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- CAT12.8.1 r1980: 1/1: ./condor/execute/dir_29781/ds/sub-15/sub-15_T1w.n
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- SANLM denoising (medium): 40s
- APP: Rough bias correction:
- Initialize 10s
- Estimate background 10s
- Initial correction 11s
- Refine background 5s
- Final correction 10s
- Final scaling 11s
- 68s
- Correct center-of-mass 3s
- Affine registration 13s
- SPM preprocessing 1 (estimate 1 - TPM registration): 170s
- SPM preprocessing 1 (estimate 2): 74s
- SPM preprocessing 2 (write):
- Write Segmentation 30s
- Update Segmentation 36s
- Update Skull-Stripping 74s
- Update probability maps 15s
- 155s
- Global intensity correction: 27s
- SANLM denoising after intensity normalization (medium): 28s
- Fast Optimized Shooting registration 42s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 8s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.00) 29s
- Estimate local tissue thresholds (WM) 32s
- Estimate local tissue thresholds (GM) 46s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 51s
- 175s
- ROI segmentation (partitioning):
- Atlas -> subject space 14s
- Major structures 7s
- Ventricle detection 26s
- Blood vessel detection 21s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.11) 60s
- Manual stroke lesion detection 0s
- Closing of deep structures 4s
- Side alignment 8s
- Final corrections 7s
- 148s
- Blood vessel correction (BVCstr=0.50): 3s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 58s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 8s
- Level 1 cleanup (brain masking) 4s
- Level 2 cleanup (CSF correction) 3s
- Level 3 cleanup (CSF/WM PVE) 5s
- 20s
- 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 | 0.0929 0.0000 0.0929 | 32.0000
- 2 | 2.50 | 0.0879 0.0019 0.0897 | 29.4886
- 3 | 2.50 | 0.0864 0.0029 0.0893 | 26.9772
- 4 | 2.50 | 0.0857 0.0033 0.0890 | 24.6107
- 5 | 2.50 | 0.0851 0.0036 0.0886 | 22.6548
- 6 | 2.50 | 0.0846 0.0037 0.0883 | 20.6989
- 7 | 2.50 | 0.0841 0.0039 0.0879 | 18.9688
- 8 | 2.50 | 0.0835 0.0040 0.0876 | 17.4455
- 9 | 2.50 | 0.0830 0.0042 0.0872 | 15.9223
- 10 | 2.50 | 0.0824 0.0043 0.0868 | 14.6627
- 11 | 2.50 | 0.0819 0.0045 0.0864 | 13.4764
- 12 | 2.50 | 0.0813 0.0045 0.0859 | 12.3015
- 13 | 2.50 | 0.0808 0.0047 0.0855 | 11.3776
- 14 | 2.50 | 0.0802 0.0048 0.0850 | 10.4537
- 15 | 2.25 | 0.0817 0.0050 0.0867 | 9.5920
- 16 | 2.25 | 0.0772 0.0072 0.0844 | 8.8725
- 17 | 2.25 | 0.0754 0.0080 0.0833 | 8.1530
- 18 | 2.25 | 0.0742 0.0083 0.0825 | 7.5234
- 29 | 2.00 | 0.0757 0.0040 0.0797 | 3.3283
- 30 | 2.00 | 0.0692 0.0069 0.0761 | 3.1221
- 31 | 2.00 | 0.0670 0.0079 0.0749 | 2.9160
- 43 | 1.75 | 0.0658 0.0045 0.0703 | 1.5785
- 44 | 1.75 | 0.0611 0.0070 0.0681 | 1.5194
- 45 | 1.75 | 0.0595 0.0079 0.0674 | 1.4626
- 57 | 1.50 | 0.0580 0.0058 0.0639 | 1.0900
- 58 | 1.50 | 0.0547 0.0080 0.0627 | 1.0730
- 59 | 1.50 | 0.0536 0.0087 0.0623 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 159s
- Prepare output 16s
- 175s
- Jacobian determinant (RMS): 0.014 0.051 0.079 0.105 0.129 | 0.135740
- Template Matching: 0.093 0.223 0.201 0.179 0.161 | 0.160851
- Write result maps: 39s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 33s
- CSF distance: 16s
- PBT2x thickness: 47s
- 103s
- Create initial surface 80s
- Topology correction: 97s
- Surface refinement: 75s
- Reduction of surface collisions with optimization: 73s
- Spherical mapping with areal smoothing 79s
- Spherical registration 276s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 37s
- CSF distance: 16s
- PBT2x thickness: 48s
- 108s
- Create initial surface 83s
- Topology correction: 98s
- Surface refinement: 89s
- Reduction of surface collisions with optimization: 76s
- Spherical mapping with areal smoothing 82s
- Spherical registration 293s
- Final surface processing results:
- Average thickness (FS): 2.6552 0.6503 mm
- Surface intensity / position RMSE: 0.0713 / 0.0718
- Euler number / defect number / defect size: 22.0 / 9.5 / 0.85%
- Display thickness: /var/lib/condor/execute/dir_29781/ds/sub-15/surf/lh.thickness.sub-15_T1w
- Display thickness: /var/lib/condor/execute/dir_29781/ds/sub-15/surf/rh.thickness.sub-15_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_29781/ds/sub-15/sub-15_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1735s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 14s
- ROI estimation of 'neuromorphometrics' atlas 53s
- 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 20s
- ROI estimation of 'mori' atlas 30s
- ROI estimation of 'anatomy3' atlas 42s
- ROI estimation of 'julichbrain' atlas 56s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 23s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 40s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 90s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 134s
- Write results 135s
- 572s
- Quality check: 9s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_29781/ds/sub-15/report/catreport_sub-15_T1w.pdf
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- CAT preprocessing takes 61 minute(s) and 41 second(s).
- Image Quality Rating (IQR): 84.03% (B)
- GM volume (GMV): 48.20% (764.64 / 1586.41 ml)
- GM thickness (GMT): 2.66 0.65 mm
- Segmentations are saved in /var/lib/condor/execute/dir_29781/ds/sub-15/mri
- Reports are saved in /var/lib/condor/execute/dir_29781/ds/sub-15/report
- Labels are saved in /var/lib/condor/execute/dir_29781/ds/sub-15/label
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