Spherical mapping with areal smoothing 86s
- Spherical registration 322s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 42s
- CSF distance: 17s
- PBT2x thickness: 51s
- 116s
- Create initial surface 85s
- Topology correction: 80s
- Surface refinement: 95s
- Reduction of surface collisions with optimization: 56s
- Spherical mapping with areal smoothing 83s
- Spherical registration 340s
- Final surface processing results:
- Average thickness (FS): 2.3394 0.5957 mm
- Surface intensity / position RMSE: 0.0625 / 0.0616
- Euler number / defect number / defect size: 18.0 / 10.0 / 0.55%
- Display thickness: /var/lib/condor/execute/dir_3344642/ds/IBA_TRT/sub-0027229/ses-1/surf/lh.thickness.sub-0027229_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3344642/ds/IBA_TRT/sub-0027229/ses-1/surf/rh.thickness.sub-0027229_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3344642/ds/IBA_TRT/sub-0027229/ses-1/sub-0027229_ses-1_run-1_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1814s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 34s
- ROI estimation of 'lpba40' atlas 10s
- ROI estimation of 'hammers' atlas 24s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 9s
- ROI estimation of 'aal3' atlas 14s
- ROI estimation of 'mori' atlas 20s
- ROI estimation of 'anatomy3' atlas 29s
- ROI estimation of 'julichbrain' atlas 40s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 16s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 28s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 66s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 119s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 11s
- Write results 13s
- 433s
- Quality check: 16s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3344642/ds/IBA_TRT/sub-0027229/ses-1/report/catreport_sub-0027229_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 56 minute(s) and 25 second(s).
- Image Quality Rating (IQR): 84.68% (B)
- GM volume (GMV): 37.83% (553.03 / 1461.95 ml)
- GM thickness (GMT): 2.34 0.60 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3344642/ds/IBA_TRT/sub-0027229/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_3344642/ds/IBA_TRT/sub-0027229/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_3344642/ds/IBA_TRT/sub-0027229/ses-1/label
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