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- CAT12.8.1 r1980: 1/1: ./execute/dir_2912350/ds/sub-22/sub-22_T1w.n
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- SANLM denoising (medium): 253s
- APP: Rough bias correction:
- Initialize 14s
- Estimate background 13s
- Initial correction 15s
- Refine background 6s
- Final correction 13s
- Final scaling 14s
- 90s
- Correct center-of-mass 4s
- Affine registration 17s
- SPM preprocessing 1 (estimate 1 - TPM registration): 164s
- SPM preprocessing 1 (estimate 2): 88s
- SPM preprocessing 2 (write):
- Write Segmentation 37s
- Update Segmentation 40s
- Update Skull-Stripping 89s
- Update probability maps 17s
- 183s
- Global intensity correction: 34s
- SANLM denoising after intensity normalization (medium): 51s
- Fast Optimized Shooting registration 55s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 9s
- Prepare partitions 4s
- Prepare segments (LASmod = 1.00) 32s
- Estimate local tissue thresholds (WM) 42s
- Estimate local tissue thresholds (GM) 64s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 75s
- 235s
- ROI segmentation (partitioning):
- Atlas -> subject space 16s
- Major structures 8s
- Ventricle detection 34s
- Blood vessel detection 25s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.01) 62s
- Manual stroke lesion detection 0s
- Closing of deep structures 4s
- Side alignment 8s
- Final corrections 9s
- 165s
- Blood vessel correction (BVCstr=0.50): 3s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 61s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 9s
- Level 1 cleanup (brain masking) 5s
- Level 2 cleanup (CSF correction) 3s
- Level 3 cleanup (CSF/WM PVE) 6s
- 23s
- 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 | 0.0849 0.0000 0.0849 | 32.0000
- 2 | 2.50 | 0.0812 0.0015 0.0827 | 29.4886
- 3 | 2.50 | 0.0801 0.0023 0.0824 | 26.9772
- 4 | 2.50 | 0.0796 0.0026 0.0822 | 24.6107
- 5 | 2.50 | 0.0791 0.0028 0.0820 | 22.6548
- 6 | 2.50 | 0.0788 0.0029 0.0817 | 20.6989
- 7 | 2.50 | 0.0784 0.0031 0.0815 | 18.9688
- 8 | 2.50 | 0.0780 0.0032 0.0812 | 17.4455
- 9 | 2.50 | 0.0776 0.0033 0.0809 | 15.9223
- 10 | 2.50 | 0.0771 0.0035 0.0806 | 14.6627
- 11 | 2.50 | 0.0767 0.0036 0.0803 | 13.4764
- 12 | 2.50 | 0.0762 0.0037 0.0799 | 12.3015
- 13 | 2.50 | 0.0758 0.0039 0.0796 | 11.3776
- 14 | 2.50 | 0.0753 0.0039 0.0793 | 10.4537
- 15 | 2.25 | 0.0752 0.0041 0.0792 | 9.5920
- 16 | 2.25 | 0.0714 0.0059 0.0773 | 8.8725
- 29 | 2.00 | 0.0719 0.0027 0.0746 | 3.3283
- 30 | 2.00 | 0.0651 0.0054 0.0705 | 3.1221
- 31 | 2.00 | 0.0628 0.0065 0.0693 | 2.9160
- 43 | 1.75 | 0.0616 0.0038 0.0654 | 1.5785
- 44 | 1.75 | 0.0575 0.0059 0.0634 | 1.5194
- 45 | 1.75 | 0.0560 0.0067 0.0627 | 1.4626
- 57 | 1.50 | 0.0545 0.0050 0.0594 | 1.0900
- 58 | 1.50 | 0.0515 0.0069 0.0584 | 1.0730
- 59 | 1.50 | 0.0505 0.0075 0.0580 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 198s
- Prepare output 22s
- 220s
- Jacobian determinant (RMS): 0.014 0.052 0.076 0.101 0.122 | 0.128122
- Template Matching: 0.085 0.214 0.188 0.168 0.151 | 0.151499
- Write result maps: 49s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 49s
- CSF distance: 19s
- PBT2x thickness: 56s
- 131s
- Create initial surface 87s
- Topology correction: 115s
- Surface refinement: 76s
- Reduction of surface collisions with optimization: 78s
- Spherical mapping with areal smoothing 100s
- Spherical registration 329s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 38s
- CSF distance: 18s
- PBT2x thickness: 55s
- 118s
- Create initial surface 86s
- Topology correction: 116s
- Surface refinement: 118s
- Reduction of surface collisions with optimization: 83s
- Spherical mapping with areal smoothing 108s
- Spherical registration 368s
- Final surface processing results:
- Average thickness (FS): 2.4885 0.6185 mm
- Surface intensity / position RMSE: 0.0730 / 0.0704
- Euler number / defect number / defect size: 16.0 / 17.0 / 0.37%
- Display thickness: /var/lib/condor/execute/dir_2912350/ds/sub-22/surf/lh.thickness.sub-22_T1w
- Display thickness: /var/lib/condor/execute/dir_2912350/ds/sub-22/surf/rh.thickness.sub-22_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2912350/ds/sub-22/sub-22_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 2053s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 17s
- ROI estimation of 'neuromorphometrics' atlas 61s
- ROI estimation of 'lpba40' atlas 17s
- ROI estimation of 'hammers' atlas 43s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 15s
- ROI estimation of 'aal3' atlas 24s
- ROI estimation of 'mori' atlas 36s
- ROI estimation of 'anatomy3' atlas 52s
- ROI estimation of 'julichbrain' atlas 71s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 28s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 48s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 113s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 169s
- Write results 170s
- 699s
- Quality check: 10s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2912350/ds/sub-22/report/catreport_sub-22_T1w.pdf
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- CAT preprocessing takes 77 minute(s) and 3 second(s).
- Image Quality Rating (IQR): 86.03% (B)
- GM volume (GMV): 49.25% (677.29 / 1375.32 ml)
- GM thickness (GMT): 2.49 0.62 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2912350/ds/sub-22/mri
- Reports are saved in /var/lib/condor/execute/dir_2912350/ds/sub-22/report
- Labels are saved in /var/lib/condor/execute/dir_2912350/ds/sub-22/label
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