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- CAT12.8.1 r1980: 1/1: ./ds/sub-432/sub-432_ses-20130521_T1w.n
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- SANLM denoising (medium): 18s
- Internal resampling (3.90x0.78x0.78mm > 1.00x0.78x0.78mm): 2s
- APP: Rough bias correction:
- Initialize 13s
- Estimate background 13s
- Initial correction 23s
- Refine background 6s
- Final correction 15s
- Final scaling 11s
- 93s
- Correct center-of-mass 4s
- Affine registration 20s
- SPM preprocessing 1 (estimate 1 - TPM registration): 149s
- SPM preprocessing 1 (estimate 2): 143s
- SPM preprocessing 2 (write):
- Write Segmentation 32s
- Update Segmentation 40s
- Update Skull-Stripping 85s
- Update probability maps 24s
- 181s
- Global intensity correction: 31s
- SANLM denoising after intensity normalization (medium): 12s
- Fast Optimized Shooting registration 52s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 7s
- Prepare partitions 5s
- Prepare segments (LASmod = 1.44) 29s
- Estimate local tissue thresholds (WM) 28s
- Estimate local tissue thresholds (GM) 35s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 48s
- 158s
- ROI segmentation (partitioning):
- Atlas -> subject space 14s
- Major structures 6s
- Ventricle detection 24s
- Blood vessel detection 21s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.38) 42s
- Manual stroke lesion detection 0s
- Closing of deep structures 3s
- Side alignment 7s
- Final corrections 8s
- 125s
- Blood vessel correction (BVCstr=0.50): 3s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 55s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.970.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 8s
- Level 1 cleanup (brain masking) 5s
- Level 2 cleanup (CSF correction) 3s
- Level 3 cleanup (CSF/WM PVE) 5s
- 21s
- 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 | 0.0989 0.0000 0.0989 | 32.0000
- 2 | 2.50 | 0.0932 0.0020 0.0952 | 29.4886
- 3 | 2.50 | 0.0914 0.0032 0.0946 | 26.9772
- 4 | 2.50 | 0.0905 0.0036 0.0942 | 24.6107
- 5 | 2.50 | 0.0898 0.0039 0.0938 | 22.6548
- 6 | 2.50 | 0.0892 0.0041 0.0934 | 20.6989
- 7 | 2.50 | 0.0886 0.0043 0.0929 | 18.9688
- 8 | 2.50 | 0.0880 0.0045 0.0925 | 17.4455
- 9 | 2.50 | 0.0873 0.0047 0.0920 | 15.9223
- 10 | 2.50 | 0.0866 0.0049 0.0915 | 14.6627
- 11 | 2.50 | 0.0860 0.0051 0.0911 | 13.4764
- 12 | 2.50 | 0.0853 0.0052 0.0905 | 12.3015
- 13 | 2.50 | 0.0846 0.0054 0.0900 | 11.3776
- 14 | 2.50 | 0.0839 0.0056 0.0895 | 10.4537
- 15 | 2.25 | 0.0860 0.0058 0.0918 | 9.5920
- 16 | 2.25 | 0.0814 0.0082 0.0896 | 8.8725
- 17 | 2.25 | 0.0794 0.0091 0.0885 | 8.1530
- 18 | 2.25 | 0.0781 0.0095 0.0876 | 7.5234
- 19 | 2.25 | 0.0770 0.0097 0.0867 | 6.9630
- 20 | 2.25 | 0.0761 0.0097 0.0858 | 6.4027
- 21 | 2.25 | 0.0752 0.0098 0.0850 | 5.9447
- 22 | 2.25 | 0.0744 0.0098 0.0841 | 5.5083
- 29 | 2.00 | 0.0757 0.0063 0.0820 | 3.3283
- 30 | 2.00 | 0.0706 0.0088 0.0794 | 3.1221
- 31 | 2.00 | 0.0687 0.0096 0.0783 | 2.9160
- 43 | 1.75 | 0.0678 0.0055 0.0733 | 1.5785
- 44 | 1.75 | 0.0629 0.0082 0.0711 | 1.5194
- 45 | 1.75 | 0.0613 0.0091 0.0703 | 1.4626
- 57 | 1.50 | 0.0602 0.0068 0.0670 | 1.0900
- 58 | 1.50 | 0.0567 0.0092 0.0659 | 1.0730
- 59 | 1.50 | 0.0556 0.0098 0.0654 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 215s
- Prepare output 18s
- 233s
- Jacobian determinant (RMS): 0.016 0.063 0.107 0.138 0.169 | 0.175909
- Template Matching: 0.099 0.223 0.206 0.184 0.167 | 0.166810
- Write result maps: 93s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 41s
- CSF distance: 17s
- PBT2x thickness: 53s
- 119s
- Create initial surface 102s
- Topology correction: 116s
- Surface refinement: 95s
- Reduction of surface collisions with optimization: 77s
- Spherical mapping with areal smoothing 109s
- Spherical registration 347s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 53s
- CSF distance: 18s
- PBT2x thickness: 53s
- 131s
- Create initial surface 98s
- Topology correction: 132s
- Surface refinement: 128s
- Reduction of surface collisions with optimization: 73s
- Spherical mapping with areal smoothing 99s
- Spherical registration 358s
- Final surface processing results:
- Average thickness (FS): 2.1295 0.6301 mm
- Surface intensity / position RMSE: 0.0792 / 0.0928
- Euler number / defect number / defect size: 180.0 / 88.0 / 4.96%
- Display thickness: /var/lib/condor/execute/dir_710498/ds/sub-432/surf/lh.thickness.sub-432_ses-20130521_T1w
- Display thickness: /var/lib/condor/execute/dir_710498/ds/sub-432/surf/rh.thickness.sub-432_ses-20130521_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_710498/ds/sub-432/sub-432_ses-20130521_T1w.nii
- Surface ROI estimation: 25s
- Surface and thickness estimation takes: 2130s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 15s
- ROI estimation of 'neuromorphometrics' atlas 54s
- ROI estimation of 'lpba40' atlas 16s
- ROI estimation of 'hammers' atlas 37s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 16s
- ROI estimation of 'aal3' atlas 23s
- ROI estimation of 'mori' atlas 30s
- ROI estimation of 'anatomy3' atlas 40s
- ROI estimation of 'julichbrain' atlas 52s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 21s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 37s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 88s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 145s
- Write results 146s
- 581s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_710498/ds/sub-432/report/catreport_sub-432_ses-20130521_T1w.pdf
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- CAT preprocessing takes 70 minute(s) and 39 second(s).
- Image Quality Rating (IQR): 61.13% (D-)
- GM volume (GMV): 39.36% (563.44 / 1431.59 ml)
- GM thickness (GMT): 2.13 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_710498/ds/sub-432/mri
- Reports are saved in /var/lib/condor/execute/dir_710498/ds/sub-432/report
- Labels are saved in /var/lib/condor/execute/dir_710498/ds/sub-432/label
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