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- CAT12.8.1 r2040: 1/1: ./sub-0026136/ses-2/sub-0026136_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 65s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 8s
- Initial correction 7s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 43s
- Correct center-of-mass 5s
- Affine registration 21s
- SPM preprocessing 1 (estimate 1 - TPM registration): 89s
- SPM preprocessing 1 (estimate 2): 72s
- SPM preprocessing 2 (write):
- Write Segmentation 20s
- Update Segmentation 22s
- Update Skull-Stripping 48s
- Update probability maps 10s
- 100s
- Global intensity correction: 18s
- SANLM denoising after intensity normalization (medium): 29s
- Fast Optimized Shooting registration 42s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 16s
- Estimate local tissue thresholds (WM) 20s
- Estimate local tissue thresholds (GM) 32s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 49s
- 128s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 16s
- Blood vessel detection 12s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.49) 24s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 75s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 37s
- AMAP peaks: [CSF,GM,WM] = [0.370.05,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 5s
- Level 1 cleanup (brain masking) 4s
- 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 | 0.0985 0.0000 0.0985 | 32.0000
- 2 | 2.50 | 0.0947 0.0015 0.0963 | 29.4886
- 3 | 2.50 | 0.0936 0.0024 0.0960 | 26.9772
- 4 | 2.50 | 0.0930 0.0027 0.0957 | 24.6107
- 5 | 2.50 | 0.0926 0.0029 0.0955 | 22.6548
- 6 | 2.50 | 0.0921 0.0031 0.0952 | 20.6989
- 7 | 2.50 | 0.0917 0.0033 0.0950 | 18.9688
- 8 | 2.50 | 0.0912 0.0034 0.0947 | 17.4455
- 9 | 2.50 | 0.0908 0.0036 0.0943 | 15.9223
- 10 | 2.50 | 0.0902 0.0038 0.0940 | 14.6627
- 11 | 2.50 | 0.0897 0.0040 0.0937 | 13.4764
- 12 | 2.50 | 0.0892 0.0041 0.0933 | 12.3015
- 13 | 2.50 | 0.0886 0.0043 0.0930 | 11.3776
- 14 | 2.50 | 0.0881 0.0045 0.0926 | 10.4537
- 15 | 2.25 | 0.0926 0.0046 0.0972 | 9.5920
- 16 | 2.25 | 0.0871 0.0075 0.0946 | 8.8725
- 17 | 2.25 | 0.0849 0.0086 0.0935 | 8.1530
- 18 | 2.25 | 0.0834 0.0092 0.0925 | 7.5234
- 19 | 2.25 | 0.0822 0.0095 0.0917 | 6.9630
- 20 | 2.25 | 0.0812 0.0096 0.0908 | 6.4027
- 21 | 2.25 | 0.0801 0.0099 0.0900 | 5.9447
- 22 | 2.25 | 0.0792 0.0100 0.0892 | 5.5083
- 23 | 2.25 | 0.0783 0.0100 0.0883 | 5.0803
- 24 | 2.25 | 0.0773 0.0102 0.0875 | 4.7404
- 25 | 2.25 | 0.0765 0.0102 0.0867 | 4.4005
- 26 | 2.25 | 0.0757 0.0102 0.0859 | 4.0868
- 27 | 2.25 | 0.0749 0.0103 0.0852 | 3.8221
- 29 | 2.00 | 0.0758 0.0092 0.0850 | 3.3283
- 30 | 2.00 | 0.0726 0.0107 0.0833 | 3.1221
- 43 | 1.75 | 0.0710 0.0057 0.0767 | 1.5785
- 44 | 1.75 | 0.0645 0.0093 0.0738 | 1.5194
- 45 | 1.75 | 0.0625 0.0104 0.0729 | 1.4626
- 57 | 1.50 | 0.0608 0.0077 0.0685 | 1.0900
- 58 | 1.50 | 0.0569 0.0103 0.0673 | 1.0730
- 59 | 1.50 | 0.0558 0.0111 0.0669 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 231s
- Prepare output 13s
- 245s
- Jacobian determinant (RMS): 0.014 0.059 0.126 0.169 0.213 | 0.226924
- Template Matching: 0.098 0.225 0.218 0.188 0.167 | 0.167291
- Write result maps: 37s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 43s
- CSF distance: 17s
- PBT2x thickness: 49s
- 116s
- Create initial surface 86s
- Topology correction: 76s
- Surface refinement: 68s
- Reduction of surface collisions with optimization: 52s
- Spherical mapping with areal smoothing 81s
- Spherical registration 336s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 39s
- CSF distance: 17s
- PBT2x thickness: 49s
- 111s
- Create initial surface 85s
- Topology correction: 76s
- Surface refinement: 89s
- Reduction of surface collisions with optimization: 52s
- Spherical mapping with areal smoothing 81s
- Spherical registration 334s
- Final surface processing results:
- Average thickness (FS): 2.4345 0.6666 mm
- Surface intensity / position RMSE: 0.0606 / 0.0565
- Euler number / defect number / defect size: 6.0 / 6.0 / 0.04%
- Display thickness: /var/lib/condor/execute/dir_2217283/ds/UM/sub-0026136/ses-2/surf/lh.thickness.sub-0026136_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2217283/ds/UM/sub-0026136/ses-2/surf/rh.thickness.sub-0026136_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2217283/ds/UM/sub-0026136/ses-2/sub-0026136_ses-2_run-1_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 1740s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 11s
- ROI estimation of 'neuromorphometrics' atlas 43s
- ROI estimation of 'lpba40' atlas 11s
- ROI estimation of 'hammers' atlas 26s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 9s
- ROI estimation of 'aal3' atlas 15s
- ROI estimation of 'mori' atlas 24s
- ROI estimation of 'anatomy3' atlas 34s
- ROI estimation of 'julichbrain' atlas 46s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 32s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 70s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 116s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 9s
- Write results 11s
- 467s
- Quality check: 14s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2217283/ds/UM/sub-0026136/ses-2/report/catreport_sub-0026136_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 55 minute(s) and 46 second(s).
- Image Quality Rating (IQR): 82.09% (B-)
- GM volume (GMV): 38.53% (550.92 / 1429.91 ml)
- GM thickness (GMT): 2.43 0.67 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2217283/ds/UM/sub-0026136/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_2217283/ds/UM/sub-0026136/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_2217283/ds/UM/sub-0026136/ses-2/label
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