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- CAT12.8.1 r1980: 1/1: ./dir_20365/ds/sub-0496/sub-0496_ses-01_T1w.n
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- SANLM denoising (medium): 142s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 11s
- Initial correction 15s
- Refine background 4s
- Final correction 8s
- Final scaling 6s
- 61s
- Correct center-of-mass 5s
- Affine registration 16s
- SPM preprocessing 1 (estimate 1 - TPM registration): 88s
- SPM preprocessing 1 (estimate 2): 61s
- SPM preprocessing 2 (write):
- Write Segmentation 22s
- Update Segmentation 23s
- Update Skull-Stripping 55s
- Update probability maps 12s
- 111s
- Global intensity correction: 23s
- SANLM denoising after intensity normalization (medium): 26s
- Fast Optimized Shooting registration 36s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 7s
- Prepare segments (LASmod = 1.13) 17s
- Estimate local tissue thresholds (WM) 23s
- Estimate local tissue thresholds (GM) 31s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 42s
- 130s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 4s
- Ventricle detection 21s
- Blood vessel detection 10s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 31s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 6s
- 87s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 36s
- 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 | 0.0827 0.0000 0.0827 | 32.0000
- 2 | 2.50 | 0.0802 0.0011 0.0814 | 29.4886
- 3 | 2.50 | 0.0795 0.0017 0.0812 | 26.9772
- 4 | 2.50 | 0.0792 0.0019 0.0811 | 24.6107
- 5 | 2.50 | 0.0789 0.0020 0.0809 | 22.6548
- 6 | 2.50 | 0.0787 0.0021 0.0808 | 20.6989
- 7 | 2.50 | 0.0785 0.0021 0.0806 | 18.9688
- 8 | 2.50 | 0.0782 0.0022 0.0804 | 17.4455
- 9 | 2.50 | 0.0779 0.0023 0.0802 | 15.9223
- 10 | 2.50 | 0.0777 0.0024 0.0800 | 14.6627
- 11 | 2.50 | 0.0774 0.0024 0.0798 | 13.4764
- 12 | 2.50 | 0.0771 0.0025 0.0796 | 12.3015
- 13 | 2.50 | 0.0768 0.0026 0.0794 | 11.3776
- 14 | 2.50 | 0.0766 0.0026 0.0792 | 10.4537
- 15 | 2.25 | 0.0757 0.0027 0.0783 | 9.5920
- 16 | 2.25 | 0.0729 0.0040 0.0769 | 8.8725
- 29 | 2.00 | 0.0743 0.0018 0.0761 | 3.3283
- 30 | 2.00 | 0.0689 0.0040 0.0729 | 3.1221
- 31 | 2.00 | 0.0670 0.0049 0.0719 | 2.9160
- 43 | 1.75 | 0.0661 0.0028 0.0689 | 1.5785
- 44 | 1.75 | 0.0619 0.0050 0.0669 | 1.5194
- 45 | 1.75 | 0.0605 0.0058 0.0663 | 1.4626
- 57 | 1.50 | 0.0593 0.0042 0.0635 | 1.0900
- 58 | 1.50 | 0.0562 0.0062 0.0624 | 1.0730
- 59 | 1.50 | 0.0552 0.0069 0.0621 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 155s
- Prepare output 11s
- 166s
- Jacobian determinant (RMS): 0.011 0.037 0.054 0.077 0.101 | 0.108413
- Template Matching: 0.083 0.219 0.201 0.182 0.166 | 0.165540
- Write result maps: 32s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 27s
- CSF distance: 14s
- PBT2x thickness: 41s
- 87s
- Create initial surface 75s
- Topology correction: 88s
- Surface refinement: 87s
- Reduction of surface collisions with optimization: 62s
- Spherical mapping with areal smoothing 79s
- Spherical registration 288s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 25s
- CSF distance: 13s
- PBT2x thickness: 40s
- 84s
- Create initial surface 74s
- Topology correction: 87s
- Surface refinement: 79s
- Reduction of surface collisions with optimization: 67s
- Spherical mapping with areal smoothing 74s
- Spherical registration 278s
- Final surface processing results:
- Average thickness (FS): 2.4942 0.6368 mm
- Surface intensity / position RMSE: 0.0779 / 0.0886
- Euler number / defect number / defect size: 36.0 / 26.0 / 1.62%
- Display thickness: /var/lib/condor/execute/dir_20365/ds/sub-0496/surf/lh.thickness.sub-0496_ses-01_T1w
- Display thickness: /var/lib/condor/execute/dir_20365/ds/sub-0496/surf/rh.thickness.sub-0496_ses-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_20365/ds/sub-0496/sub-0496_ses-01_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1608s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 11s
- ROI estimation of 'neuromorphometrics' atlas 40s
- ROI estimation of 'lpba40' atlas 11s
- 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 34s
- ROI estimation of 'julichbrain' atlas 45s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 18s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 31s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 72s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 110s
- Write results 111s
- 453s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_20365/ds/sub-0496/report/catreport_sub-0496_ses-01_T1w.pdf
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- CAT preprocessing takes 53 minute(s) and 22 second(s).
- Image Quality Rating (IQR): 78.55% (C+)
- GM volume (GMV): 50.60% (667.29 / 1318.64 ml)
- GM thickness (GMT): 2.49 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_20365/ds/sub-0496/mri
- Reports are saved in /var/lib/condor/execute/dir_20365/ds/sub-0496/report
- Labels are saved in /var/lib/condor/execute/dir_20365/ds/sub-0496/label
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