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- CAT12.8.1 r2040: 1/1: ./sub-0026136/ses-1/sub-0026136_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 62s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 7s
- Initial correction 7s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 41s
- Correct center-of-mass 6s
- Affine registration 16s
- SPM preprocessing 1 (estimate 1 - TPM registration): 82s
- SPM preprocessing 1 (estimate 2): 68s
- SPM preprocessing 2 (write):
- Write Segmentation 19s
- Update Segmentation 21s
- Update Skull-Stripping 45s
- Update probability maps 9s
- 94s
- Global intensity correction: 18s
- SANLM denoising after intensity normalization (medium): 29s
- Fast Optimized Shooting registration 41s
- 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) 31s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 47s
- 122s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 3s
- Ventricle detection 13s
- Blood vessel detection 12s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.50) 25s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 72s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 35s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- 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 | 0.0987 0.0000 0.0987 | 32.0000
- 2 | 2.50 | 0.0949 0.0015 0.0965 | 29.4886
- 3 | 2.50 | 0.0938 0.0024 0.0962 | 26.9772
- 4 | 2.50 | 0.0932 0.0027 0.0959 | 24.6107
- 5 | 2.50 | 0.0927 0.0029 0.0957 | 22.6548
- 6 | 2.50 | 0.0923 0.0031 0.0954 | 20.6989
- 7 | 2.50 | 0.0919 0.0033 0.0951 | 18.9688
- 8 | 2.50 | 0.0914 0.0035 0.0949 | 17.4455
- 9 | 2.50 | 0.0909 0.0036 0.0945 | 15.9223
- 10 | 2.50 | 0.0904 0.0038 0.0942 | 14.6627
- 11 | 2.50 | 0.0899 0.0040 0.0939 | 13.4764
- 12 | 2.50 | 0.0894 0.0041 0.0935 | 12.3015
- 13 | 2.50 | 0.0888 0.0043 0.0931 | 11.3776
- 14 | 2.50 | 0.0883 0.0045 0.0927 | 10.4537
- 15 | 2.25 | 0.0928 0.0046 0.0974 | 9.5920
- 16 | 2.25 | 0.0873 0.0075 0.0948 | 8.8725
- 17 | 2.25 | 0.0851 0.0086 0.0937 | 8.1530
- 18 | 2.25 | 0.0836 0.0091 0.0927 | 7.5234
- 19 | 2.25 | 0.0824 0.0095 0.0919 | 6.9630
- 20 | 2.25 | 0.0814 0.0096 0.0910 | 6.4027
- 21 | 2.25 | 0.0804 0.0098 0.0902 | 5.9447
- 22 | 2.25 | 0.0794 0.0099 0.0894 | 5.5083
- 23 | 2.25 | 0.0785 0.0100 0.0885 | 5.0803
- 24 | 2.25 | 0.0776 0.0101 0.0877 | 4.7404
- 25 | 2.25 | 0.0768 0.0101 0.0869 | 4.4005
- 26 | 2.25 | 0.0760 0.0101 0.0861 | 4.0868
- 27 | 2.25 | 0.0752 0.0102 0.0854 | 3.8221
- 28 | 2.25 | 0.0745 0.0101 0.0846 | 3.5574
- 29 | 2.00 | 0.0753 0.0098 0.0851 | 3.3283
- 30 | 2.00 | 0.0726 0.0108 0.0835 | 3.1221
- 43 | 1.75 | 0.0712 0.0057 0.0769 | 1.5785
- 44 | 1.75 | 0.0647 0.0093 0.0741 | 1.5194
- 45 | 1.75 | 0.0628 0.0104 0.0732 | 1.4626
- 57 | 1.50 | 0.0610 0.0077 0.0688 | 1.0900
- 58 | 1.50 | 0.0572 0.0104 0.0675 | 1.0730
- 59 | 1.50 | 0.0560 0.0111 0.0671 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 227s
- Prepare output 13s
- 240s
- Jacobian determinant (RMS): 0.013 0.058 0.127 0.168 0.213 | 0.226525
- Template Matching: 0.099 0.223 0.218 0.188 0.168 | 0.167958
- Write result maps: 37s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 52s
- CSF distance: 18s
- PBT2x thickness: 49s
- 126s
- Create initial surface 87s
- Topology correction: 76s
- Surface refinement: 79s
- Reduction of surface collisions with optimization: 54s
- Spherical mapping with areal smoothing 87s
- Spherical registration 320s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 39s
- CSF distance: 17s
- PBT2x thickness: 48s
- 110s
- Create initial surface 83s
- Topology correction: 75s
- Surface refinement: 60s
- Reduction of surface collisions with optimization: 50s
- Spherical mapping with areal smoothing 77s
- Spherical registration 320s
- Final surface processing results:
- Average thickness (FS): 2.4445 0.6717 mm
- Surface intensity / position RMSE: 0.0597 / 0.0568
- Euler number / defect number / defect size: 8.0 / 6.0 / 0.19%
- Display thickness: /var/lib/condor/execute/dir_2217283/ds/UM/sub-0026136/ses-1/surf/lh.thickness.sub-0026136_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2217283/ds/UM/sub-0026136/ses-1/surf/rh.thickness.sub-0026136_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2217283/ds/UM/sub-0026136/ses-1/sub-0026136_ses-1_run-1_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1699s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 8s
- ROI estimation of 'neuromorphometrics' atlas 31s
- ROI estimation of 'lpba40' atlas 9s
- ROI estimation of 'hammers' atlas 21s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 8s
- ROI estimation of 'aal3' atlas 13s
- ROI estimation of 'mori' atlas 20s
- ROI estimation of 'anatomy3' atlas 28s
- ROI estimation of 'julichbrain' atlas 38s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 26s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 62s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 93s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s
- Write results 10s
- 384s
- Quality check: 14s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2217283/ds/UM/sub-0026136/ses-1/report/catreport_sub-0026136_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 52 minute(s) and 49 second(s).
- Image Quality Rating (IQR): 81.99% (B-)
- GM volume (GMV): 38.28% (556.90 / 1454.77 ml)
- GM thickness (GMT): 2.44 0.67 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2217283/ds/UM/sub-0026136/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_2217283/ds/UM/sub-0026136/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_2217283/ds/UM/sub-0026136/ses-1/label
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