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- CAT12.8.1 r1980: 1/1: ./execute/dir_2739317/ds/sub-86/sub-86_T1w.n
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- SANLM denoising (medium): 93s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 14s
- Initial correction 13s
- Refine background 6s
- Final correction 7s
- Final scaling 10s
- 65s
- Correct center-of-mass 17s
- Affine registration 10s
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- WARNING 01: cat_run_job1639:StrokeLesionButNoCorrection
- There are 1.23 cm of zeros within the brain but Stroke Lesion
- Correction (SLC) inactive (available in the expert mode).
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- SPM preprocessing 1 (estimate 1 - TPM registration): 17s
- Use initial fine affine registration. 13s
- Use previous fine affine registration. 69s
- SPM preprocessing 1 (estimate 2): 59s
- SPM preprocessing 2 (write):
- Write Segmentation 21s
- Update Segmentation 22s
- Update Skull-Stripping 49s
- Update probability maps 12s
- 104s
- Global intensity correction: 19s
- SANLM denoising after intensity normalization (medium): 15s
- Fast Optimized Shooting registration 41s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 17s
- Estimate local tissue thresholds (WM) 25s
- Estimate local tissue thresholds (GM) 33s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 35s
- 120s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 19s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.48 > WMHCstr'=0.07) 36s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 89s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 34s
- AMAP peaks: [CSF,GM,WM] = [0.350.04,0.670.08,0.980.05]
- Final cleanup (gcutstr=0.24):
- 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
- 13s
- 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 | 0.1108 0.0000 0.1108 | 32.0000
- 2 | 2.50 | 0.1057 0.0019 0.1076 | 29.4886
- 3 | 2.50 | 0.1040 0.0031 0.1071 | 26.9772
- 4 | 2.50 | 0.1031 0.0036 0.1067 | 24.6107
- 5 | 2.50 | 0.1024 0.0040 0.1064 | 22.6548
- 6 | 2.50 | 0.1017 0.0042 0.1060 | 20.6989
- 7 | 2.50 | 0.1010 0.0045 0.1055 | 18.9688
- 8 | 2.50 | 0.1003 0.0048 0.1051 | 17.4455
- 9 | 2.50 | 0.0996 0.0050 0.1046 | 15.9223
- 10 | 2.50 | 0.0989 0.0053 0.1042 | 14.6627
- 11 | 2.50 | 0.0981 0.0056 0.1037 | 13.4764
- 12 | 2.50 | 0.0973 0.0058 0.1031 | 12.3015
- 13 | 2.50 | 0.0965 0.0061 0.1026 | 11.3776
- 14 | 2.50 | 0.0957 0.0064 0.1020 | 10.4537
- 15 | 2.25 | 0.1045 0.0067 0.1111 | 9.5920
- 16 | 2.25 | 0.0985 0.0099 0.1085 | 8.8725
- 17 | 2.25 | 0.0959 0.0112 0.1071 | 8.1530
- 18 | 2.25 | 0.0941 0.0118 0.1059 | 7.5234
- 19 | 2.25 | 0.0926 0.0123 0.1048 | 6.9630
- 20 | 2.25 | 0.0911 0.0125 0.1036 | 6.4027
- 21 | 2.25 | 0.0897 0.0129 0.1026 | 5.9447
- 22 | 2.25 | 0.0883 0.0131 0.1015 | 5.5083
- 23 | 2.25 | 0.0870 0.0133 0.1003 | 5.0803
- 24 | 2.25 | 0.0855 0.0136 0.0991 | 4.7404
- 25 | 2.25 | 0.0843 0.0137 0.0979 | 4.4005
- 26 | 2.25 | 0.0830 0.0138 0.0968 | 4.0868
- 27 | 2.25 | 0.0818 0.0139 0.0957 | 3.8221
- 28 | 2.25 | 0.0807 0.0140 0.0946 | 3.5574
- 29 | 2.00 | 0.0813 0.0138 0.0951 | 3.3283
- 30 | 2.00 | 0.0785 0.0144 0.0929 | 3.1221
- 31 | 2.00 | 0.0772 0.0144 0.0916 | 2.9160
- 32 | 2.00 | 0.0760 0.0145 0.0906 | 2.7495
- 33 | 2.00 | 0.0751 0.0145 0.0896 | 2.5890
- 34 | 2.00 | 0.0741 0.0144 0.0886 | 2.4330
- 43 | 1.75 | 0.0734 0.0096 0.0830 | 1.5785
- 44 | 1.75 | 0.0682 0.0126 0.0808 | 1.5194
- 45 | 1.75 | 0.0660 0.0138 0.0798 | 1.4626
- 57 | 1.50 | 0.0651 0.0106 0.0757 | 1.0900
- Problem with Shooting (dets: 0.00133101 .. 1.99458)
- 58 | 1.50 | 0.0603 0.0138 0.0741 | 1.0730
- 59 | 1.50 | 0.0584 0.0149 0.0733 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 259s
- Prepare output 14s
- 273s
- Jacobian determinant (RMS): 0.016 0.077 0.194 0.321 2.074 | 0.626112
- Template Matching: 0.111 0.104 0.222 0.198 0.175 | 0.175236
- Write result maps: 29s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 57s
- CSF distance: 23s
- PBT2x thickness: 64s
- 151s
- Create initial surface 110s
- Topology correction: 128s
- Surface refinement: 103s
- Reduction of surface collisions with optimization: 95s
- Spherical mapping with areal smoothing 115s
- Spherical registration 355s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 61s
- CSF distance: 23s
- PBT2x thickness: 64s
- 156s
- Create initial surface 111s
- Topology correction: 122s
- Surface refinement: 97s
- Reduction of surface collisions with optimization: 90s
- Spherical mapping with areal smoothing 109s
- Spherical registration 327s
- Final surface processing results:
- Average thickness (FS): 2.4555 0.6144 mm
- Surface intensity / position RMSE: 0.0715 / 0.0769
- Euler number / defect number / defect size: 34.0 / 20.0 / 1.50%
- Display thickness: /var/lib/condor/execute/dir_2739317/ds/sub-86/surf/lh.thickness.sub-86_T1w
- Display thickness: /var/lib/condor/execute/dir_2739317/ds/sub-86/surf/rh.thickness.sub-86_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2739317/ds/sub-86/sub-86_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 2188s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 31s
- ROI estimation of 'lpba40' atlas 9s
- ROI estimation of 'hammers' atlas 22s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 8s
- ROI estimation of 'aal3' atlas 12s
- ROI estimation of 'mori' atlas 18s
- ROI estimation of 'anatomy3' atlas 26s
- ROI estimation of 'julichbrain' atlas 35s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 14s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 24s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 56s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 84s
- Write results 85s
- 350s
- Quality check: 5s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2739317/ds/sub-86/report/catreport_sub-86_T1w.pdf
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- CAT preprocessing takes 62 minute(s) and 6 second(s).
- Image Quality Rating (IQR): 80.56% (B-)
- GM volume (GMV): 42.61% (676.81 / 1588.23 ml)
- GM thickness (GMT): 2.46 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2739317/ds/sub-86/mri
- Reports are saved in /var/lib/condor/execute/dir_2739317/ds/sub-86/report
- Labels are saved in /var/lib/condor/execute/dir_2739317/ds/sub-86/label
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