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- CAT12.8.1 r2040: 1/1: ./sub-0027248/ses-1/sub-0027248_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 52s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 7s
- Initial correction 7s
- Refine background 4s
- Final correction 5s
- Final scaling 5s
- 42s
- Correct center-of-mass 6s
- Affine registration 11s
- SPM preprocessing 1 (estimate 1 - TPM registration): 86s
- SPM preprocessing 1 (estimate 2): 59s
- SPM preprocessing 2 (write):
- Write Segmentation 20s
- Update Segmentation 22s
- Update Skull-Stripping 48s
- Update probability maps 10s
- 100s
- Global intensity correction: 18s
- SANLM denoising after intensity normalization (medium): 27s
- Fast Optimized Shooting registration 39s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 16s
- Estimate local tissue thresholds (WM) 21s
- Estimate local tissue thresholds (GM) 34s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 50s
- 131s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 16s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.03) 25s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 3s
- Final corrections 5s
- 74s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 37s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.670.08,0.990.05]
- 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 | 0.0867 0.0000 0.0867 | 32.0000
- 2 | 2.50 | 0.0838 0.0012 0.0851 | 29.4886
- 3 | 2.50 | 0.0830 0.0019 0.0848 | 26.9772
- 4 | 2.50 | 0.0825 0.0021 0.0847 | 24.6107
- 5 | 2.50 | 0.0822 0.0023 0.0845 | 22.6548
- 6 | 2.50 | 0.0819 0.0024 0.0843 | 20.6989
- 7 | 2.50 | 0.0816 0.0025 0.0841 | 18.9688
- 8 | 2.50 | 0.0813 0.0026 0.0839 | 17.4455
- 9 | 2.50 | 0.0810 0.0027 0.0836 | 15.9223
- 10 | 2.50 | 0.0806 0.0028 0.0834 | 14.6627
- 11 | 2.50 | 0.0803 0.0029 0.0832 | 13.4764
- 12 | 2.50 | 0.0799 0.0030 0.0829 | 12.3015
- 13 | 2.50 | 0.0796 0.0031 0.0827 | 11.3776
- 14 | 2.50 | 0.0792 0.0032 0.0824 | 10.4537
- 15 | 2.25 | 0.0791 0.0033 0.0824 | 9.5920
- 16 | 2.25 | 0.0760 0.0048 0.0808 | 8.8725
- 17 | 2.25 | 0.0747 0.0054 0.0801 | 8.1530
- 29 | 2.00 | 0.0768 0.0025 0.0792 | 3.3283
- 30 | 2.00 | 0.0710 0.0049 0.0759 | 3.1221
- 31 | 2.00 | 0.0689 0.0059 0.0748 | 2.9160
- 43 | 1.75 | 0.0679 0.0034 0.0712 | 1.5785
- 44 | 1.75 | 0.0634 0.0057 0.0691 | 1.5194
- 45 | 1.75 | 0.0618 0.0065 0.0683 | 1.4626
- 57 | 1.50 | 0.0603 0.0048 0.0651 | 1.0900
- 58 | 1.50 | 0.0571 0.0069 0.0639 | 1.0730
- 59 | 1.50 | 0.0560 0.0075 0.0635 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 205s
- Prepare output 14s
- 219s
- Jacobian determinant (RMS): 0.012 0.045 0.069 0.096 0.122 | 0.129316
- Template Matching: 0.087 0.224 0.207 0.185 0.168 | 0.167918
- Write result maps: 43s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 37s
- CSF distance: 18s
- PBT2x thickness: 54s
- 116s
- Create initial surface 95s
- Topology correction: 88s
- Surface refinement: 100s
- Reduction of surface collisions with optimization: 67s
- Spherical mapping with areal smoothing 97s
- Spherical registration 326s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 34s
- CSF distance: 18s
- PBT2x thickness: 56s
- 115s
- Create initial surface 97s
- Topology correction: 91s
- Surface refinement: 79s
- Reduction of surface collisions with optimization: 67s
- Spherical mapping with areal smoothing 89s
- Spherical registration 334s
- Final surface processing results:
- Average thickness (FS): 2.5155 0.6801 mm
- Surface intensity / position RMSE: 0.0690 / 0.0792
- Euler number / defect number / defect size: 20.0 / 11.5 / 0.68%
- Display thickness: /var/lib/condor/execute/dir_3501056/ds/IBA_TRT/sub-0027248/ses-1/surf/lh.thickness.sub-0027248_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3501056/ds/IBA_TRT/sub-0027248/ses-1/surf/rh.thickness.sub-0027248_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3501056/ds/IBA_TRT/sub-0027248/ses-1/sub-0027248_ses-1_run-1_T1w.nii
- Surface ROI estimation: 13s
- Surface and thickness estimation takes: 1872s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 13s
- ROI estimation of 'neuromorphometrics' atlas 37s
- ROI estimation of 'lpba40' atlas 11s
- ROI estimation of 'hammers' atlas 26s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 11s
- ROI estimation of 'aal3' atlas 20s
- ROI estimation of 'mori' atlas 25s
- ROI estimation of 'anatomy3' atlas 31s
- ROI estimation of 'julichbrain' atlas 45s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 21s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 35s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 70s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 117s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 11s
- Write results 13s
- 478s
- Quality check: 14s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3501056/ds/IBA_TRT/sub-0027248/ses-1/report/catreport_sub-0027248_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 56 minute(s) and 59 second(s).
- Image Quality Rating (IQR): 85.28% (B)
- GM volume (GMV): 49.48% (663.36 / 1340.76 ml)
- GM thickness (GMT): 2.52 0.68 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3501056/ds/IBA_TRT/sub-0027248/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_3501056/ds/IBA_TRT/sub-0027248/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_3501056/ds/IBA_TRT/sub-0027248/ses-1/label
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