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- CAT12.8.1 r2040: 1/1: ./sub-0027273/ses-1/sub-0027273_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 59s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 5s
- Initial correction 4s
- Refine background 3s
- Final correction 4s
- Final scaling 4s
- 31s
- Correct center-of-mass 4s
- Affine registration 7s
- SPM preprocessing 1 (estimate 1 - TPM registration): 66s
- SPM preprocessing 1 (estimate 2): 47s
- SPM preprocessing 2 (write):
- Write Segmentation 15s
- Update Segmentation 17s
- Update Skull-Stripping 35s
- Update probability maps 8s
- 75s
- Global intensity correction: 14s
- SANLM denoising after intensity normalization (medium): 26s
- Fast Optimized Shooting registration 30s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.00) 13s
- Estimate local tissue thresholds (WM) 15s
- Estimate local tissue thresholds (GM) 22s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 34s
- 93s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 13s
- Blood vessel detection 9s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.04) 21s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 61s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 30s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 2s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 3s
- 10s
- 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 | 0.0871 0.0000 0.0871 | 32.0000
- 2 | 2.50 | 0.0840 0.0013 0.0853 | 29.4886
- 3 | 2.50 | 0.0832 0.0020 0.0851 | 26.9772
- 4 | 2.50 | 0.0827 0.0022 0.0849 | 24.6107
- 5 | 2.50 | 0.0824 0.0024 0.0848 | 22.6548
- 6 | 2.50 | 0.0821 0.0025 0.0846 | 20.6989
- 7 | 2.50 | 0.0818 0.0026 0.0844 | 18.9688
- 8 | 2.50 | 0.0815 0.0027 0.0842 | 17.4455
- 9 | 2.50 | 0.0811 0.0028 0.0839 | 15.9223
- 10 | 2.50 | 0.0808 0.0029 0.0837 | 14.6627
- 11 | 2.50 | 0.0805 0.0030 0.0834 | 13.4764
- 12 | 2.50 | 0.0801 0.0030 0.0831 | 12.3015
- 13 | 2.50 | 0.0797 0.0032 0.0829 | 11.3776
- 14 | 2.50 | 0.0794 0.0032 0.0826 | 10.4537
- 15 | 2.25 | 0.0785 0.0033 0.0818 | 9.5920
- 16 | 2.25 | 0.0755 0.0048 0.0803 | 8.8725
- 17 | 2.25 | 0.0744 0.0053 0.0796 | 8.1530
- 29 | 2.00 | 0.0757 0.0024 0.0781 | 3.3283
- 30 | 2.00 | 0.0702 0.0047 0.0750 | 3.1221
- 31 | 2.00 | 0.0683 0.0057 0.0740 | 2.9160
- 43 | 1.75 | 0.0674 0.0032 0.0706 | 1.5785
- 44 | 1.75 | 0.0632 0.0055 0.0686 | 1.5194
- 45 | 1.75 | 0.0617 0.0063 0.0680 | 1.4626
- 57 | 1.50 | 0.0604 0.0046 0.0650 | 1.0900
- 58 | 1.50 | 0.0572 0.0067 0.0639 | 1.0730
- 59 | 1.50 | 0.0562 0.0073 0.0635 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 171s
- Prepare output 10s
- 181s
- Jacobian determinant (RMS): 0.012 0.045 0.068 0.094 0.119 | 0.125703
- Template Matching: 0.087 0.223 0.205 0.185 0.169 | 0.168570
- Write result maps: 31s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 35s
- CSF distance: 16s
- PBT2x thickness: 45s
- 103s
- Create initial surface 86s
- Topology correction: 92s
- Surface refinement: 83s
- Reduction of surface collisions with optimization: 71s
- Spherical mapping with areal smoothing 86s
- Spherical registration 307s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 28s
- CSF distance: 15s
- PBT2x thickness: 43s
- 92s
- Create initial surface 83s
- Topology correction: 89s
- Surface refinement: 77s
- Reduction of surface collisions with optimization: 66s
- Spherical mapping with areal smoothing 82s
- Spherical registration 298s
- Final surface processing results:
- Average thickness (FS): 2.5666 0.6125 mm
- Surface intensity / position RMSE: 0.0661 / 0.0609
- Euler number / defect number / defect size: 12.0 / 8.5 / 0.56%
- Display thickness: /var/lib/condor/execute/dir_2615109/ds/UWM/sub-0027273/ses-1/surf/lh.thickness.sub-0027273_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2615109/ds/UWM/sub-0027273/ses-1/surf/rh.thickness.sub-0027273_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2615109/ds/UWM/sub-0027273/ses-1/sub-0027273_ses-1_run-1_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1708s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 26s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 18s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 6s
- ROI estimation of 'aal3' atlas 11s
- ROI estimation of 'mori' atlas 16s
- ROI estimation of 'anatomy3' atlas 24s
- ROI estimation of 'julichbrain' atlas 30s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 22s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 53s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 79s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s
- Write results 8s
- 320s
- Quality check: 11s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2615109/ds/UWM/sub-0027273/ses-1/report/catreport_sub-0027273_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 47 minute(s) and 54 second(s).
- Image Quality Rating (IQR): 81.95% (B-)
- GM volume (GMV): 50.02% (711.47 / 1422.35 ml)
- GM thickness (GMT): 2.57 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2615109/ds/UWM/sub-0027273/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_2615109/ds/UWM/sub-0027273/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_2615109/ds/UWM/sub-0027273/ses-1/label
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