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- CAT12.8.1 r1980: 1/1: ./ds/sub-271/sub-271_ses-20110518_T1w.n
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- SANLM denoising (medium): 30s
- Internal resampling (3.90x0.56x0.56mm > 1.00x1.00x1.00mm): 1s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 7s
- Initial correction 8s
- Refine background 3s
- Final correction 7s
- Final scaling 5s
- 41s
- Correct center-of-mass 3s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 78s
- SPM preprocessing 1 (estimate 2): 78s
- SPM preprocessing 2 (write):
- Write Segmentation 16s
- Update Segmentation 21s
- Update Skull-Stripping 39s
- Update probability maps 10s
- 86s
- Global intensity correction: 14s
- SANLM denoising after intensity normalization (medium): 10s
- Fast Optimized Shooting registration 40s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.30) 15s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 25s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 27s
- 92s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 11s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.29) 21s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 4s
- 61s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 31s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.970.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 3s
- 11s
- 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 | 0.0967 0.0000 0.0967 | 32.0000
- 2 | 2.50 | 0.0923 0.0017 0.0940 | 29.4886
- 3 | 2.50 | 0.0909 0.0027 0.0936 | 26.9772
- 4 | 2.50 | 0.0902 0.0031 0.0933 | 24.6107
- 5 | 2.50 | 0.0897 0.0034 0.0930 | 22.6548
- 6 | 2.50 | 0.0892 0.0035 0.0927 | 20.6989
- 7 | 2.50 | 0.0887 0.0037 0.0924 | 18.9688
- 8 | 2.50 | 0.0881 0.0039 0.0920 | 17.4455
- 9 | 2.50 | 0.0876 0.0041 0.0917 | 15.9223
- 10 | 2.50 | 0.0870 0.0043 0.0913 | 14.6627
- 11 | 2.50 | 0.0864 0.0044 0.0909 | 13.4764
- 12 | 2.50 | 0.0858 0.0046 0.0904 | 12.3015
- 13 | 2.50 | 0.0852 0.0048 0.0900 | 11.3776
- 14 | 2.50 | 0.0846 0.0049 0.0895 | 10.4537
- 15 | 2.25 | 0.0876 0.0051 0.0928 | 9.5920
- 16 | 2.25 | 0.0831 0.0074 0.0905 | 8.8725
- 17 | 2.25 | 0.0810 0.0084 0.0894 | 8.1530
- 18 | 2.25 | 0.0796 0.0089 0.0885 | 7.5234
- 19 | 2.25 | 0.0786 0.0091 0.0877 | 6.9630
- 20 | 2.25 | 0.0776 0.0092 0.0868 | 6.4027
- 21 | 2.25 | 0.0767 0.0093 0.0860 | 5.9447
- 22 | 2.25 | 0.0759 0.0093 0.0852 | 5.5083
- 23 | 2.25 | 0.0751 0.0093 0.0844 | 5.0803
- 24 | 2.25 | 0.0744 0.0093 0.0837 | 4.7404
- 29 | 2.00 | 0.0756 0.0069 0.0825 | 3.3283
- 30 | 2.00 | 0.0714 0.0089 0.0803 | 3.1221
- 31 | 2.00 | 0.0697 0.0096 0.0793 | 2.9160
- 43 | 1.75 | 0.0685 0.0054 0.0739 | 1.5785
- 44 | 1.75 | 0.0634 0.0082 0.0716 | 1.5194
- 45 | 1.75 | 0.0617 0.0092 0.0709 | 1.4626
- 57 | 1.50 | 0.0606 0.0069 0.0674 | 1.0900
- 58 | 1.50 | 0.0570 0.0092 0.0663 | 1.0730
- 59 | 1.50 | 0.0559 0.0099 0.0659 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 224s
- Prepare output 12s
- 235s
- Jacobian determinant (RMS): 0.015 0.060 0.107 0.137 0.170 | 0.180751
- Template Matching: 0.097 0.223 0.209 0.185 0.168 | 0.167801
- Write result maps: 66s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 32s
- CSF distance: 14s
- PBT2x thickness: 45s
- 97s
- Create initial surface 87s
- Topology correction: 94s
- Surface refinement: 119s
- Reduction of surface collisions with optimization: 54s
- Spherical mapping with areal smoothing 90s
- Spherical registration 334s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 37s
- CSF distance: 14s
- PBT2x thickness: 45s
- 103s
- Create initial surface 86s
- Topology correction: 80s
- Surface refinement: 91s
- Reduction of surface collisions with optimization: 51s
- Spherical mapping with areal smoothing 91s
- Spherical registration 361s
- Final surface processing results:
- Average thickness (FS): 2.0936 0.5846 mm
- Surface intensity / position RMSE: 0.0694 / 0.0786
- Euler number / defect number / defect size: 72.0 / 34.5 / 1.90%
- Display thickness: /var/lib/condor/execute/dir_710418/ds/sub-271/surf/lh.thickness.sub-271_ses-20110518_T1w
- Display thickness: /var/lib/condor/execute/dir_710418/ds/sub-271/surf/rh.thickness.sub-271_ses-20110518_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_710418/ds/sub-271/sub-271_ses-20110518_T1w.nii
- Surface ROI estimation: 13s
- Surface and thickness estimation takes: 1846s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 6s
- ROI estimation of 'neuromorphometrics' atlas 24s
- ROI estimation of 'lpba40' atlas 7s
- ROI estimation of 'hammers' atlas 16s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 5s
- ROI estimation of 'aal3' atlas 9s
- ROI estimation of 'mori' atlas 13s
- ROI estimation of 'anatomy3' atlas 19s
- ROI estimation of 'julichbrain' atlas 26s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 10s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 18s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 41s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 61s
- Write results 63s
- 259s
- Quality check: 10s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_710418/ds/sub-271/report/catreport_sub-271_ses-20110518_T1w.pdf
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- CAT preprocessing takes 51 minute(s) and 29 second(s).
- Image Quality Rating (IQR): 62.11% (D-)
- GM volume (GMV): 38.45% (484.41 / 1259.73 ml)
- GM thickness (GMT): 2.09 0.58 mm
- Segmentations are saved in /var/lib/condor/execute/dir_710418/ds/sub-271/mri
- Reports are saved in /var/lib/condor/execute/dir_710418/ds/sub-271/report
- Labels are saved in /var/lib/condor/execute/dir_710418/ds/sub-271/label
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