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- CAT12.8.1 r2040: 1/1: ./sub-0025953/ses-1/sub-0025953_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 24s
- Internal resampling (1.33x1.00x1.00mm > 1.00x1.00x1.00mm): 1s
- APP: Rough bias correction:
- Initialize 4s
- Estimate background 4s
- Initial correction 4s
- Refine background 2s
- Final correction 3s
- Final scaling 3s
- 23s
- Correct center-of-mass 2s
- Affine registration 6s
- SPM preprocessing 1 (estimate 1 - TPM registration): 51s
- SPM preprocessing 1 (estimate 2): 49s
- SPM preprocessing 2 (write):
- Write Segmentation 12s
- Update Segmentation 13s
- Update Skull-Stripping 27s
- Update probability maps 6s
- 58s
- Global intensity correction: 10s
- SANLM denoising after intensity normalization (medium): 20s
- Fast Optimized Shooting registration 22s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 2s
- Prepare partitions 1s
- Prepare segments (LASmod = 1.08) 10s
- Estimate local tissue thresholds (WM) 12s
- Estimate local tissue thresholds (GM) 18s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 27s
- 72s
- ROI segmentation (partitioning):
- Atlas -> subject space 5s
- Major structures 2s
- Ventricle detection 8s
- Blood vessel detection 6s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 14s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 3s
- 42s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 23s
- AMAP peaks: [CSF,GM,WM] = [0.370.05,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 3s
- Level 1 cleanup (brain masking) 2s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 7s
- 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 | 0.0824 0.0000 0.0824 | 32.0000
- 2 | 2.50 | 0.0797 0.0012 0.0809 | 29.4886
- 3 | 2.50 | 0.0790 0.0018 0.0808 | 26.9772
- 4 | 2.50 | 0.0786 0.0020 0.0806 | 24.6107
- 5 | 2.50 | 0.0783 0.0022 0.0805 | 22.6548
- 6 | 2.50 | 0.0781 0.0022 0.0803 | 20.6989
- 7 | 2.50 | 0.0778 0.0023 0.0801 | 18.9688
- 8 | 2.50 | 0.0775 0.0024 0.0799 | 17.4455
- 9 | 2.50 | 0.0772 0.0025 0.0797 | 15.9223
- 10 | 2.50 | 0.0769 0.0026 0.0795 | 14.6627
- 11 | 2.50 | 0.0766 0.0027 0.0793 | 13.4764
- 12 | 2.50 | 0.0763 0.0027 0.0790 | 12.3015
- 13 | 2.50 | 0.0760 0.0028 0.0788 | 11.3776
- 14 | 2.50 | 0.0757 0.0029 0.0786 | 10.4537
- 15 | 2.25 | 0.0748 0.0029 0.0777 | 9.5920
- 16 | 2.25 | 0.0718 0.0044 0.0762 | 8.8725
- 29 | 2.00 | 0.0729 0.0020 0.0749 | 3.3283
- 30 | 2.00 | 0.0668 0.0044 0.0713 | 3.1221
- 31 | 2.00 | 0.0648 0.0054 0.0702 | 2.9160
- 43 | 1.75 | 0.0638 0.0031 0.0669 | 1.5785
- 44 | 1.75 | 0.0596 0.0053 0.0649 | 1.5194
- 45 | 1.75 | 0.0582 0.0061 0.0643 | 1.4626
- 57 | 1.50 | 0.0567 0.0044 0.0612 | 1.0900
- 58 | 1.50 | 0.0537 0.0064 0.0601 | 1.0730
- 59 | 1.50 | 0.0527 0.0071 0.0598 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 110s
- Prepare output 7s
- 117s
- Jacobian determinant (RMS): 0.010 0.038 0.058 0.082 0.105 | 0.111279
- Template Matching: 0.082 0.215 0.194 0.175 0.158 | 0.158119
- Write result maps: 37s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 20s
- CSF distance: 10s
- PBT2x thickness: 31s
- 66s
- Create initial surface 60s
- Topology correction: 70s
- Surface refinement: 62s
- Reduction of surface collisions with optimization: 51s
- Spherical mapping with areal smoothing 60s
- Spherical registration 182s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 18s
- CSF distance: 10s
- PBT2x thickness: 31s
- 65s
- Create initial surface 60s
- Topology correction: 72s
- Surface refinement: 55s
- Reduction of surface collisions with optimization: 52s
- Spherical mapping with areal smoothing 63s
- Spherical registration 197s
- Final surface processing results:
- Average thickness (FS): 2.4992 0.6272 mm
- Surface intensity / position RMSE: 0.0658 / 0.0629
- Euler number / defect number / defect size: 14.0 / 14.0 / 0.19%
- Display thickness: /var/lib/condor/execute/dir_1954942/ds/BNU_2/sub-0025953/ses-1/surf/lh.thickness.sub-0025953_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1954942/ds/BNU_2/sub-0025953/ses-1/surf/rh.thickness.sub-0025953_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1954942/ds/BNU_2/sub-0025953/ses-1/sub-0025953_ses-1_run-1_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1187s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 6s
- ROI estimation of 'neuromorphometrics' atlas 22s
- ROI estimation of 'lpba40' atlas 6s
- ROI estimation of 'hammers' atlas 16s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 6s
- ROI estimation of 'aal3' atlas 9s
- ROI estimation of 'mori' atlas 13s
- ROI estimation of 'anatomy3' atlas 19s
- ROI estimation of 'julichbrain' atlas 24s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 10s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 18s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 40s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 58s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 5s
- Write results 6s
- 254s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1954942/ds/BNU_2/sub-0025953/ses-1/report/catreport_sub-0025953_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 34 minute(s) and 28 second(s).
- Image Quality Rating (IQR): 82.08% (B-)
- GM volume (GMV): 48.27% (742.16 / 1537.53 ml)
- GM thickness (GMT): 2.50 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1954942/ds/BNU_2/sub-0025953/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_1954942/ds/BNU_2/sub-0025953/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_1954942/ds/BNU_2/sub-0025953/ses-1/label
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