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- CAT12.8.1 r1980: 1/1: ./condor/execute/dir_19713/ds/sub-29/sub-29_T1w.n
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- SANLM denoising (medium): 80s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 6s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 38s
- Correct center-of-mass 5s
- Affine registration 9s
- SPM preprocessing 1 (estimate 1 - TPM registration): 71s
- SPM preprocessing 1 (estimate 2): 47s
- SPM preprocessing 2 (write):
- Write Segmentation 16s
- Update Segmentation 18s
- Update Skull-Stripping 40s
- Update probability maps 8s
- 82s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 7s
- Fast Optimized Shooting registration 31s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 4s
- Prepare segments (LASmod = 1.00) 13s
- Estimate local tissue thresholds (WM) 19s
- Estimate local tissue thresholds (GM) 26s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 35s
- 105s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 18s
- Blood vessel detection 9s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 25s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 3s
- Final corrections 5s
- 72s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 33s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.07,0.980.05]
- 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 | 0.0820 0.0000 0.0820 | 32.0000
- 2 | 2.50 | 0.0797 0.0010 0.0808 | 29.4886
- 3 | 2.50 | 0.0791 0.0015 0.0807 | 26.9772
- 4 | 2.50 | 0.0788 0.0017 0.0805 | 24.6107
- 5 | 2.50 | 0.0786 0.0018 0.0804 | 22.6548
- 6 | 2.50 | 0.0784 0.0019 0.0803 | 20.6989
- 7 | 2.50 | 0.0782 0.0020 0.0801 | 18.9688
- 8 | 2.50 | 0.0779 0.0021 0.0800 | 17.4455
- 9 | 2.50 | 0.0777 0.0021 0.0798 | 15.9223
- 10 | 2.50 | 0.0775 0.0022 0.0797 | 14.6627
- 11 | 2.50 | 0.0772 0.0022 0.0795 | 13.4764
- 12 | 2.50 | 0.0770 0.0023 0.0793 | 12.3015
- 13 | 2.50 | 0.0768 0.0024 0.0791 | 11.3776
- 14 | 2.50 | 0.0765 0.0024 0.0789 | 10.4537
- 15 | 2.25 | 0.0759 0.0024 0.0784 | 9.5920
- 16 | 2.25 | 0.0734 0.0037 0.0771 | 8.8725
- 29 | 2.00 | 0.0759 0.0017 0.0775 | 3.3283
- 30 | 2.00 | 0.0698 0.0041 0.0739 | 3.1221
- 31 | 2.00 | 0.0677 0.0051 0.0728 | 2.9160
- 43 | 1.75 | 0.0670 0.0029 0.0699 | 1.5785
- 44 | 1.75 | 0.0622 0.0055 0.0676 | 1.5194
- 45 | 1.75 | 0.0606 0.0063 0.0669 | 1.4626
- 57 | 1.50 | 0.0592 0.0045 0.0637 | 1.0900
- 58 | 1.50 | 0.0558 0.0068 0.0625 | 1.0730
- 59 | 1.50 | 0.0546 0.0075 0.0621 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 163s
- Prepare output 10s
- 174s
- Jacobian determinant (RMS): 0.010 0.032 0.049 0.076 0.102 | 0.108731
- Template Matching: 0.082 0.220 0.203 0.182 0.164 | 0.163879
- Write result maps: 25s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 26s
- CSF distance: 14s
- PBT2x thickness: 40s
- 86s
- Create initial surface 79s
- Topology correction: 94s
- Surface refinement: 73s
- Reduction of surface collisions with optimization: 71s
- Spherical mapping with areal smoothing 82s
- Spherical registration 294s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 28s
- CSF distance: 14s
- PBT2x thickness: 43s
- 91s
- Create initial surface 77s
- Topology correction: 90s
- Surface refinement: 82s
- Reduction of surface collisions with optimization: 71s
- Spherical mapping with areal smoothing 80s
- Spherical registration 289s
- Final surface processing results:
- Average thickness (FS): 2.7527 0.6743 mm
- Surface intensity / position RMSE: 0.0714 / 0.0759
- Euler number / defect number / defect size: 20.0 / 10.0 / 1.28%
- Display thickness: /var/lib/condor/execute/dir_19713/ds/sub-29/surf/lh.thickness.sub-29_T1w
- Display thickness: /var/lib/condor/execute/dir_19713/ds/sub-29/surf/rh.thickness.sub-29_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_19713/ds/sub-29/sub-29_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1652s
- 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 25s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 8s
- ROI estimation of 'aal3' atlas 13s
- ROI estimation of 'mori' atlas 20s
- ROI estimation of 'anatomy3' atlas 31s
- ROI estimation of 'julichbrain' atlas 39s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 29s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 59s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 95s
- Write results 96s
- 391s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_19713/ds/sub-29/report/catreport_sub-29_T1w.pdf
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- CAT preprocessing takes 49 minute(s) and 3 second(s).
- Image Quality Rating (IQR): 83.75% (B)
- GM volume (GMV): 51.75% (751.37 / 1451.91 ml)
- GM thickness (GMT): 2.75 0.68 mm
- Segmentations are saved in /var/lib/condor/execute/dir_19713/ds/sub-29/mri
- Reports are saved in /var/lib/condor/execute/dir_19713/ds/sub-29/report
- Labels are saved in /var/lib/condor/execute/dir_19713/ds/sub-29/label
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