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- CAT12.8.1 r1980: 1/1: ./dir_12363/ds/sub-015/sub-015_ses-t2_T1w.n
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- SANLM denoising (medium): 9s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 5s
- Initial correction 5s
- Refine background 2s
- Final correction 4s
- Final scaling 4s
- 30s
- Correct center-of-mass 7s
- Affine registration 7s
- SPM preprocessing 1 (estimate 1 - TPM registration): 53s
- SPM preprocessing 1 (estimate 2): 61s
- SPM preprocessing 2 (write):
- Write Segmentation 13s
- Update Segmentation 14s
- Update Skull-Stripping 31s
- Update probability maps 7s
- 64s
- Global intensity correction: 12s
- SANLM denoising after intensity normalization (medium): 5s
- Fast Optimized Shooting registration 26s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.19) 11s
- Estimate local tissue thresholds (WM) 13s
- Estimate local tissue thresholds (GM) 16s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 13s
- 60s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 2s
- Ventricle detection 9s
- Blood vessel detection 7s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 19s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 3s
- 50s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 25s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 3s
- Level 1 cleanup (brain masking) 2s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 9s
- 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 | 0.0823 0.0000 0.0823 | 32.0000
- 2 | 2.50 | 0.0796 0.0012 0.0808 | 29.4886
- 3 | 2.50 | 0.0788 0.0019 0.0807 | 26.9772
- 4 | 2.50 | 0.0784 0.0021 0.0805 | 24.6107
- 5 | 2.50 | 0.0780 0.0023 0.0803 | 22.6548
- 6 | 2.50 | 0.0777 0.0024 0.0801 | 20.6989
- 7 | 2.50 | 0.0774 0.0025 0.0799 | 18.9688
- 8 | 2.50 | 0.0771 0.0026 0.0797 | 17.4455
- 9 | 2.50 | 0.0768 0.0027 0.0795 | 15.9223
- 10 | 2.50 | 0.0764 0.0028 0.0793 | 14.6627
- 11 | 2.50 | 0.0761 0.0029 0.0790 | 13.4764
- 12 | 2.50 | 0.0757 0.0030 0.0787 | 12.3015
- 13 | 2.50 | 0.0753 0.0031 0.0785 | 11.3776
- 14 | 2.50 | 0.0750 0.0032 0.0782 | 10.4537
- 15 | 2.25 | 0.0739 0.0033 0.0772 | 9.5920
- 16 | 2.25 | 0.0709 0.0048 0.0756 | 8.8725
- 29 | 2.00 | 0.0715 0.0022 0.0736 | 3.3283
- 30 | 2.00 | 0.0652 0.0046 0.0698 | 3.1221
- 31 | 2.00 | 0.0629 0.0057 0.0686 | 2.9160
- 43 | 1.75 | 0.0614 0.0033 0.0647 | 1.5785
- 44 | 1.75 | 0.0573 0.0054 0.0627 | 1.5194
- 45 | 1.75 | 0.0559 0.0061 0.0620 | 1.4626
- 57 | 1.50 | 0.0542 0.0045 0.0587 | 1.0900
- 58 | 1.50 | 0.0514 0.0063 0.0577 | 1.0730
- Shooting registration with 2.50:-0.25:1.50 mm takes: 119s
- Prepare output 8s
- 127s
- Jacobian determinant (RMS): 0.012 0.043 0.065 0.092 0.115 | 0.120079
- Template Matching: 0.082 0.213 0.189 0.168 0.154 | 0.154316
- Write result maps: 18s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 26s
- CSF distance: 10s
- PBT2x thickness: 29s
- 69s
- Create initial surface 60s
- Topology correction: 56s
- Surface refinement: 49s
- Reduction of surface collisions with optimization: 39s
- Spherical mapping with areal smoothing 52s
- Spherical registration 246s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 25s
- CSF distance: 10s
- PBT2x thickness: 29s
- 69s
- Create initial surface 60s
- Topology correction: 55s
- Surface refinement: 63s
- Reduction of surface collisions with optimization: 38s
- Spherical mapping with areal smoothing 52s
- Spherical registration 249s
- Final surface processing results:
- Average thickness (FS): 2.3551 0.6046 mm
- Surface intensity / position RMSE: 0.0628 / 0.0651
- Euler number / defect number / defect size: 14.0 / 11.5 / 0.46%
- Display thickness: /var/lib/condor/execute/dir_12363/ds/sub-015/surf/lh.thickness.sub-015_ses-t2_T1w
- Display thickness: /var/lib/condor/execute/dir_12363/ds/sub-015/surf/rh.thickness.sub-015_ses-t2_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_12363/ds/sub-015/sub-015_ses-t2_T1w.nii
- Surface ROI estimation: 6s
- Surface and thickness estimation takes: 1222s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 6s
- ROI estimation of 'neuromorphometrics' atlas 21s
- ROI estimation of 'lpba40' atlas 6s
- ROI estimation of 'hammers' atlas 15s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 5s
- ROI estimation of 'aal3' atlas 9s
- ROI estimation of 'mori' atlas 14s
- ROI estimation of 'anatomy3' atlas 20s
- ROI estimation of 'julichbrain' atlas 26s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 19s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 42s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 63s
- Write results 64s
- 260s
- Quality check: 4s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_12363/ds/sub-015/report/catreport_sub-015_ses-t2_T1w.pdf
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- CAT preprocessing takes 35 minute(s) and 13 second(s).
- Image Quality Rating (IQR): 84.33% (B)
- GM volume (GMV): 43.50% (530.78 / 1220.19 ml)
- GM thickness (GMT): 2.36 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_12363/ds/sub-015/mri
- Reports are saved in /var/lib/condor/execute/dir_12363/ds/sub-015/report
- Labels are saved in /var/lib/condor/execute/dir_12363/ds/sub-015/label
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