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- CAT12.8.1 r2040: 1/1: ./sub-0025965/ses-1/sub-0025965_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 7s
- Estimate background 6s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 6s
- 41s
- Correct center-of-mass 3s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 75s
- SPM preprocessing 1 (estimate 2): 75s
- SPM preprocessing 2 (write):
- Write Segmentation 18s
- Update Segmentation 20s
- Update Skull-Stripping 44s
- Update probability maps 9s
- 91s
- Global intensity correction: 17s
- SANLM denoising after intensity normalization (medium): 26s
- Fast Optimized Shooting registration 39s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 14s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 27s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 36s
- 106s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 3s
- Ventricle detection 14s
- Blood vessel detection 9s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.24) 24s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 70s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 32s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 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 | 0.0905 0.0000 0.0905 | 32.0000
- 2 | 2.50 | 0.0874 0.0013 0.0887 | 29.4886
- 3 | 2.50 | 0.0864 0.0020 0.0884 | 26.9772
- 4 | 2.50 | 0.0859 0.0023 0.0882 | 24.6107
- 5 | 2.50 | 0.0855 0.0025 0.0880 | 22.6548
- 6 | 2.50 | 0.0852 0.0026 0.0878 | 20.6989
- 7 | 2.50 | 0.0848 0.0027 0.0876 | 18.9688
- 8 | 2.50 | 0.0845 0.0029 0.0874 | 17.4455
- 9 | 2.50 | 0.0841 0.0030 0.0871 | 15.9223
- 10 | 2.50 | 0.0838 0.0031 0.0868 | 14.6627
- 11 | 2.50 | 0.0834 0.0032 0.0866 | 13.4764
- 12 | 2.50 | 0.0830 0.0033 0.0863 | 12.3015
- 13 | 2.50 | 0.0826 0.0034 0.0860 | 11.3776
- 14 | 2.50 | 0.0822 0.0034 0.0857 | 10.4537
- 15 | 2.25 | 0.0833 0.0035 0.0869 | 9.5920
- 16 | 2.25 | 0.0797 0.0053 0.0851 | 8.8725
- 17 | 2.25 | 0.0783 0.0060 0.0843 | 8.1530
- 18 | 2.25 | 0.0774 0.0062 0.0837 | 7.5234
- 19 | 2.25 | 0.0767 0.0064 0.0831 | 6.9630
- 20 | 2.25 | 0.0761 0.0064 0.0825 | 6.4027
- 21 | 2.25 | 0.0755 0.0064 0.0820 | 5.9447
- 22 | 2.25 | 0.0750 0.0064 0.0814 | 5.5083
- 23 | 2.25 | 0.0745 0.0064 0.0809 | 5.0803
- 29 | 2.00 | 0.0764 0.0044 0.0808 | 3.3283
- 30 | 2.00 | 0.0723 0.0063 0.0787 | 3.1221
- 31 | 2.00 | 0.0709 0.0070 0.0779 | 2.9160
- 43 | 1.75 | 0.0702 0.0039 0.0741 | 1.5785
- 44 | 1.75 | 0.0653 0.0066 0.0719 | 1.5194
- 45 | 1.75 | 0.0638 0.0075 0.0713 | 1.4626
- 57 | 1.50 | 0.0625 0.0054 0.0680 | 1.0900
- 58 | 1.50 | 0.0590 0.0078 0.0668 | 1.0730
- 59 | 1.50 | 0.0578 0.0085 0.0664 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 238s
- Prepare output 11s
- 248s
- Jacobian determinant (RMS): 0.011 0.042 0.074 0.102 0.132 | 0.140945
- Template Matching: 0.090 0.223 0.213 0.191 0.173 | 0.173486
- Write result maps: 92s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 42s
- CSF distance: 18s
- PBT2x thickness: 52s
- 120s
- Create initial surface 87s
- Topology correction: 91s
- Surface refinement: 77s
- Reduction of surface collisions with optimization: 57s
- Spherical mapping with areal smoothing 83s
- Spherical registration 247s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 41s
- CSF distance: 17s
- PBT2x thickness: 51s
- 117s
- Create initial surface 86s
- Topology correction: 90s
- Surface refinement: 69s
- Reduction of surface collisions with optimization: 55s
- Spherical mapping with areal smoothing 81s
- Spherical registration 263s
- Final surface processing results:
- Average thickness (FS): 2.4538 0.6277 mm
- Surface intensity / position RMSE: 0.0651 / 0.0686
- Euler number / defect number / defect size: 20.0 / 8.5 / 0.74%
- Display thickness: /var/lib/condor/execute/dir_2321434/ds/BNU_2/sub-0025965/ses-1/surf/lh.thickness.sub-0025965_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2321434/ds/BNU_2/sub-0025965/ses-1/surf/rh.thickness.sub-0025965_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2321434/ds/BNU_2/sub-0025965/ses-1/sub-0025965_ses-1_run-1_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1626s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 14s
- ROI estimation of 'neuromorphometrics' atlas 52s
- ROI estimation of 'lpba40' atlas 15s
- ROI estimation of 'hammers' atlas 38s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 13s
- ROI estimation of 'aal3' atlas 23s
- ROI estimation of 'mori' atlas 34s
- ROI estimation of 'anatomy3' atlas 50s
- ROI estimation of 'julichbrain' atlas 65s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 25s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 34s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 105s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 156s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 11s
- Write results 12s
- 639s
- Quality check: 13s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2321434/ds/BNU_2/sub-0025965/ses-1/report/catreport_sub-0025965_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 55 minute(s) and 42 second(s).
- Image Quality Rating (IQR): 84.08% (B)
- GM volume (GMV): 45.80% (681.02 / 1487.07 ml)
- GM thickness (GMT): 2.45 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2321434/ds/BNU_2/sub-0025965/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_2321434/ds/BNU_2/sub-0025965/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_2321434/ds/BNU_2/sub-0025965/ses-1/label
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