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- CAT12.8.1 r2040: 1/1: ./sub-0025955/ses-1/sub-0025955_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 36s
- Internal resampling (1.33x1.00x1.00mm > 1.00x1.00x1.00mm): 1s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 6s
- Initial correction 6s
- Refine background 3s
- Final correction 4s
- Final scaling 5s
- 36s
- Correct center-of-mass 4s
- Affine registration 9s
- SPM preprocessing 1 (estimate 1 - TPM registration): 73s
- SPM preprocessing 1 (estimate 2): 71s
- SPM preprocessing 2 (write):
- Write Segmentation 16s
- Update Segmentation 18s
- Update Skull-Stripping 41s
- Update probability maps 8s
- 84s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 28s
- Fast Optimized Shooting registration 31s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 14s
- Estimate local tissue thresholds (WM) 17s
- Estimate local tissue thresholds (GM) 27s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 38s
- 105s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 4s
- Ventricle detection 13s
- Blood vessel detection 9s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.01) 23s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 3s
- Final corrections 4s
- 65s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 32s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.670.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 3s
- 11s
- 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 | 0.0854 0.0000 0.0854 | 32.0000
- 2 | 2.50 | 0.0825 0.0012 0.0837 | 29.4886
- 3 | 2.50 | 0.0816 0.0019 0.0835 | 26.9772
- 4 | 2.50 | 0.0811 0.0022 0.0833 | 24.6107
- 5 | 2.50 | 0.0808 0.0024 0.0831 | 22.6548
- 6 | 2.50 | 0.0805 0.0025 0.0829 | 20.6989
- 7 | 2.50 | 0.0801 0.0026 0.0827 | 18.9688
- 8 | 2.50 | 0.0798 0.0027 0.0825 | 17.4455
- 9 | 2.50 | 0.0795 0.0028 0.0823 | 15.9223
- 10 | 2.50 | 0.0791 0.0030 0.0820 | 14.6627
- 11 | 2.50 | 0.0787 0.0031 0.0818 | 13.4764
- 12 | 2.50 | 0.0784 0.0031 0.0815 | 12.3015
- 13 | 2.50 | 0.0780 0.0033 0.0812 | 11.3776
- 14 | 2.50 | 0.0776 0.0033 0.0810 | 10.4537
- 15 | 2.25 | 0.0776 0.0034 0.0810 | 9.5920
- 16 | 2.25 | 0.0744 0.0050 0.0795 | 8.8725
- 29 | 2.00 | 0.0758 0.0023 0.0781 | 3.3283
- 30 | 2.00 | 0.0694 0.0049 0.0742 | 3.1221
- 31 | 2.00 | 0.0671 0.0059 0.0730 | 2.9160
- 43 | 1.75 | 0.0661 0.0034 0.0695 | 1.5785
- 44 | 1.75 | 0.0617 0.0058 0.0674 | 1.5194
- 45 | 1.75 | 0.0602 0.0066 0.0668 | 1.4626
- 57 | 1.50 | 0.0588 0.0048 0.0636 | 1.0900
- 58 | 1.50 | 0.0556 0.0069 0.0625 | 1.0730
- 59 | 1.50 | 0.0545 0.0075 0.0621 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 169s
- Prepare output 10s
- 179s
- Jacobian determinant (RMS): 0.012 0.046 0.069 0.098 0.124 | 0.130830
- Template Matching: 0.085 0.223 0.201 0.181 0.164 | 0.163567
- Write result maps: 55s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 28s
- CSF distance: 15s
- PBT2x thickness: 46s
- 96s
- Create initial surface 87s
- Topology correction: 98s
- Surface refinement: 85s
- Reduction of surface collisions with optimization: 73s
- Spherical mapping with areal smoothing 83s
- Spherical registration 294s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 28s
- CSF distance: 15s
- PBT2x thickness: 45s
- 93s
- Create initial surface 83s
- Topology correction: 99s
- Surface refinement: 82s
- Reduction of surface collisions with optimization: 75s
- Spherical mapping with areal smoothing 84s
- Spherical registration 301s
- Final surface processing results:
- Average thickness (FS): 2.5218 0.5981 mm
- Surface intensity / position RMSE: 0.0688 / 0.0706
- Euler number / defect number / defect size: 22.0 / 12.0 / 0.65%
- Display thickness: /var/lib/condor/execute/dir_565640/ds/BNU_2/sub-0025955/ses-1/surf/lh.thickness.sub-0025955_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_565640/ds/BNU_2/sub-0025955/ses-1/surf/rh.thickness.sub-0025955_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_565640/ds/BNU_2/sub-0025955/ses-1/sub-0025955_ses-1_run-1_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 1731s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 8s
- ROI estimation of 'neuromorphometrics' atlas 29s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 20s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 12s
- ROI estimation of 'mori' atlas 19s
- ROI estimation of 'anatomy3' atlas 28s
- ROI estimation of 'julichbrain' atlas 43s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 18s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 32s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 70s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 106s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 9s
- Write results 11s
- 413s
- Quality check: 12s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_565640/ds/BNU_2/sub-0025955/ses-1/report/catreport_sub-0025955_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 51 minute(s) and 21 second(s).
- Image Quality Rating (IQR): 80.85% (B-)
- GM volume (GMV): 51.92% (745.36 / 1435.49 ml)
- GM thickness (GMT): 2.52 0.60 mm
- Segmentations are saved in /var/lib/condor/execute/dir_565640/ds/BNU_2/sub-0025955/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_565640/ds/BNU_2/sub-0025955/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_565640/ds/BNU_2/sub-0025955/ses-1/label
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