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- CAT12.8.1 r1980: 1/1: ./dir_29941/ds/sub-0539/sub-0539_ses-01_T1w.n
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- SANLM denoising (medium): 158s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 8s
- Initial correction 16s
- Refine background 4s
- Final correction 9s
- Final scaling 7s
- 61s
- Correct center-of-mass 4s
- Affine registration 18s
- SPM preprocessing 1 (estimate 1 - TPM registration): 86s
- SPM preprocessing 1 (estimate 2): 62s
- SPM preprocessing 2 (write):
- Write Segmentation 21s
- Update Segmentation 23s
- Update Skull-Stripping 53s
- Update probability maps 11s
- 108s
- Global intensity correction: 21s
- SANLM denoising after intensity normalization (medium): 15s
- Fast Optimized Shooting registration 34s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 7s
- Prepare segments (LASmod = 1.18) 17s
- Estimate local tissue thresholds (WM) 23s
- Estimate local tissue thresholds (GM) 31s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 43s
- 129s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 4s
- Ventricle detection 21s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 33s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 6s
- 89s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 37s
- 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
- 13s
- 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 | 0.0856 0.0000 0.0856 | 32.0000
- 2 | 2.50 | 0.0826 0.0013 0.0838 | 29.4886
- 3 | 2.50 | 0.0817 0.0019 0.0836 | 26.9772
- 4 | 2.50 | 0.0813 0.0022 0.0835 | 24.6107
- 5 | 2.50 | 0.0810 0.0023 0.0833 | 22.6548
- 6 | 2.50 | 0.0807 0.0024 0.0831 | 20.6989
- 7 | 2.50 | 0.0804 0.0025 0.0829 | 18.9688
- 8 | 2.50 | 0.0801 0.0026 0.0826 | 17.4455
- 9 | 2.50 | 0.0798 0.0026 0.0824 | 15.9223
- 10 | 2.50 | 0.0794 0.0027 0.0822 | 14.6627
- 11 | 2.50 | 0.0791 0.0028 0.0819 | 13.4764
- 12 | 2.50 | 0.0788 0.0028 0.0816 | 12.3015
- 13 | 2.50 | 0.0784 0.0029 0.0814 | 11.3776
- 14 | 2.50 | 0.0781 0.0030 0.0811 | 10.4537
- 15 | 2.25 | 0.0777 0.0031 0.0808 | 9.5920
- 16 | 2.25 | 0.0748 0.0044 0.0792 | 8.8725
- 29 | 2.00 | 0.0763 0.0020 0.0783 | 3.3283
- 30 | 2.00 | 0.0704 0.0044 0.0747 | 3.1221
- 31 | 2.00 | 0.0684 0.0053 0.0737 | 2.9160
- 43 | 1.75 | 0.0676 0.0031 0.0707 | 1.5785
- 44 | 1.75 | 0.0632 0.0054 0.0686 | 1.5194
- 45 | 1.75 | 0.0617 0.0062 0.0679 | 1.4626
- 57 | 1.50 | 0.0606 0.0045 0.0651 | 1.0900
- 58 | 1.50 | 0.0574 0.0066 0.0640 | 1.0730
- 59 | 1.50 | 0.0563 0.0073 0.0636 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 150s
- Prepare output 11s
- 162s
- Jacobian determinant (RMS): 0.010 0.036 0.054 0.077 0.101 | 0.107999
- Template Matching: 0.086 0.224 0.205 0.185 0.169 | 0.168966
- Write result maps: 30s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 32s
- CSF distance: 14s
- PBT2x thickness: 43s
- 94s
- Create initial surface 80s
- Topology correction: 93s
- Surface refinement: 100s
- Reduction of surface collisions with optimization: 67s
- Spherical mapping with areal smoothing 76s
- Spherical registration 295s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 36s
- CSF distance: 15s
- PBT2x thickness: 43s
- 100s
- Create initial surface 82s
- Topology correction: 95s
- Surface refinement: 101s
- Reduction of surface collisions with optimization: 70s
- Spherical mapping with areal smoothing 78s
- Spherical registration 285s
- Final surface processing results:
- Average thickness (FS): 2.4317 0.6172 mm
- Surface intensity / position RMSE: 0.0754 / 0.0826
- Euler number / defect number / defect size: 54.0 / 26.5 / 1.65%
- Display thickness: /var/lib/condor/execute/dir_29941/ds/sub-0539/surf/lh.thickness.sub-0539_ses-01_T1w
- Display thickness: /var/lib/condor/execute/dir_29941/ds/sub-0539/surf/rh.thickness.sub-0539_ses-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_29941/ds/sub-0539/sub-0539_ses-01_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1716s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 11s
- ROI estimation of 'neuromorphometrics' atlas 40s
- ROI estimation of 'lpba40' atlas 12s
- ROI estimation of 'hammers' atlas 28s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 10s
- ROI estimation of 'aal3' atlas 16s
- ROI estimation of 'mori' atlas 24s
- ROI estimation of 'anatomy3' atlas 35s
- ROI estimation of 'julichbrain' atlas 46s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 18s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 32s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 73s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 110s
- Write results 111s
- 460s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_29941/ds/sub-0539/report/catreport_sub-0539_ses-01_T1w.pdf
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- CAT preprocessing takes 55 minute(s) and 9 second(s).
- Image Quality Rating (IQR): 81.86% (B-)
- GM volume (GMV): 47.82% (693.43 / 1450.04 ml)
- GM thickness (GMT): 2.43 0.62 mm
- Segmentations are saved in /var/lib/condor/execute/dir_29941/ds/sub-0539/mri
- Reports are saved in /var/lib/condor/execute/dir_29941/ds/sub-0539/report
- Labels are saved in /var/lib/condor/execute/dir_29941/ds/sub-0539/label
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