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- CAT12.8.1 r1980: 1/1: ./execute/dir_25440/ds/sub-01/sub-01_ses-01_T1w.n
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- SANLM denoising (medium): 56s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 10s
- Initial correction 10s
- Refine background 4s
- Final correction 8s
- Final scaling 8s
- 56s
- Correct center-of-mass 5s
- Affine registration 11s
- SPM preprocessing 1 (estimate 1 - TPM registration): 92s
- SPM preprocessing 1 (estimate 2): 83s
- SPM preprocessing 2 (write):
- Write Segmentation 21s
- Update Segmentation 22s
- Update Skull-Stripping 52s
- Update probability maps 10s
- 105s
- Global intensity correction: 19s
- SANLM denoising after intensity normalization (medium): 11s
- Fast Optimized Shooting registration 39s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.02) 18s
- Estimate local tissue thresholds (WM) 25s
- Estimate local tissue thresholds (GM) 35s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 32s
- 121s
- ROI segmentation (partitioning):
- Atlas -> subject space 10s
- Major structures 4s
- Ventricle detection 16s
- Blood vessel detection 12s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.02) 34s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 87s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 39s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.07,0.980.04]
- 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 | 0.0847 0.0000 0.0847 | 32.0000
- 2 | 2.50 | 0.0820 0.0012 0.0832 | 29.4886
- 3 | 2.50 | 0.0812 0.0018 0.0830 | 26.9772
- 4 | 2.50 | 0.0808 0.0020 0.0828 | 24.6107
- 5 | 2.50 | 0.0805 0.0022 0.0827 | 22.6548
- 6 | 2.50 | 0.0802 0.0023 0.0825 | 20.6989
- 7 | 2.50 | 0.0799 0.0024 0.0823 | 18.9688
- 8 | 2.50 | 0.0797 0.0025 0.0821 | 17.4455
- 9 | 2.50 | 0.0794 0.0025 0.0819 | 15.9223
- 10 | 2.50 | 0.0790 0.0026 0.0817 | 14.6627
- 11 | 2.50 | 0.0787 0.0027 0.0815 | 13.4764
- 12 | 2.50 | 0.0784 0.0028 0.0812 | 12.3015
- 13 | 2.50 | 0.0781 0.0029 0.0810 | 11.3776
- 14 | 2.50 | 0.0778 0.0029 0.0807 | 10.4537
- 15 | 2.25 | 0.0782 0.0030 0.0812 | 9.5920
- 16 | 2.25 | 0.0752 0.0045 0.0797 | 8.8725
- 17 | 2.25 | 0.0740 0.0051 0.0791 | 8.1530
- 29 | 2.00 | 0.0760 0.0023 0.0783 | 3.3283
- 30 | 2.00 | 0.0702 0.0048 0.0750 | 3.1221
- 31 | 2.00 | 0.0682 0.0057 0.0740 | 2.9160
- 43 | 1.75 | 0.0674 0.0033 0.0707 | 1.5785
- 44 | 1.75 | 0.0628 0.0057 0.0686 | 1.5194
- 45 | 1.75 | 0.0613 0.0066 0.0678 | 1.4626
- 57 | 1.50 | 0.0600 0.0048 0.0648 | 1.0900
- 58 | 1.50 | 0.0566 0.0070 0.0636 | 1.0730
- 59 | 1.50 | 0.0555 0.0077 0.0632 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 200s
- Prepare output 14s
- 213s
- Jacobian determinant (RMS): 0.009 0.035 0.054 0.078 0.103 | 0.110836
- Template Matching: 0.085 0.222 0.205 0.184 0.166 | 0.166365
- Write result maps: 32s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 37s
- CSF distance: 19s
- PBT2x thickness: 58s
- 122s
- Create initial surface 92s
- Topology correction: 112s
- Surface refinement: 111s
- Reduction of surface collisions with optimization: 83s
- Spherical mapping with areal smoothing 100s
- Spherical registration 332s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 37s
- CSF distance: 20s
- PBT2x thickness: 57s
- 121s
- Create initial surface 90s
- Topology correction: 115s
- Surface refinement: 110s
- Reduction of surface collisions with optimization: 80s
- Spherical mapping with areal smoothing 94s
- Spherical registration 279s
- Final surface processing results:
- Average thickness (FS): 2.5133 0.6117 mm
- Surface intensity / position RMSE: 0.0701 / 0.0734
- Euler number / defect number / defect size: 24.0 / 10.0 / 0.65%
- Display thickness: /var/lib/condor/execute/dir_25440/ds/sub-01/surf/lh.thickness.sub-01_ses-01_T1w
- Display thickness: /var/lib/condor/execute/dir_25440/ds/sub-01/surf/rh.thickness.sub-01_ses-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_25440/ds/sub-01/sub-01_ses-01_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1948s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 10s
- ROI estimation of 'neuromorphometrics' atlas 36s
- ROI estimation of 'lpba40' atlas 10s
- ROI estimation of 'hammers' atlas 25s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 9s
- ROI estimation of 'aal3' atlas 15s
- ROI estimation of 'mori' atlas 23s
- ROI estimation of 'anatomy3' atlas 29s
- ROI estimation of 'julichbrain' atlas 35s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 14s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 22s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 48s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 73s
- Write results 74s
- 353s
- Quality check: 5s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_25440/ds/sub-01/report/catreport_sub-01_ses-01_T1w.pdf
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- CAT preprocessing takes 56 minute(s) and 26 second(s).
- Image Quality Rating (IQR): 84.81% (B)
- GM volume (GMV): 48.32% (731.39 / 1513.64 ml)
- GM thickness (GMT): 2.51 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_25440/ds/sub-01/mri
- Reports are saved in /var/lib/condor/execute/dir_25440/ds/sub-01/report
- Labels are saved in /var/lib/condor/execute/dir_25440/ds/sub-01/label
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