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- CAT12.8.1 r1980: 1/1: ./sub-NC233_ses-20190512_acq-highres_run-01_T1w.n
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- SANLM denoising (medium): 53s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 8s
- Initial correction 7s
- Refine background 4s
- Final correction 6s
- Final scaling 7s
- 49s
- Correct center-of-mass 6s
- Affine registration 12s
- SPM preprocessing 1 (estimate 1 - TPM registration): 87s
- SPM preprocessing 1 (estimate 2): 86s
- SPM preprocessing 2 (write):
- Write Segmentation 22s
- Update Segmentation 25s
- Update Skull-Stripping 53s
- Update probability maps 11s
- 110s
- Global intensity correction: 21s
- SANLM denoising after intensity normalization (medium): 12s
- Fast Optimized Shooting registration 44s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.06) 19s
- Estimate local tissue thresholds (WM) 21s
- Estimate local tissue thresholds (GM) 28s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 26s
- 106s
- ROI segmentation (partitioning):
- Atlas -> subject space 10s
- Major structures 4s
- Ventricle detection 18s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.03) 28s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 5s
- Final corrections 5s
- 84s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 49s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 5s
- Level 1 cleanup (brain masking) 4s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 3s
- 14s
- 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 | 0.0847 0.0000 0.0847 | 32.0000
- 2 | 2.50 | 0.0819 0.0012 0.0831 | 29.4886
- 3 | 2.50 | 0.0810 0.0018 0.0829 | 26.9772
- 4 | 2.50 | 0.0807 0.0021 0.0827 | 24.6107
- 5 | 2.50 | 0.0803 0.0022 0.0826 | 22.6548
- 6 | 2.50 | 0.0801 0.0023 0.0824 | 20.6989
- 7 | 2.50 | 0.0798 0.0024 0.0822 | 18.9688
- 8 | 2.50 | 0.0795 0.0025 0.0820 | 17.4455
- 9 | 2.50 | 0.0792 0.0025 0.0818 | 15.9223
- 10 | 2.50 | 0.0789 0.0026 0.0815 | 14.6627
- 11 | 2.50 | 0.0786 0.0027 0.0813 | 13.4764
- 12 | 2.50 | 0.0783 0.0028 0.0811 | 12.3015
- 13 | 2.50 | 0.0780 0.0029 0.0808 | 11.3776
- 14 | 2.50 | 0.0777 0.0029 0.0806 | 10.4537
- 15 | 2.25 | 0.0770 0.0030 0.0800 | 9.5920
- 16 | 2.25 | 0.0741 0.0043 0.0785 | 8.8725
- 29 | 2.00 | 0.0756 0.0019 0.0775 | 3.3283
- 30 | 2.00 | 0.0698 0.0042 0.0741 | 3.1221
- 31 | 2.00 | 0.0679 0.0052 0.0731 | 2.9160
- 43 | 1.75 | 0.0669 0.0030 0.0699 | 1.5785
- 44 | 1.75 | 0.0627 0.0052 0.0679 | 1.5194
- 45 | 1.75 | 0.0612 0.0061 0.0673 | 1.4626
- 57 | 1.50 | 0.0599 0.0044 0.0643 | 1.0900
- 58 | 1.50 | 0.0567 0.0065 0.0632 | 1.0730
- 59 | 1.50 | 0.0556 0.0072 0.0628 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 226s
- Prepare output 11s
- 237s
- Jacobian determinant (RMS): 0.011 0.040 0.058 0.081 0.104 | 0.111298
- Template Matching: 0.085 0.222 0.204 0.184 0.167 | 0.166832
- Write result maps: 39s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 52s
- CSF distance: 19s
- PBT2x thickness: 60s
- 140s
- Create initial surface 109s
- Topology correction: 150s
- Surface refinement: 93s
- Reduction of surface collisions with optimization: 97s
- Spherical mapping with areal smoothing 105s
- Spherical registration 278s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 52s
- CSF distance: 19s
- PBT2x thickness: 60s
- 139s
- Create initial surface 110s
- Topology correction: 121s
- Surface refinement: 115s
- Reduction of surface collisions with optimization: 100s
- Spherical mapping with areal smoothing 107s
- Spherical registration 280s
- Final surface processing results:
- Average thickness (FS): 2.3725 0.6124 mm
- Surface intensity / position RMSE: 0.0636 / 0.0615
- Euler number / defect number / defect size: 26.0 / 11.0 / 0.49%
- Display thickness: /var/lib/condor/execute/dir_11697/ds/sub-NC233/surf/lh.thickness.sub-NC233_ses-20190512_acq-highres_run-01_T1w
- Display thickness: /var/lib/condor/execute/dir_11697/ds/sub-NC233/surf/rh.thickness.sub-NC233_ses-20190512_acq-highres_run-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_11697/ds/sub-NC233/sub-NC233_ses-20190512_acq-highres_run-01_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 2059s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 16s
- ROI estimation of 'neuromorphometrics' atlas 59s
- ROI estimation of 'lpba40' atlas 15s
- ROI estimation of 'hammers' atlas 38s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 13s
- ROI estimation of 'aal3' atlas 21s
- ROI estimation of 'mori' atlas 31s
- ROI estimation of 'anatomy3' atlas 46s
- ROI estimation of 'julichbrain' atlas 60s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 22s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 31s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 98s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 159s
- Write results 161s
- 615s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_11697/ds/sub-NC233/report/catreport_sub-NC233_ses-20190512_acq-highres_run-01_T1w.pdf
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- CAT preprocessing takes 63 minute(s) and 27 second(s).
- Image Quality Rating (IQR): 81.53% (B-)
- GM volume (GMV): 46.45% (710.74 / 1530.19 ml)
- GM thickness (GMT): 2.37 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_11697/ds/sub-NC233/mri
- Reports are saved in /var/lib/condor/execute/dir_11697/ds/sub-NC233/report
- Labels are saved in /var/lib/condor/execute/dir_11697/ds/sub-NC233/label
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