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- CAT12.8.1 r1980: 1/1: ./execute/dir_29033/ds/sub-OXF10/sub-OXF10_T1w.n
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- SANLM denoising (medium): 48s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 6s
- Initial correction 5s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 32s
- Correct center-of-mass 4s
- Affine registration 8s
- SPM preprocessing 1 (estimate 1 - TPM registration): 78s
- SPM preprocessing 1 (estimate 2): 84s
- SPM preprocessing 2 (write):
- Write Segmentation 14s
- Update Segmentation 20s
- Update Skull-Stripping 35s
- Update probability maps 6s
- 75s
- Global intensity correction: 12s
- SANLM denoising after intensity normalization (medium): 27s
- Fast Optimized Shooting registration 39s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.04) 17s
- Estimate local tissue thresholds (WM) 15s
- Estimate local tissue thresholds (GM) 23s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 28s
- 93s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 18s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.02) 29s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 5s
- Final corrections 3s
- 80s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 50s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- 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 | 0.0851 0.0000 0.0851 | 32.0000
- 2 | 2.50 | 0.0822 0.0012 0.0834 | 29.4886
- 3 | 2.50 | 0.0813 0.0019 0.0832 | 26.9772
- 4 | 2.50 | 0.0808 0.0022 0.0830 | 24.6107
- 5 | 2.50 | 0.0805 0.0023 0.0828 | 22.6548
- 6 | 2.50 | 0.0802 0.0024 0.0826 | 20.6989
- 7 | 2.50 | 0.0799 0.0025 0.0824 | 18.9688
- 8 | 2.50 | 0.0795 0.0026 0.0821 | 17.4455
- 9 | 2.50 | 0.0792 0.0027 0.0819 | 15.9223
- 10 | 2.50 | 0.0788 0.0028 0.0816 | 14.6627
- 11 | 2.50 | 0.0785 0.0029 0.0814 | 13.4764
- 12 | 2.50 | 0.0782 0.0029 0.0811 | 12.3015
- 13 | 2.50 | 0.0778 0.0031 0.0808 | 11.3776
- 14 | 2.50 | 0.0775 0.0031 0.0806 | 10.4537
- 15 | 2.25 | 0.0776 0.0032 0.0808 | 9.5920
- 16 | 2.25 | 0.0745 0.0048 0.0792 | 8.8725
- 29 | 2.00 | 0.0762 0.0022 0.0784 | 3.3283
- 30 | 2.00 | 0.0698 0.0047 0.0746 | 3.1221
- 31 | 2.00 | 0.0677 0.0058 0.0735 | 2.9160
- 43 | 1.75 | 0.0670 0.0033 0.0703 | 1.5785
- 44 | 1.75 | 0.0624 0.0057 0.0681 | 1.5194
- 45 | 1.75 | 0.0608 0.0066 0.0674 | 1.4626
- 57 | 1.50 | 0.0596 0.0048 0.0645 | 1.0900
- 58 | 1.50 | 0.0563 0.0070 0.0633 | 1.0730
- 59 | 1.50 | 0.0551 0.0078 0.0629 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 229s
- Prepare output 10s
- 238s
- Jacobian determinant (RMS): 0.010 0.037 0.056 0.080 0.106 | 0.114084
- Template Matching: 0.085 0.223 0.203 0.182 0.165 | 0.165273
- Write result maps: 22s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 49s
- CSF distance: 20s
- PBT2x thickness: 60s
- 138s
- Create initial surface 111s
- Topology correction: 123s
- Surface refinement: 106s
- Reduction of surface collisions with optimization: 99s
- Spherical mapping with areal smoothing 109s
- Spherical registration 269s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 53s
- CSF distance: 20s
- PBT2x thickness: 59s
- 140s
- Create initial surface 107s
- Topology correction: 120s
- Surface refinement: 107s
- Reduction of surface collisions with optimization: 96s
- Spherical mapping with areal smoothing 104s
- Spherical registration 262s
- Final surface processing results:
- Average thickness (FS): 2.4651 0.5866 mm
- Surface intensity / position RMSE: 0.0649 / 0.0639
- Euler number / defect number / defect size: 12.0 / 6.5 / 0.70%
- Display thickness: /var/lib/condor/execute/dir_29033/ds/sub-OXF10/surf/lh.thickness.sub-OXF10_T1w
- Display thickness: /var/lib/condor/execute/dir_29033/ds/sub-OXF10/surf/rh.thickness.sub-OXF10_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_29033/ds/sub-OXF10/sub-OXF10_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1987s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 8s
- ROI estimation of 'neuromorphometrics' atlas 29s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 20s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 12s
- ROI estimation of 'mori' atlas 18s
- ROI estimation of 'anatomy3' atlas 25s
- ROI estimation of 'julichbrain' atlas 33s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 16s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 54s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 80s
- Write results 82s
- 327s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_29033/ds/sub-OXF10/report/catreport_sub-OXF10_T1w.pdf
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- CAT preprocessing takes 55 minute(s) and 27 second(s).
- Image Quality Rating (IQR): 86.07% (B)
- GM volume (GMV): 47.05% (720.82 / 1532.02 ml)
- GM thickness (GMT): 2.46 0.59 mm
- Segmentations are saved in /var/lib/condor/execute/dir_29033/ds/sub-OXF10/mri
- Reports are saved in /var/lib/condor/execute/dir_29033/ds/sub-OXF10/report
- Labels are saved in /var/lib/condor/execute/dir_29033/ds/sub-OXF10/label
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