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- CAT12.8.1 r2040: 1/1: ./sub-0025966/ses-2/sub-0025966_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 54s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 6s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 38s
- Correct center-of-mass 4s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 95s
- SPM preprocessing 1 (estimate 2): 57s
- SPM preprocessing 2 (write):
- Write Segmentation 18s
- Update Segmentation 21s
- Update Skull-Stripping 44s
- Update probability maps 9s
- 91s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 34s
- Fast Optimized Shooting registration 33s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.09) 16s
- Estimate local tissue thresholds (WM) 19s
- Estimate local tissue thresholds (GM) 27s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 42s
- 114s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 16s
- Blood vessel detection 10s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.12) 27s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 4s
- 76s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 38s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.04]
- 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 | 0.0852 0.0000 0.0852 | 32.0000
- 2 | 2.50 | 0.0826 0.0012 0.0838 | 29.4886
- 3 | 2.50 | 0.0819 0.0017 0.0836 | 26.9772
- 4 | 2.50 | 0.0815 0.0020 0.0835 | 24.6107
- 5 | 2.50 | 0.0812 0.0021 0.0833 | 22.6548
- 6 | 2.50 | 0.0810 0.0022 0.0832 | 20.6989
- 7 | 2.50 | 0.0807 0.0023 0.0830 | 18.9688
- 8 | 2.50 | 0.0804 0.0024 0.0828 | 17.4455
- 9 | 2.50 | 0.0801 0.0025 0.0826 | 15.9223
- 10 | 2.50 | 0.0798 0.0026 0.0824 | 14.6627
- 11 | 2.50 | 0.0795 0.0027 0.0822 | 13.4764
- 12 | 2.50 | 0.0792 0.0028 0.0819 | 12.3015
- 13 | 2.50 | 0.0788 0.0029 0.0817 | 11.3776
- 14 | 2.50 | 0.0785 0.0029 0.0815 | 10.4537
- 15 | 2.25 | 0.0779 0.0030 0.0809 | 9.5920
- 16 | 2.25 | 0.0749 0.0045 0.0794 | 8.8725
- 29 | 2.00 | 0.0762 0.0020 0.0782 | 3.3283
- 30 | 2.00 | 0.0697 0.0046 0.0743 | 3.1221
- 31 | 2.00 | 0.0675 0.0057 0.0732 | 2.9160
- 43 | 1.75 | 0.0664 0.0033 0.0697 | 1.5785
- 44 | 1.75 | 0.0618 0.0057 0.0675 | 1.5194
- 45 | 1.75 | 0.0603 0.0065 0.0668 | 1.4626
- 57 | 1.50 | 0.0587 0.0047 0.0634 | 1.0900
- 58 | 1.50 | 0.0554 0.0069 0.0622 | 1.0730
- 59 | 1.50 | 0.0543 0.0075 0.0618 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 181s
- Prepare output 11s
- 192s
- Jacobian determinant (RMS): 0.011 0.039 0.060 0.086 0.110 | 0.117239
- Template Matching: 0.085 0.225 0.202 0.181 0.163 | 0.162924
- Write result maps: 35s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 44s
- CSF distance: 17s
- PBT2x thickness: 50s
- 118s
- Create initial surface 101s
- Topology correction: 108s
- Surface refinement: 119s
- Reduction of surface collisions with optimization: 84s
- Spherical mapping with areal smoothing 89s
- Spherical registration 320s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 32s
- CSF distance: 17s
- PBT2x thickness: 49s
- 106s
- Create initial surface 100s
- Topology correction: 107s
- Surface refinement: 96s
- Reduction of surface collisions with optimization: 86s
- Spherical mapping with areal smoothing 103s
- Spherical registration 338s
- Final surface processing results:
- Average thickness (FS): 2.5293 0.6602 mm
- Surface intensity / position RMSE: 0.0676 / 0.0904
- Euler number / defect number / defect size: 26.0 / 10.5 / 1.53%
- Display thickness: /var/lib/condor/execute/dir_2997796/ds/BNU_2/sub-0025966/ses-2/surf/lh.thickness.sub-0025966_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2997796/ds/BNU_2/sub-0025966/ses-2/surf/rh.thickness.sub-0025966_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2997796/ds/BNU_2/sub-0025966/ses-2/sub-0025966_ses-2_run-1_T1w.nii
- Surface ROI estimation: 13s
- Surface and thickness estimation takes: 1987s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 15s
- ROI estimation of 'neuromorphometrics' atlas 50s
- ROI estimation of 'lpba40' atlas 14s
- ROI estimation of 'hammers' atlas 34s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 12s
- ROI estimation of 'aal3' atlas 21s
- ROI estimation of 'mori' atlas 29s
- ROI estimation of 'anatomy3' atlas 41s
- ROI estimation of 'julichbrain' atlas 48s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 19s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 35s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 67s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 90s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s
- Write results 9s
- 487s
- Quality check: 13s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2997796/ds/BNU_2/sub-0025966/ses-2/report/catreport_sub-0025966_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 57 minute(s) and 48 second(s).
- Image Quality Rating (IQR): 83.94% (B)
- GM volume (GMV): 45.66% (786.51 / 1722.43 ml)
- GM thickness (GMT): 2.53 0.66 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2997796/ds/BNU_2/sub-0025966/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_2997796/ds/BNU_2/sub-0025966/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_2997796/ds/BNU_2/sub-0025966/ses-2/label
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