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- CAT12.8.1 r1980: 1/1: ./dir_16316/ds/sub-1296/sub-1296_ses-01_T1w.n
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- SANLM denoising (medium): 176s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 9s
- Initial correction 15s
- Refine background 4s
- Final correction 9s
- Final scaling 8s
- 62s
- Correct center-of-mass 5s
- Affine registration 16s
- SPM preprocessing 1 (estimate 1 - TPM registration): 10s
- Use initial fine affine registration. 72s
- SPM preprocessing 1 (estimate 2): 78s
- SPM preprocessing 2 (write):
- Write Segmentation 22s
- Update Segmentation 22s
- Update Skull-Stripping 54s
- Update probability maps 12s
- 109s
- Global intensity correction: 22s
- SANLM denoising after intensity normalization (medium): 13s
- Fast Optimized Shooting registration 35s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 7s
- Prepare segments (LASmod = 1.00) 16s
- Estimate local tissue thresholds (WM) 24s
- Estimate local tissue thresholds (GM) 34s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 40s
- 130s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 4s
- Ventricle detection 17s
- Blood vessel detection 10s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 35s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 6s
- 86s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 35s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- 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 | 0.0828 0.0000 0.0828 | 32.0000
- 2 | 2.50 | 0.0798 0.0012 0.0810 | 29.4886
- 3 | 2.50 | 0.0790 0.0018 0.0808 | 26.9772
- 4 | 2.50 | 0.0787 0.0019 0.0806 | 24.6107
- 5 | 2.50 | 0.0784 0.0020 0.0804 | 22.6548
- 6 | 2.50 | 0.0782 0.0020 0.0803 | 20.6989
- 7 | 2.50 | 0.0780 0.0021 0.0801 | 18.9688
- 8 | 2.50 | 0.0778 0.0021 0.0799 | 17.4455
- 9 | 2.50 | 0.0776 0.0021 0.0797 | 15.9223
- 10 | 2.50 | 0.0773 0.0022 0.0795 | 14.6627
- 11 | 2.50 | 0.0771 0.0022 0.0793 | 13.4764
- 12 | 2.50 | 0.0769 0.0022 0.0791 | 12.3015
- 13 | 2.50 | 0.0766 0.0023 0.0789 | 11.3776
- 14 | 2.50 | 0.0764 0.0023 0.0787 | 10.4537
- 15 | 2.25 | 0.0755 0.0023 0.0779 | 9.5920
- 16 | 2.25 | 0.0730 0.0035 0.0765 | 8.8725
- 29 | 2.00 | 0.0752 0.0016 0.0767 | 3.3283
- 30 | 2.00 | 0.0697 0.0038 0.0734 | 3.1221
- 31 | 2.00 | 0.0680 0.0046 0.0726 | 2.9160
- 43 | 1.75 | 0.0676 0.0026 0.0702 | 1.5785
- 44 | 1.75 | 0.0632 0.0050 0.0682 | 1.5194
- 45 | 1.75 | 0.0619 0.0057 0.0676 | 1.4626
- 57 | 1.50 | 0.0610 0.0041 0.0651 | 1.0900
- 58 | 1.50 | 0.0578 0.0062 0.0640 | 1.0730
- 59 | 1.50 | 0.0568 0.0069 0.0637 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 152s
- Prepare output 11s
- 163s
- Jacobian determinant (RMS): 0.008 0.027 0.044 0.072 0.101 | 0.108168
- Template Matching: 0.083 0.219 0.204 0.186 0.170 | 0.170423
- Write result maps: 31s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 27s
- CSF distance: 14s
- PBT2x thickness: 42s
- 88s
- Create initial surface 77s
- Topology correction: 91s
- Surface refinement: 105s
- Reduction of surface collisions with optimization: 70s
- Spherical mapping with areal smoothing 90s
- Spherical registration 306s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 26s
- CSF distance: 14s
- PBT2x thickness: 41s
- 87s
- Create initial surface 77s
- Topology correction: 95s
- Surface refinement: 104s
- Reduction of surface collisions with optimization: 68s
- Spherical mapping with areal smoothing 77s
- Spherical registration 290s
- Final surface processing results:
- Average thickness (FS): 2.6252 0.7040 mm
- Surface intensity / position RMSE: 0.0961 / 0.1226
- Euler number / defect number / defect size: 108.0 / 36.0 / 4.11%
- Display thickness: /var/lib/condor/execute/dir_16316/ds/sub-1296/surf/lh.thickness.sub-1296_ses-01_T1w
- Display thickness: /var/lib/condor/execute/dir_16316/ds/sub-1296/surf/rh.thickness.sub-1296_ses-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_16316/ds/sub-1296/sub-1296_ses-01_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1723s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 11s
- ROI estimation of 'neuromorphometrics' atlas 42s
- ROI estimation of 'lpba40' atlas 12s
- ROI estimation of 'hammers' atlas 29s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 10s
- ROI estimation of 'aal3' atlas 17s
- ROI estimation of 'mori' atlas 25s
- ROI estimation of 'anatomy3' atlas 36s
- ROI estimation of 'julichbrain' atlas 48s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 19s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 33s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 75s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 112s
- Write results 113s
- 473s
- Quality check: 5s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_16316/ds/sub-1296/report/catreport_sub-1296_ses-01_T1w.pdf
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- CAT preprocessing takes 57 minute(s) and 14 second(s).
- Image Quality Rating (IQR): 80.24% (B-)
- GM volume (GMV): 56.66% (725.97 / 1281.19 ml)
- GM thickness (GMT): 2.63 0.71 mm
- Segmentations are saved in /var/lib/condor/execute/dir_16316/ds/sub-1296/mri
- Reports are saved in /var/lib/condor/execute/dir_16316/ds/sub-1296/report
- Labels are saved in /var/lib/condor/execute/dir_16316/ds/sub-1296/label
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