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- CAT12.8.1 r1980: 1/1: ./condor/execute/dir_61426/ds/sub-01/sub-01_T1w.n
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- SANLM denoising (medium): 33s
- APP: Rough bias correction:
- Initialize 4s
- Estimate background 6s
- Initial correction 6s
- Refine background 2s
- Final correction 5s
- Final scaling 5s
- 31s
- Correct center-of-mass 7s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 78s
- SPM preprocessing 1 (estimate 2): 52s
- SPM preprocessing 2 (write):
- Write Segmentation 13s
- Update Segmentation 18s
- Update Skull-Stripping 30s
- Update probability maps 5s
- 66s
- Global intensity correction: 9s
- SANLM denoising after intensity normalization (medium): 8s
- Fast Optimized Shooting registration 34s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 17s
- Estimate local tissue thresholds (WM) 16s
- Estimate local tissue thresholds (GM) 26s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 16s
- 82s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 4s
- Ventricle detection 16s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 27s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 3s
- 72s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 33s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- 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
- 12s
- 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 | 0.0825 0.0000 0.0825 | 32.0000
- 2 | 2.50 | 0.0797 0.0012 0.0809 | 29.4886
- 3 | 2.50 | 0.0789 0.0019 0.0807 | 26.9772
- 4 | 2.50 | 0.0785 0.0021 0.0806 | 24.6107
- 5 | 2.50 | 0.0781 0.0022 0.0804 | 22.6548
- 6 | 2.50 | 0.0779 0.0023 0.0802 | 20.6989
- 7 | 2.50 | 0.0776 0.0024 0.0800 | 18.9688
- 8 | 2.50 | 0.0773 0.0026 0.0798 | 17.4455
- 9 | 2.50 | 0.0769 0.0026 0.0796 | 15.9223
- 10 | 2.50 | 0.0766 0.0027 0.0793 | 14.6627
- 11 | 2.50 | 0.0763 0.0028 0.0791 | 13.4764
- 12 | 2.50 | 0.0759 0.0029 0.0788 | 12.3015
- 13 | 2.50 | 0.0756 0.0030 0.0786 | 11.3776
- 14 | 2.50 | 0.0752 0.0031 0.0783 | 10.4537
- 15 | 2.25 | 0.0740 0.0032 0.0772 | 9.5920
- 16 | 2.25 | 0.0708 0.0047 0.0755 | 8.8725
- 29 | 2.00 | 0.0714 0.0021 0.0736 | 3.3283
- 30 | 2.00 | 0.0656 0.0045 0.0700 | 3.1221
- 31 | 2.00 | 0.0636 0.0054 0.0690 | 2.9160
- 43 | 1.75 | 0.0625 0.0031 0.0656 | 1.5785
- 44 | 1.75 | 0.0586 0.0052 0.0637 | 1.5194
- 45 | 1.75 | 0.0573 0.0059 0.0632 | 1.4626
- 57 | 1.50 | 0.0559 0.0043 0.0602 | 1.0900
- 58 | 1.50 | 0.0531 0.0061 0.0592 | 1.0730
- Shooting registration with 2.50:-0.25:1.50 mm takes: 174s
- Prepare output 11s
- 185s
- Jacobian determinant (RMS): 0.012 0.043 0.064 0.089 0.113 | 0.117532
- Template Matching: 0.083 0.213 0.191 0.172 0.159 | 0.159299
- Write result maps: 18s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 36s
- CSF distance: 19s
- PBT2x thickness: 55s
- 116s
- Create initial surface 95s
- Topology correction: 91s
- Surface refinement: 117s
- Reduction of surface collisions with optimization: 78s
- Spherical mapping with areal smoothing 112s
- Spherical registration 335s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 41s
- CSF distance: 19s
- PBT2x thickness: 55s
- 120s
- Create initial surface 97s
- Topology correction: 104s
- Surface refinement: 125s
- Reduction of surface collisions with optimization: 83s
- Spherical mapping with areal smoothing 99s
- Spherical registration 359s
- Final surface processing results:
- Average thickness (FS): 2.6283 0.6401 mm
- Surface intensity / position RMSE: 0.0748 / 0.0751
- Euler number / defect number / defect size: 16.0 / 12.5 / 0.83%
- Display thickness: /var/lib/condor/execute/dir_61426/ds/sub-01/surf/lh.thickness.sub-01_T1w
- Display thickness: /var/lib/condor/execute/dir_61426/ds/sub-01/surf/rh.thickness.sub-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_61426/ds/sub-01/sub-01_T1w.nii
- Surface ROI estimation: 11s
- Surface and thickness estimation takes: 2051s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 6s
- ROI estimation of 'neuromorphometrics' atlas 19s
- ROI estimation of 'lpba40' atlas 7s
- ROI estimation of 'hammers' atlas 15s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 5s
- ROI estimation of 'aal3' atlas 8s
- ROI estimation of 'mori' atlas 13s
- ROI estimation of 'anatomy3' atlas 19s
- ROI estimation of 'julichbrain' atlas 25s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 10s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 17s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 38s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 54s
- Write results 55s
- 239s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_61426/ds/sub-01/report/catreport_sub-01_T1w.pdf
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- CAT preprocessing takes 51 minute(s) and 57 second(s).
- Image Quality Rating (IQR): 82.33% (B-)
- GM volume (GMV): 52.41% (680.82 / 1298.96 ml)
- GM thickness (GMT): 2.63 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_61426/ds/sub-01/mri
- Reports are saved in /var/lib/condor/execute/dir_61426/ds/sub-01/report
- Labels are saved in /var/lib/condor/execute/dir_61426/ds/sub-01/label
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