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- CAT12.8.1 r2040: 1/1: ./sub-0026000/ses-3/sub-0026000_ses-3_run-1_T1w.n
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- SANLM denoising (medium): 38s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 6s
- Initial correction 5s
- Refine background 3s
- Final correction 4s
- Final scaling 4s
- 35s
- Correct center-of-mass 3s
- Affine registration 22s
- SPM preprocessing 1 (estimate 1 - TPM registration): 5s
- Use initial fine affine registration. 4s
- Use previous fine affine registration. 51s
- SPM preprocessing 1 (estimate 2): 62s
- SPM preprocessing 2 (write):
- Write Segmentation 15s
- Update Segmentation 17s
- Update Skull-Stripping 39s
- Update probability maps 9s
- 80s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 21s
- Fast Optimized Shooting registration 34s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.04) 12s
- Estimate local tissue thresholds (WM) 15s
- Estimate local tissue thresholds (GM) 21s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 40s
- 97s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 13s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.44) 17s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 56s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 30s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 2s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 10s
- 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 | 0.1025 0.0000 0.1025 | 32.0000
- 2 | 2.50 | 0.0980 0.0018 0.0998 | 29.4886
- 3 | 2.50 | 0.0967 0.0027 0.0994 | 26.9772
- 4 | 2.50 | 0.0960 0.0031 0.0991 | 24.6107
- 5 | 2.50 | 0.0955 0.0033 0.0988 | 22.6548
- 6 | 2.50 | 0.0950 0.0035 0.0985 | 20.6989
- 7 | 2.50 | 0.0945 0.0037 0.0982 | 18.9688
- 8 | 2.50 | 0.0940 0.0038 0.0979 | 17.4455
- 9 | 2.50 | 0.0935 0.0040 0.0975 | 15.9223
- 10 | 2.50 | 0.0929 0.0042 0.0971 | 14.6627
- 11 | 2.50 | 0.0924 0.0043 0.0967 | 13.4764
- 12 | 2.50 | 0.0918 0.0044 0.0962 | 12.3015
- 13 | 2.50 | 0.0912 0.0046 0.0958 | 11.3776
- 14 | 2.50 | 0.0907 0.0047 0.0954 | 10.4537
- 15 | 2.25 | 0.0943 0.0049 0.0992 | 9.5920
- 16 | 2.25 | 0.0894 0.0073 0.0967 | 8.8725
- 17 | 2.25 | 0.0875 0.0082 0.0956 | 8.1530
- 18 | 2.25 | 0.0861 0.0086 0.0947 | 7.5234
- 19 | 2.25 | 0.0851 0.0088 0.0939 | 6.9630
- 20 | 2.25 | 0.0842 0.0089 0.0930 | 6.4027
- 21 | 2.25 | 0.0832 0.0090 0.0923 | 5.9447
- 22 | 2.25 | 0.0824 0.0091 0.0915 | 5.5083
- 23 | 2.25 | 0.0816 0.0091 0.0907 | 5.0803
- 24 | 2.25 | 0.0808 0.0092 0.0899 | 4.7404
- 25 | 2.25 | 0.0801 0.0091 0.0892 | 4.4005
- 26 | 2.25 | 0.0794 0.0091 0.0885 | 4.0868
- 27 | 2.25 | 0.0787 0.0091 0.0878 | 3.8221
- 28 | 2.25 | 0.0781 0.0090 0.0871 | 3.5574
- 29 | 2.00 | 0.0799 0.0087 0.0886 | 3.3283
- 30 | 2.00 | 0.0769 0.0099 0.0868 | 3.1221
- 31 | 2.00 | 0.0757 0.0103 0.0859 | 2.9160
- 32 | 2.00 | 0.0748 0.0104 0.0852 | 2.7495
- 43 | 1.75 | 0.0741 0.0060 0.0802 | 1.5785
- 44 | 1.75 | 0.0688 0.0092 0.0779 | 1.5194
- 45 | 1.75 | 0.0671 0.0101 0.0772 | 1.4626
- 57 | 1.50 | 0.0657 0.0075 0.0732 | 1.0900
- 58 | 1.50 | 0.0617 0.0102 0.0719 | 1.0730
- 59 | 1.50 | 0.0605 0.0110 0.0715 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 209s
- Prepare output 10s
- 219s
- Jacobian determinant (RMS): 0.014 0.054 0.103 0.139 0.177 | 0.186114
- Template Matching: 0.102 0.094 0.224 0.201 0.182 | 0.181548
- Write result maps: 34s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 22s
- CSF distance: 12s
- PBT2x thickness: 36s
- 75s
- Create initial surface 72s
- Topology correction: 67s
- Surface refinement: 84s
- Reduction of surface collisions with optimization: 50s
- Spherical mapping with areal smoothing 68s
- Spherical registration 298s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 28s
- CSF distance: 12s
- PBT2x thickness: 35s
- 79s
- Create initial surface 66s
- Topology correction: 63s
- Surface refinement: 64s
- Reduction of surface collisions with optimization: 48s
- Spherical mapping with areal smoothing 64s
- Spherical registration 290s
- Final surface processing results:
- Average thickness (FS): 2.3040 0.6961 mm
- Surface intensity / position RMSE: 0.0757 / 0.0906
- Euler number / defect number / defect size: 18.0 / 10.5 / 1.31%
- Display thickness: /var/lib/condor/execute/dir_3292157/ds/XHCUMS/sub-0026000/ses-3/surf/lh.thickness.sub-0026000_ses-3_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3292157/ds/XHCUMS/sub-0026000/ses-3/surf/rh.thickness.sub-0026000_ses-3_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3292157/ds/XHCUMS/sub-0026000/ses-3/sub-0026000_ses-3_run-1_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1470s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 8s
- ROI estimation of 'neuromorphometrics' atlas 27s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 19s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 12s
- ROI estimation of 'mori' atlas 18s
- ROI estimation of 'anatomy3' atlas 26s
- ROI estimation of 'julichbrain' atlas 34s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 13s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 24s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 54s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 81s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s
- Write results 8s
- 340s
- Quality check: 10s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3292157/ds/XHCUMS/sub-0026000/ses-3/report/catreport_sub-0026000_ses-3_run-1_T1w.pdf
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- CAT preprocessing takes 45 minute(s) and 26 second(s).
- Image Quality Rating (IQR): 79.17% (C+)
- GM volume (GMV): 40.54% (504.15 / 1243.61 ml)
- GM thickness (GMT): 2.30 0.70 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3292157/ds/XHCUMS/sub-0026000/ses-3/mri
- Reports are saved in /var/lib/condor/execute/dir_3292157/ds/XHCUMS/sub-0026000/ses-3/report
- Labels are saved in /var/lib/condor/execute/dir_3292157/ds/XHCUMS/sub-0026000/ses-3/label
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