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- CAT12.8.1 r1980: 1/1: ./dir_4176/ds/sub-047/sub-047_ses-t14_T1w.n
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- SANLM denoising (medium): 10s
- APP: Rough bias correction:
- Initialize 4s
- Estimate background 4s
- Initial correction 5s
- Refine background 2s
- Final correction 4s
- Final scaling 5s
- 28s
- Correct center-of-mass 3s
- Affine registration 6s
- SPM preprocessing 1 (estimate 1 - TPM registration): 52s
- SPM preprocessing 1 (estimate 2): 50s
- SPM preprocessing 2 (write):
- Write Segmentation 11s
- Update Segmentation 13s
- Update Skull-Stripping 29s
- Update probability maps 6s
- 59s
- Global intensity correction: 10s
- SANLM denoising after intensity normalization (medium): 7s
- Fast Optimized Shooting registration 25s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 10s
- Estimate local tissue thresholds (WM) 12s
- Estimate local tissue thresholds (GM) 15s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 12s
- 55s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 3s
- Ventricle detection 7s
- Blood vessel detection 6s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 18s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 3s
- 47s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 20s
- 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
- 8s
- 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 | 0.0830 0.0000 0.0830 | 32.0000
- 2 | 2.50 | 0.0799 0.0013 0.0812 | 29.4886
- 3 | 2.50 | 0.0789 0.0020 0.0810 | 26.9772
- 4 | 2.50 | 0.0785 0.0023 0.0808 | 24.6107
- 5 | 2.50 | 0.0781 0.0025 0.0806 | 22.6548
- 6 | 2.50 | 0.0777 0.0026 0.0803 | 20.6989
- 7 | 2.50 | 0.0774 0.0027 0.0801 | 18.9688
- 8 | 2.50 | 0.0770 0.0028 0.0799 | 17.4455
- 9 | 2.50 | 0.0767 0.0029 0.0796 | 15.9223
- 10 | 2.50 | 0.0763 0.0031 0.0794 | 14.6627
- 11 | 2.50 | 0.0759 0.0032 0.0791 | 13.4764
- 12 | 2.50 | 0.0755 0.0032 0.0788 | 12.3015
- 13 | 2.50 | 0.0751 0.0034 0.0785 | 11.3776
- 14 | 2.50 | 0.0747 0.0034 0.0782 | 10.4537
- 15 | 2.25 | 0.0741 0.0035 0.0777 | 9.5920
- 16 | 2.25 | 0.0708 0.0051 0.0760 | 8.8725
- 29 | 2.00 | 0.0715 0.0023 0.0739 | 3.3283
- 30 | 2.00 | 0.0652 0.0048 0.0701 | 3.1221
- 31 | 2.00 | 0.0630 0.0058 0.0689 | 2.9160
- 43 | 1.75 | 0.0616 0.0034 0.0651 | 1.5785
- 44 | 1.75 | 0.0576 0.0055 0.0631 | 1.5194
- 45 | 1.75 | 0.0562 0.0063 0.0624 | 1.4626
- 57 | 1.50 | 0.0546 0.0046 0.0592 | 1.0900
- 58 | 1.50 | 0.0517 0.0064 0.0581 | 1.0730
- 59 | 1.50 | 0.0508 0.0070 0.0578 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 127s
- Prepare output 7s
- 134s
- Jacobian determinant (RMS): 0.012 0.047 0.070 0.096 0.118 | 0.125314
- Template Matching: 0.083 0.213 0.189 0.168 0.152 | 0.152268
- Write result maps: 17s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 32s
- CSF distance: 11s
- PBT2x thickness: 33s
- 80s
- Create initial surface 54s
- Topology correction: 61s
- Surface refinement: 52s
- Reduction of surface collisions with optimization: 39s
- Spherical mapping with areal smoothing 52s
- Spherical registration 168s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 32s
- CSF distance: 11s
- PBT2x thickness: 33s
- 80s
- Create initial surface 54s
- Topology correction: 62s
- Surface refinement: 68s
- Reduction of surface collisions with optimization: 40s
- Spherical mapping with areal smoothing 55s
- Spherical registration 180s
- Final surface processing results:
- Average thickness (FS): 2.5079 0.6596 mm
- Surface intensity / position RMSE: 0.0674 / 0.0685
- Euler number / defect number / defect size: 14.0 / 14.0 / 0.38%
- Display thickness: /var/lib/condor/execute/dir_4176/ds/sub-047/surf/lh.thickness.sub-047_ses-t14_T1w
- Display thickness: /var/lib/condor/execute/dir_4176/ds/sub-047/surf/rh.thickness.sub-047_ses-t14_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_4176/ds/sub-047/sub-047_ses-t14_T1w.nii
- Surface ROI estimation: 5s
- Surface and thickness estimation takes: 1106s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 35s
- ROI estimation of 'lpba40' atlas 10s
- ROI estimation of 'hammers' atlas 25s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 9s
- ROI estimation of 'aal3' atlas 14s
- ROI estimation of 'mori' atlas 21s
- ROI estimation of 'anatomy3' atlas 30s
- ROI estimation of 'julichbrain' atlas 41s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 19s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 66s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 94s
- Write results 94s
- 390s
- Quality check: 4s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_4176/ds/sub-047/report/catreport_sub-047_ses-t14_T1w.pdf
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- CAT preprocessing takes 34 minute(s) and 53 second(s).
- Image Quality Rating (IQR): 84.45% (B)
- GM volume (GMV): 45.72% (666.11 / 1457.00 ml)
- GM thickness (GMT): 2.51 0.66 mm
- Segmentations are saved in /var/lib/condor/execute/dir_4176/ds/sub-047/mri
- Reports are saved in /var/lib/condor/execute/dir_4176/ds/sub-047/report
- Labels are saved in /var/lib/condor/execute/dir_4176/ds/sub-047/label
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