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- CAT12.8.1 r2040: 1/1: ./sub-0025892/ses-1/sub-0025892_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 31s
- Internal resampling (1.33x1.00x1.00mm > 1.00x1.00x1.00mm): 1s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 6s
- Initial correction 5s
- 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): 8s
- Use initial fine affine registration. 71s
- SPM preprocessing 1 (estimate 2): 77s
- SPM preprocessing 2 (write):
- Write Segmentation 18s
- Update Segmentation 18s
- Update Skull-Stripping 43s
- Update probability maps 10s
- 88s
- Global intensity correction: 18s
- SANLM denoising after intensity normalization (medium): 25s
- Fast Optimized Shooting registration 32s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 4s
- Prepare segments (LASmod = 1.03) 13s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 25s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 39s
- 106s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 14s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 21s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 5s
- 62s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 31s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 3s
- 10s
- 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 | 0.0832 0.0000 0.0832 | 32.0000
- 2 | 2.50 | 0.0804 0.0013 0.0816 | 29.4886
- 3 | 2.50 | 0.0795 0.0019 0.0814 | 26.9772
- 4 | 2.50 | 0.0791 0.0022 0.0812 | 24.6107
- 5 | 2.50 | 0.0787 0.0024 0.0811 | 22.6548
- 6 | 2.50 | 0.0784 0.0025 0.0809 | 20.6989
- 7 | 2.50 | 0.0781 0.0026 0.0807 | 18.9688
- 8 | 2.50 | 0.0778 0.0027 0.0805 | 17.4455
- 9 | 2.50 | 0.0774 0.0028 0.0802 | 15.9223
- 10 | 2.50 | 0.0771 0.0029 0.0800 | 14.6627
- 11 | 2.50 | 0.0767 0.0030 0.0798 | 13.4764
- 12 | 2.50 | 0.0764 0.0031 0.0795 | 12.3015
- 13 | 2.50 | 0.0760 0.0032 0.0792 | 11.3776
- 14 | 2.50 | 0.0757 0.0033 0.0789 | 10.4537
- 15 | 2.25 | 0.0752 0.0034 0.0786 | 9.5920
- 16 | 2.25 | 0.0720 0.0049 0.0770 | 8.8725
- 29 | 2.00 | 0.0732 0.0022 0.0754 | 3.3283
- 30 | 2.00 | 0.0668 0.0048 0.0716 | 3.1221
- 31 | 2.00 | 0.0646 0.0058 0.0704 | 2.9160
- 43 | 1.75 | 0.0634 0.0034 0.0668 | 1.5785
- 44 | 1.75 | 0.0591 0.0056 0.0647 | 1.5194
- 45 | 1.75 | 0.0576 0.0064 0.0640 | 1.4626
- 57 | 1.50 | 0.0561 0.0047 0.0608 | 1.0900
- 58 | 1.50 | 0.0530 0.0067 0.0597 | 1.0730
- 59 | 1.50 | 0.0520 0.0073 0.0593 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 169s
- Prepare output 10s
- 179s
- Jacobian determinant (RMS): 0.012 0.043 0.063 0.086 0.108 | 0.115120
- Template Matching: 0.083 0.216 0.194 0.173 0.156 | 0.155992
- Write result maps: 68s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 27s
- CSF distance: 13s
- PBT2x thickness: 39s
- 86s
- Create initial surface 78s
- Topology correction: 85s
- Surface refinement: 72s
- Reduction of surface collisions with optimization: 61s
- Spherical mapping with areal smoothing 75s
- Spherical registration 288s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 35s
- CSF distance: 12s
- PBT2x thickness: 37s
- 90s
- Create initial surface 77s
- Topology correction: 87s
- Surface refinement: 75s
- Reduction of surface collisions with optimization: 57s
- Spherical mapping with areal smoothing 70s
- Spherical registration 288s
- Final surface processing results:
- Average thickness (FS): 2.5064 0.6116 mm
- Surface intensity / position RMSE: 0.0663 / 0.0658
- Euler number / defect number / defect size: 10.0 / 10.0 / 0.33%
- Display thickness: /var/lib/condor/execute/dir_4190102/ds/BNU_1/sub-0025892/ses-1/surf/lh.thickness.sub-0025892_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_4190102/ds/BNU_1/sub-0025892/ses-1/surf/rh.thickness.sub-0025892_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_4190102/ds/BNU_1/sub-0025892/ses-1/sub-0025892_ses-1_run-1_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1585s
- 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 21s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 13s
- ROI estimation of 'mori' atlas 19s
- ROI estimation of 'anatomy3' atlas 27s
- ROI estimation of 'julichbrain' atlas 37s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 16s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 30s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 72s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 152s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 14s
- Write results 16s
- 457s
- Quality check: 14s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_4190102/ds/BNU_1/sub-0025892/ses-1/report/catreport_sub-0025892_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 50 minute(s) and 11 second(s).
- Image Quality Rating (IQR): 82.43% (B-)
- GM volume (GMV): 49.81% (638.49 / 1281.73 ml)
- GM thickness (GMT): 2.51 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_4190102/ds/BNU_1/sub-0025892/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_4190102/ds/BNU_1/sub-0025892/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_4190102/ds/BNU_1/sub-0025892/ses-1/label
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