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- CAT12.8.1 r2040: 1/1: ./sub-0026138/ses-1/sub-0026138_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 36s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 4s
- Initial correction 4s
- Refine background 2s
- Final correction 3s
- Final scaling 3s
- 26s
- Correct center-of-mass 3s
- Affine registration 6s
- SPM preprocessing 1 (estimate 1 - TPM registration): 53s
- SPM preprocessing 1 (estimate 2): 52s
- SPM preprocessing 2 (write):
- Write Segmentation 12s
- Update Segmentation 14s
- Update Skull-Stripping 31s
- Update probability maps 7s
- 63s
- Global intensity correction: 11s
- SANLM denoising after intensity normalization (medium): 18s
- Fast Optimized Shooting registration 26s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 2s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 10s
- Estimate local tissue thresholds (WM) 12s
- Estimate local tissue thresholds (GM) 18s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 28s
- 75s
- ROI segmentation (partitioning):
- Atlas -> subject space 5s
- Major structures 2s
- Ventricle detection 8s
- Blood vessel detection 6s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.09) 14s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 3s
- 43s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 24s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.990.04]
- 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 | 0.0876 0.0000 0.0876 | 32.0000
- 2 | 2.50 | 0.0844 0.0014 0.0858 | 29.4886
- 3 | 2.50 | 0.0834 0.0021 0.0855 | 26.9772
- 4 | 2.50 | 0.0829 0.0024 0.0853 | 24.6107
- 5 | 2.50 | 0.0826 0.0026 0.0851 | 22.6548
- 6 | 2.50 | 0.0822 0.0027 0.0849 | 20.6989
- 7 | 2.50 | 0.0819 0.0028 0.0847 | 18.9688
- 8 | 2.50 | 0.0815 0.0030 0.0844 | 17.4455
- 9 | 2.50 | 0.0811 0.0031 0.0842 | 15.9223
- 10 | 2.50 | 0.0807 0.0032 0.0839 | 14.6627
- 11 | 2.50 | 0.0803 0.0033 0.0836 | 13.4764
- 12 | 2.50 | 0.0799 0.0034 0.0833 | 12.3015
- 13 | 2.50 | 0.0795 0.0036 0.0830 | 11.3776
- 14 | 2.50 | 0.0790 0.0036 0.0827 | 10.4537
- 15 | 2.25 | 0.0788 0.0038 0.0826 | 9.5920
- 16 | 2.25 | 0.0756 0.0053 0.0809 | 8.8725
- 17 | 2.25 | 0.0742 0.0059 0.0801 | 8.1530
- 29 | 2.00 | 0.0756 0.0027 0.0784 | 3.3283
- 30 | 2.00 | 0.0697 0.0052 0.0749 | 3.1221
- 31 | 2.00 | 0.0676 0.0062 0.0738 | 2.9160
- 43 | 1.75 | 0.0664 0.0036 0.0700 | 1.5785
- 44 | 1.75 | 0.0622 0.0058 0.0680 | 1.5194
- 45 | 1.75 | 0.0607 0.0067 0.0674 | 1.4626
- 57 | 1.50 | 0.0592 0.0049 0.0641 | 1.0900
- 58 | 1.50 | 0.0560 0.0069 0.0630 | 1.0730
- 59 | 1.50 | 0.0550 0.0076 0.0626 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 135s
- Prepare output 7s
- 143s
- Jacobian determinant (RMS): 0.013 0.049 0.074 0.099 0.123 | 0.130885
- Template Matching: 0.088 0.223 0.203 0.182 0.165 | 0.164868
- Write result maps: 29s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 18s
- CSF distance: 10s
- PBT2x thickness: 28s
- 61s
- Create initial surface 51s
- Topology correction: 54s
- Surface refinement: 66s
- Reduction of surface collisions with optimization: 40s
- Spherical mapping with areal smoothing 64s
- Spherical registration 204s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 17s
- CSF distance: 9s
- PBT2x thickness: 28s
- 59s
- Create initial surface 50s
- Topology correction: 53s
- Surface refinement: 63s
- Reduction of surface collisions with optimization: 43s
- Spherical mapping with areal smoothing 75s
- Spherical registration 236s
- Final surface processing results:
- Average thickness (FS): 2.4302 0.6153 mm
- Surface intensity / position RMSE: 0.0637 / 0.0605
- Euler number / defect number / defect size: 6.0 / 5.5 / 0.06%
- Display thickness: /var/lib/condor/execute/dir_3618454/ds/UM/sub-0026138/ses-1/surf/lh.thickness.sub-0026138_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3618454/ds/UM/sub-0026138/ses-1/surf/rh.thickness.sub-0026138_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3618454/ds/UM/sub-0026138/ses-1/sub-0026138_ses-1_run-1_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1186s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 32s
- ROI estimation of 'lpba40' atlas 9s
- ROI estimation of 'hammers' atlas 22s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 9s
- ROI estimation of 'aal3' atlas 14s
- ROI estimation of 'mori' atlas 20s
- ROI estimation of 'anatomy3' atlas 31s
- ROI estimation of 'julichbrain' atlas 50s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 20s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 38s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 77s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 107s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s
- Write results 9s
- 449s
- Quality check: 9s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3618454/ds/UM/sub-0026138/ses-1/report/catreport_sub-0026138_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 39 minute(s) and 5 second(s).
- Image Quality Rating (IQR): 79.14% (C+)
- GM volume (GMV): 45.66% (587.46 / 1286.62 ml)
- GM thickness (GMT): 2.43 0.62 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3618454/ds/UM/sub-0026138/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_3618454/ds/UM/sub-0026138/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_3618454/ds/UM/sub-0026138/ses-1/label
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