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- CAT12.8.1 r2040: 1/1: ./sub-0027241/ses-2/sub-0027241_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 64s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 7s
- Initial correction 7s
- Refine background 3s
- Final correction 5s
- Final scaling 6s
- 43s
- Correct center-of-mass 5s
- Affine registration 11s
- SPM preprocessing 1 (estimate 1 - TPM registration): 84s
- SPM preprocessing 1 (estimate 2): 82s
- SPM preprocessing 2 (write):
- Write Segmentation 21s
- Update Segmentation 24s
- Update Skull-Stripping 51s
- Update probability maps 10s
- 106s
- Global intensity correction: 19s
- SANLM denoising after intensity normalization (medium): 34s
- Fast Optimized Shooting registration 43s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.00) 18s
- Estimate local tissue thresholds (WM) 24s
- Estimate local tissue thresholds (GM) 38s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 53s
- 144s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 4s
- Ventricle detection 22s
- Blood vessel detection 13s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.01) 30s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 90s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 45s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.670.08,0.990.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 6s
- Level 1 cleanup (brain masking) 4s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 4s
- 15s
- 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 | 0.0844 0.0000 0.0844 | 32.0000
- 2 | 2.50 | 0.0818 0.0012 0.0830 | 29.4886
- 3 | 2.50 | 0.0811 0.0018 0.0828 | 26.9772
- 4 | 2.50 | 0.0807 0.0020 0.0827 | 24.6107
- 5 | 2.50 | 0.0804 0.0021 0.0825 | 22.6548
- 6 | 2.50 | 0.0802 0.0022 0.0824 | 20.6989
- 7 | 2.50 | 0.0799 0.0023 0.0822 | 18.9688
- 8 | 2.50 | 0.0796 0.0024 0.0820 | 17.4455
- 9 | 2.50 | 0.0793 0.0025 0.0818 | 15.9223
- 10 | 2.50 | 0.0790 0.0026 0.0816 | 14.6627
- 11 | 2.50 | 0.0788 0.0026 0.0814 | 13.4764
- 12 | 2.50 | 0.0785 0.0027 0.0812 | 12.3015
- 13 | 2.50 | 0.0781 0.0028 0.0809 | 11.3776
- 14 | 2.50 | 0.0779 0.0028 0.0807 | 10.4537
- 15 | 2.25 | 0.0771 0.0029 0.0800 | 9.5920
- 16 | 2.25 | 0.0744 0.0043 0.0786 | 8.8725
- 29 | 2.00 | 0.0758 0.0019 0.0777 | 3.3283
- 30 | 2.00 | 0.0699 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 | 0.0613 0.0060 0.0673 | 1.4626
- 57 | 1.50 | 0.0599 0.0043 0.0642 | 1.0900
- 58 | 1.50 | 0.0568 0.0064 0.0631 | 1.0730
- 59 | 1.50 | 0.0557 0.0070 0.0627 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 202s
- Prepare output 14s
- 216s
- Jacobian determinant (RMS): 0.011 0.040 0.058 0.081 0.103 | 0.109407
- Template Matching: 0.084 0.223 0.204 0.184 0.167 | 0.167147
- Write result maps: 41s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 48s
- CSF distance: 21s
- PBT2x thickness: 62s
- 139s
- Create initial surface 108s
- Topology correction: 122s
- Surface refinement: 96s
- Reduction of surface collisions with optimization: 88s
- Spherical mapping with areal smoothing 111s
- Spherical registration 334s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 42s
- CSF distance: 20s
- PBT2x thickness: 60s
- 129s
- Create initial surface 103s
- Topology correction: 119s
- Surface refinement: 104s
- Reduction of surface collisions with optimization: 87s
- Spherical mapping with areal smoothing 112s
- Spherical registration 342s
- Final surface processing results:
- Average thickness (FS): 2.3870 0.6468 mm
- Surface intensity / position RMSE: 0.0690 / 0.0849
- Euler number / defect number / defect size: 22.0 / 12.5 / 1.00%
- Display thickness: /var/lib/condor/execute/dir_3344799/ds/IBA_TRT/sub-0027241/ses-2/surf/lh.thickness.sub-0027241_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3344799/ds/IBA_TRT/sub-0027241/ses-2/surf/rh.thickness.sub-0027241_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3344799/ds/IBA_TRT/sub-0027241/ses-2/sub-0027241_ses-2_run-1_T1w.nii
- Surface ROI estimation: 11s
- Surface and thickness estimation takes: 2114s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 10s
- ROI estimation of 'neuromorphometrics' atlas 39s
- ROI estimation of 'lpba40' atlas 11s
- ROI estimation of 'hammers' atlas 27s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 10s
- ROI estimation of 'aal3' atlas 15s
- ROI estimation of 'mori' atlas 23s
- ROI estimation of 'anatomy3' atlas 33s
- ROI estimation of 'julichbrain' atlas 42s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 29s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 69s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 107s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 10s
- Write results 11s
- 446s
- Quality check: 16s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3344799/ds/IBA_TRT/sub-0027241/ses-2/report/catreport_sub-0027241_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 61 minute(s) and 56 second(s).
- Image Quality Rating (IQR): 82.83% (B-)
- GM volume (GMV): 47.84% (739.56 / 1545.79 ml)
- GM thickness (GMT): 2.39 0.65 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3344799/ds/IBA_TRT/sub-0027241/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_3344799/ds/IBA_TRT/sub-0027241/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_3344799/ds/IBA_TRT/sub-0027241/ses-2/label
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