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- CAT12.8.1 r2040: 1/1: ./sub-0025978/ses-1/sub-0025978_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 33s
- Internal resampling (1.33x1.00x1.00mm > 1.00x1.00x1.00mm): 1s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 5s
- Initial correction 5s
- Refine background 3s
- Final correction 4s
- Final scaling 4s
- 34s
- Correct center-of-mass 4s
- Affine registration 8s
- SPM preprocessing 1 (estimate 1 - TPM registration): 71s
- SPM preprocessing 1 (estimate 2): 57s
- SPM preprocessing 2 (write):
- Write Segmentation 15s
- Update Segmentation 16s
- Update Skull-Stripping 38s
- Update probability maps 8s
- 78s
- Global intensity correction: 15s
- SANLM denoising after intensity normalization (medium): 23s
- Fast Optimized Shooting registration 32s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 12s
- Estimate local tissue thresholds (WM) 17s
- Estimate local tissue thresholds (GM) 25s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 38s
- 101s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 14s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 21s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 62s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 30s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.670.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 3s
- 11s
- 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 | 0.0814 0.0000 0.0814 | 32.0000
- 2 | 2.50 | 0.0791 0.0011 0.0802 | 29.4886
- 3 | 2.50 | 0.0784 0.0017 0.0801 | 26.9772
- 4 | 2.50 | 0.0780 0.0019 0.0799 | 24.6107
- 5 | 2.50 | 0.0778 0.0020 0.0798 | 22.6548
- 6 | 2.50 | 0.0775 0.0021 0.0796 | 20.6989
- 7 | 2.50 | 0.0772 0.0022 0.0795 | 18.9688
- 8 | 2.50 | 0.0770 0.0023 0.0793 | 17.4455
- 9 | 2.50 | 0.0767 0.0024 0.0791 | 15.9223
- 10 | 2.50 | 0.0764 0.0025 0.0789 | 14.6627
- 11 | 2.50 | 0.0761 0.0026 0.0787 | 13.4764
- 12 | 2.50 | 0.0758 0.0026 0.0785 | 12.3015
- 13 | 2.50 | 0.0755 0.0027 0.0782 | 11.3776
- 14 | 2.50 | 0.0752 0.0028 0.0780 | 10.4537
- 15 | 2.25 | 0.0732 0.0029 0.0761 | 9.5920
- 16 | 2.25 | 0.0706 0.0042 0.0748 | 8.8725
- 29 | 2.00 | 0.0709 0.0019 0.0728 | 3.3283
- 30 | 2.00 | 0.0653 0.0041 0.0694 | 3.1221
- 31 | 2.00 | 0.0634 0.0050 0.0684 | 2.9160
- 43 | 1.75 | 0.0621 0.0029 0.0650 | 1.5785
- 44 | 1.75 | 0.0584 0.0049 0.0632 | 1.5194
- 45 | 1.75 | 0.0571 0.0055 0.0627 | 1.4626
- 57 | 1.50 | 0.0556 0.0040 0.0596 | 1.0900
- 58 | 1.50 | 0.0529 0.0058 0.0586 | 1.0730
- Shooting registration with 2.50:-0.25:1.50 mm takes: 147s
- Prepare output 10s
- 157s
- Jacobian determinant (RMS): 0.011 0.041 0.060 0.083 0.103 | 0.107282
- Template Matching: 0.081 0.212 0.190 0.171 0.159 | 0.158621
- Write result maps: 55s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 25s
- CSF distance: 14s
- PBT2x thickness: 42s
- 88s
- Create initial surface 83s
- Topology correction: 94s
- Surface refinement: 79s
- Reduction of surface collisions with optimization: 66s
- Spherical mapping with areal smoothing 87s
- Spherical registration 299s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 24s
- CSF distance: 13s
- PBT2x thickness: 41s
- 85s
- Create initial surface 81s
- Topology correction: 88s
- Surface refinement: 94s
- Reduction of surface collisions with optimization: 65s
- Spherical mapping with areal smoothing 77s
- Spherical registration 299s
- Final surface processing results:
- Average thickness (FS): 2.5498 0.6277 mm
- Surface intensity / position RMSE: 0.0685 / 0.0703
- Euler number / defect number / defect size: 16.0 / 11.5 / 0.64%
- Display thickness: /var/lib/condor/execute/dir_2997985/ds/BNU_2/sub-0025978/ses-1/surf/lh.thickness.sub-0025978_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2997985/ds/BNU_2/sub-0025978/ses-1/surf/rh.thickness.sub-0025978_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2997985/ds/BNU_2/sub-0025978/ses-1/sub-0025978_ses-1_run-1_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1678s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 8s
- ROI estimation of 'neuromorphometrics' atlas 29s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 20s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 12s
- ROI estimation of 'mori' atlas 17s
- ROI estimation of 'anatomy3' atlas 25s
- ROI estimation of 'julichbrain' atlas 33s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 13s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 23s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 52s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 78s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s
- Write results 8s
- 335s
- Quality check: 10s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2997985/ds/BNU_2/sub-0025978/ses-1/report/catreport_sub-0025978_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 47 minute(s) and 46 second(s).
- Image Quality Rating (IQR): 80.99% (B-)
- GM volume (GMV): 50.74% (673.05 / 1326.42 ml)
- GM thickness (GMT): 2.55 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2997985/ds/BNU_2/sub-0025978/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_2997985/ds/BNU_2/sub-0025978/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_2997985/ds/BNU_2/sub-0025978/ses-1/label
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