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- CAT12.8.1 r2040: 1/1: ./sub-0025883/ses-1/sub-0025883_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 37s
- Internal resampling (1.33x1.00x1.00mm > 1.00x1.00x1.00mm): 1s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 6s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 41s
- Correct center-of-mass 3s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 91s
- SPM preprocessing 1 (estimate 2): 63s
- SPM preprocessing 2 (write):
- Write Segmentation 18s
- Update Segmentation 21s
- Update Skull-Stripping 45s
- Update probability maps 9s
- 94s
- Global intensity correction: 17s
- SANLM denoising after intensity normalization (medium): 27s
- Fast Optimized Shooting registration 34s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 15s
- Estimate local tissue thresholds (WM) 20s
- Estimate local tissue thresholds (GM) 29s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 43s
- 117s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 16s
- Blood vessel detection 10s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.04) 24s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 72s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 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
- 12s
- 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 | 0.0844 0.0000 0.0844 | 32.0000
- 2 | 2.50 | 0.0819 0.0012 0.0830 | 29.4886
- 3 | 2.50 | 0.0811 0.0018 0.0829 | 26.9772
- 4 | 2.50 | 0.0807 0.0020 0.0827 | 24.6107
- 5 | 2.50 | 0.0804 0.0021 0.0826 | 22.6548
- 6 | 2.50 | 0.0802 0.0022 0.0824 | 20.6989
- 7 | 2.50 | 0.0799 0.0023 0.0822 | 18.9688
- 8 | 2.50 | 0.0796 0.0024 0.0820 | 17.4455
- 9 | 2.50 | 0.0793 0.0025 0.0818 | 15.9223
- 10 | 2.50 | 0.0790 0.0026 0.0816 | 14.6627
- 11 | 2.50 | 0.0787 0.0027 0.0814 | 13.4764
- 12 | 2.50 | 0.0784 0.0027 0.0811 | 12.3015
- 13 | 2.50 | 0.0781 0.0028 0.0809 | 11.3776
- 14 | 2.50 | 0.0777 0.0029 0.0806 | 10.4537
- 15 | 2.25 | 0.0769 0.0030 0.0798 | 9.5920
- 16 | 2.25 | 0.0739 0.0044 0.0783 | 8.8725
- 29 | 2.00 | 0.0752 0.0020 0.0772 | 3.3283
- 30 | 2.00 | 0.0693 0.0044 0.0737 | 3.1221
- 31 | 2.00 | 0.0673 0.0053 0.0727 | 2.9160
- 43 | 1.75 | 0.0664 0.0031 0.0695 | 1.5785
- 44 | 1.75 | 0.0622 0.0053 0.0674 | 1.5194
- 45 | 1.75 | 0.0607 0.0060 0.0668 | 1.4626
- 57 | 1.50 | 0.0592 0.0044 0.0636 | 1.0900
- 58 | 1.50 | 0.0561 0.0064 0.0625 | 1.0730
- 59 | 1.50 | 0.0551 0.0070 0.0621 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 180s
- Prepare output 12s
- 192s
- Jacobian determinant (RMS): 0.012 0.041 0.061 0.084 0.107 | 0.113707
- Template Matching: 0.084 0.222 0.202 0.182 0.165 | 0.165318
- Write result maps: 70s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 35s
- CSF distance: 17s
- PBT2x thickness: 49s
- 107s
- Create initial surface 95s
- Topology correction: 107s
- Surface refinement: 113s
- Reduction of surface collisions with optimization: 85s
- Spherical mapping with areal smoothing 86s
- Spherical registration 288s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 33s
- CSF distance: 17s
- PBT2x thickness: 50s
- 106s
- Create initial surface 94s
- Topology correction: 106s
- Surface refinement: 97s
- Reduction of surface collisions with optimization: 85s
- Spherical mapping with areal smoothing 95s
- Spherical registration 321s
- Final surface processing results:
- Average thickness (FS): 2.5148 0.6382 mm
- Surface intensity / position RMSE: 0.0650 / 0.0629
- Euler number / defect number / defect size: 24.0 / 16.0 / 0.66%
- Display thickness: /var/lib/condor/execute/dir_478244/ds/BNU_1/sub-0025883/ses-1/surf/lh.thickness.sub-0025883_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_478244/ds/BNU_1/sub-0025883/ses-1/surf/rh.thickness.sub-0025883_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_478244/ds/BNU_1/sub-0025883/ses-1/sub-0025883_ses-1_run-1_T1w.nii
- Surface ROI estimation: 14s
- Surface and thickness estimation takes: 1903s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 18s
- ROI estimation of 'neuromorphometrics' atlas 64s
- ROI estimation of 'lpba40' atlas 18s
- ROI estimation of 'hammers' atlas 48s
- ROI estimation of 'thalamus' atlas 4s
- ROI estimation of 'ibsr' atlas 17s
- ROI estimation of 'aal3' atlas 30s
- ROI estimation of 'mori' atlas 42s
- ROI estimation of 'anatomy3' atlas 57s
- ROI estimation of 'julichbrain' atlas 70s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 27s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 44s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 83s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 100s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s
- Write results 9s
- 632s
- Quality check: 12s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_478244/ds/BNU_1/sub-0025883/ses-1/report/catreport_sub-0025883_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 59 minute(s) and 4 second(s).
- Image Quality Rating (IQR): 81.94% (B-)
- GM volume (GMV): 48.70% (797.02 / 1636.48 ml)
- GM thickness (GMT): 2.51 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_478244/ds/BNU_1/sub-0025883/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_478244/ds/BNU_1/sub-0025883/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_478244/ds/BNU_1/sub-0025883/ses-1/label
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