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- CAT12.8.1 r2040: 1/1: ./sub-0027238/ses-1/sub-0027238_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 54s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 8s
- Initial correction 7s
- Refine background 4s
- Final correction 5s
- Final scaling 6s
- 46s
- Correct center-of-mass 7s
- Affine registration 12s
- SPM preprocessing 1 (estimate 1 - TPM registration): 88s
- SPM preprocessing 1 (estimate 2): 94s
- SPM preprocessing 2 (write):
- Write Segmentation 21s
- Update Segmentation 23s
- Update Skull-Stripping 50s
- Update probability maps 10s
- 104s
- Global intensity correction: 19s
- SANLM denoising after intensity normalization (medium): 28s
- Fast Optimized Shooting registration 40s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 16s
- Estimate local tissue thresholds (WM) 22s
- Estimate local tissue thresholds (GM) 35s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 50s
- 133s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 19s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.12) 25s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 78s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 40s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.670.08,0.980.04]
- 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 | 0.0860 0.0000 0.0860 | 32.0000
- 2 | 2.50 | 0.0832 0.0012 0.0844 | 29.4886
- 3 | 2.50 | 0.0824 0.0018 0.0843 | 26.9772
- 4 | 2.50 | 0.0820 0.0020 0.0841 | 24.6107
- 5 | 2.50 | 0.0817 0.0022 0.0839 | 22.6548
- 6 | 2.50 | 0.0815 0.0023 0.0837 | 20.6989
- 7 | 2.50 | 0.0812 0.0024 0.0836 | 18.9688
- 8 | 2.50 | 0.0809 0.0025 0.0834 | 17.4455
- 9 | 2.50 | 0.0806 0.0025 0.0831 | 15.9223
- 10 | 2.50 | 0.0803 0.0026 0.0829 | 14.6627
- 11 | 2.50 | 0.0800 0.0027 0.0827 | 13.4764
- 12 | 2.50 | 0.0797 0.0028 0.0824 | 12.3015
- 13 | 2.50 | 0.0793 0.0029 0.0822 | 11.3776
- 14 | 2.50 | 0.0790 0.0029 0.0820 | 10.4537
- 15 | 2.25 | 0.0785 0.0030 0.0815 | 9.5920
- 16 | 2.25 | 0.0757 0.0044 0.0801 | 8.8725
- 17 | 2.25 | 0.0745 0.0049 0.0794 | 8.1530
- 29 | 2.00 | 0.0765 0.0022 0.0788 | 3.3283
- 30 | 2.00 | 0.0708 0.0046 0.0755 | 3.1221
- 31 | 2.00 | 0.0689 0.0056 0.0745 | 2.9160
- 43 | 1.75 | 0.0680 0.0032 0.0712 | 1.5785
- 44 | 1.75 | 0.0635 0.0056 0.0691 | 1.5194
- 45 | 1.75 | 0.0620 0.0064 0.0684 | 1.4626
- 57 | 1.50 | 0.0606 0.0046 0.0652 | 1.0900
- 58 | 1.50 | 0.0573 0.0068 0.0642 | 1.0730
- 59 | 1.50 | 0.0562 0.0075 0.0637 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 209s
- Prepare output 14s
- 223s
- Jacobian determinant (RMS): 0.011 0.040 0.060 0.084 0.109 | 0.115429
- Template Matching: 0.086 0.224 0.207 0.186 0.169 | 0.168727
- Write result maps: 45s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 51s
- CSF distance: 20s
- PBT2x thickness: 56s
- 134s
- Create initial surface 99s
- Topology correction: 110s
- Surface refinement: 89s
- Reduction of surface collisions with optimization: 74s
- Spherical mapping with areal smoothing 97s
- Spherical registration 344s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 37s
- CSF distance: 19s
- PBT2x thickness: 55s
- 117s
- Create initial surface 96s
- Topology correction: 115s
- Surface refinement: 91s
- Reduction of surface collisions with optimization: 75s
- Spherical mapping with areal smoothing 99s
- Spherical registration 320s
- Final surface processing results:
- Average thickness (FS): 2.3977 0.6173 mm
- Surface intensity / position RMSE: 0.0672 / 0.0872
- Euler number / defect number / defect size: 18.0 / 16.0 / 0.48%
- Display thickness: /var/lib/condor/execute/dir_138838/ds/IBA_TRT/sub-0027238/ses-1/surf/lh.thickness.sub-0027238_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_138838/ds/IBA_TRT/sub-0027238/ses-1/surf/rh.thickness.sub-0027238_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_138838/ds/IBA_TRT/sub-0027238/ses-1/sub-0027238_ses-1_run-1_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 1969s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 10s
- ROI estimation of 'neuromorphometrics' atlas 37s
- ROI estimation of 'lpba40' atlas 11s
- ROI estimation of 'hammers' atlas 26s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 9s
- ROI estimation of 'aal3' atlas 16s
- ROI estimation of 'mori' atlas 23s
- ROI estimation of 'anatomy3' atlas 34s
- ROI estimation of 'julichbrain' atlas 43s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 31s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 76s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 128s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 11s
- Write results 13s
- 477s
- Quality check: 17s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_138838/ds/IBA_TRT/sub-0027238/ses-1/report/catreport_sub-0027238_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 60 minute(s) and 15 second(s).
- Image Quality Rating (IQR): 85.66% (B)
- GM volume (GMV): 47.53% (676.87 / 1424.07 ml)
- GM thickness (GMT): 2.40 0.62 mm
- Segmentations are saved in /var/lib/condor/execute/dir_138838/ds/IBA_TRT/sub-0027238/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_138838/ds/IBA_TRT/sub-0027238/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_138838/ds/IBA_TRT/sub-0027238/ses-1/label
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