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- CAT12.8.1 r2040: 1/1: ./sub-0025627/ses-1/sub-0025627_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 65s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 7s
- Initial correction 8s
- Refine background 3s
- Final correction 6s
- Final scaling 6s
- 44s
- Correct center-of-mass 5s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 95s
- SPM preprocessing 1 (estimate 2): 106s
- SPM preprocessing 2 (write):
- Write Segmentation 21s
- Update Segmentation 23s
- Update Skull-Stripping 49s
- Update probability maps 10s
- 105s
- Global intensity correction: 19s
- SANLM denoising after intensity normalization (medium): 34s
- Fast Optimized Shooting registration 41s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.05) 17s
- Estimate local tissue thresholds (WM) 24s
- Estimate local tissue thresholds (GM) 37s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 51s
- 141s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 4s
- Ventricle detection 16s
- Blood vessel detection 13s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.07) 30s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 83s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 39s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 5s
- Level 1 cleanup (brain masking) 4s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 4s
- 15s
- 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 | 0.0845 0.0000 0.0845 | 32.0000
- 2 | 2.50 | 0.0818 0.0012 0.0830 | 29.4886
- 3 | 2.50 | 0.0810 0.0018 0.0828 | 26.9772
- 4 | 2.50 | 0.0806 0.0021 0.0826 | 24.6107
- 5 | 2.50 | 0.0802 0.0022 0.0824 | 22.6548
- 6 | 2.50 | 0.0799 0.0023 0.0822 | 20.6989
- 7 | 2.50 | 0.0796 0.0024 0.0821 | 18.9688
- 8 | 2.50 | 0.0793 0.0025 0.0819 | 17.4455
- 9 | 2.50 | 0.0790 0.0026 0.0816 | 15.9223
- 10 | 2.50 | 0.0787 0.0027 0.0814 | 14.6627
- 11 | 2.50 | 0.0784 0.0028 0.0812 | 13.4764
- 12 | 2.50 | 0.0780 0.0029 0.0809 | 12.3015
- 13 | 2.50 | 0.0777 0.0030 0.0807 | 11.3776
- 14 | 2.50 | 0.0774 0.0030 0.0804 | 10.4537
- 15 | 2.25 | 0.0762 0.0031 0.0794 | 9.5920
- 16 | 2.25 | 0.0733 0.0046 0.0779 | 8.8725
- 29 | 2.00 | 0.0744 0.0021 0.0765 | 3.3283
- 30 | 2.00 | 0.0680 0.0047 0.0727 | 3.1221
- 31 | 2.00 | 0.0659 0.0057 0.0716 | 2.9160
- 43 | 1.75 | 0.0649 0.0033 0.0682 | 1.5785
- 44 | 1.75 | 0.0606 0.0055 0.0661 | 1.5194
- 45 | 1.75 | 0.0592 0.0063 0.0655 | 1.4626
- 57 | 1.50 | 0.0575 0.0046 0.0621 | 1.0900
- 58 | 1.50 | 0.0544 0.0066 0.0610 | 1.0730
- 59 | 1.50 | 0.0534 0.0072 0.0606 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 215s
- Prepare output 14s
- 229s
- Jacobian determinant (RMS): 0.011 0.039 0.058 0.081 0.102 | 0.108638
- Template Matching: 0.084 0.220 0.198 0.177 0.160 | 0.160253
- Write result maps: 43s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 53s
- CSF distance: 20s
- PBT2x thickness: 61s
- 142s
- Create initial surface 107s
- Topology correction: 122s
- Surface refinement: 108s
- Reduction of surface collisions with optimization: 94s
- Spherical mapping with areal smoothing 123s
- Spherical registration 343s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 57s
- CSF distance: 21s
- PBT2x thickness: 61s
- 146s
- Create initial surface 105s
- Topology correction: 124s
- Surface refinement: 127s
- Reduction of surface collisions with optimization: 88s
- Spherical mapping with areal smoothing 121s
- Spherical registration 364s
- Final surface processing results:
- Average thickness (FS): 2.5065 0.5966 mm
- Surface intensity / position RMSE: 0.0616 / 0.0621
- Euler number / defect number / defect size: 12.0 / 7.0 / 0.46%
- Display thickness: /var/lib/condor/execute/dir_92055/ds/JHNU/sub-0025627/ses-1/surf/lh.thickness.sub-0025627_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_92055/ds/JHNU/sub-0025627/ses-1/surf/rh.thickness.sub-0025627_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_92055/ds/JHNU/sub-0025627/ses-1/sub-0025627_ses-1_run-1_T1w.nii
- Surface ROI estimation: 11s
- Surface and thickness estimation takes: 2238s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 11s
- ROI estimation of 'neuromorphometrics' atlas 36s
- ROI estimation of 'lpba40' atlas 11s
- ROI estimation of 'hammers' atlas 25s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 9s
- ROI estimation of 'aal3' atlas 15s
- ROI estimation of 'mori' atlas 22s
- ROI estimation of 'anatomy3' atlas 31s
- ROI estimation of 'julichbrain' atlas 44s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 18s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 31s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 70s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 110s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 10s
- Write results 12s
- 445s
- Quality check: 16s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_92055/ds/JHNU/sub-0025627/ses-1/report/catreport_sub-0025627_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 64 minute(s) and 46 second(s).
- Image Quality Rating (IQR): 82.39% (B-)
- GM volume (GMV): 46.92% (716.85 / 1527.96 ml)
- GM thickness (GMT): 2.51 0.60 mm
- Segmentations are saved in /var/lib/condor/execute/dir_92055/ds/JHNU/sub-0025627/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_92055/ds/JHNU/sub-0025627/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_92055/ds/JHNU/sub-0025627/ses-1/label
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