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- CAT12.8.1 r1980: 1/1: ./condor/execute/dir_60985/ds/sub-20/sub-20_T1w.n
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- SANLM denoising (medium): 25s
- APP: Rough bias correction:
- Initialize 3s
- Estimate background 6s
- Initial correction 5s
- Refine background 2s
- Final correction 4s
- Final scaling 4s
- 27s
- Correct center-of-mass 6s
- Affine registration 7s
- SPM preprocessing 1 (estimate 1 - TPM registration): 61s
- SPM preprocessing 1 (estimate 2): 44s
- SPM preprocessing 2 (write):
- Write Segmentation 12s
- Update Segmentation 17s
- Update Skull-Stripping 29s
- Update probability maps 5s
- 62s
- Global intensity correction: 9s
- SANLM denoising after intensity normalization (medium): 8s
- Fast Optimized Shooting registration 32s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 1s
- Prepare segments (LASmod = 1.00) 15s
- Estimate local tissue thresholds (WM) 15s
- Estimate local tissue thresholds (GM) 26s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 21s
- 84s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 4s
- Ventricle detection 17s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.06) 28s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 2s
- 73s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 32s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.04]
- 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 | 0.0827 0.0000 0.0827 | 32.0000
- 2 | 2.50 | 0.0806 0.0010 0.0816 | 29.4886
- 3 | 2.50 | 0.0800 0.0015 0.0815 | 26.9772
- 4 | 2.50 | 0.0797 0.0017 0.0814 | 24.6107
- 5 | 2.50 | 0.0794 0.0018 0.0812 | 22.6548
- 6 | 2.50 | 0.0792 0.0019 0.0811 | 20.6989
- 7 | 2.50 | 0.0790 0.0019 0.0810 | 18.9688
- 8 | 2.50 | 0.0788 0.0020 0.0808 | 17.4455
- 9 | 2.50 | 0.0786 0.0021 0.0807 | 15.9223
- 10 | 2.50 | 0.0783 0.0021 0.0805 | 14.6627
- 11 | 2.50 | 0.0781 0.0022 0.0803 | 13.4764
- 12 | 2.50 | 0.0779 0.0023 0.0801 | 12.3015
- 13 | 2.50 | 0.0776 0.0023 0.0800 | 11.3776
- 14 | 2.50 | 0.0774 0.0024 0.0798 | 10.4537
- 15 | 2.25 | 0.0759 0.0024 0.0783 | 9.5920
- 16 | 2.25 | 0.0734 0.0037 0.0770 | 8.8725
- 29 | 2.00 | 0.0751 0.0017 0.0768 | 3.3283
- 30 | 2.00 | 0.0693 0.0040 0.0733 | 3.1221
- 31 | 2.00 | 0.0673 0.0049 0.0723 | 2.9160
- 43 | 1.75 | 0.0664 0.0028 0.0692 | 1.5785
- 44 | 1.75 | 0.0620 0.0051 0.0671 | 1.5194
- 45 | 1.75 | 0.0607 0.0059 0.0665 | 1.4626
- 57 | 1.50 | 0.0591 0.0042 0.0633 | 1.0900
- 58 | 1.50 | 0.0560 0.0062 0.0623 | 1.0730
- 59 | 1.50 | 0.0551 0.0068 0.0619 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 204s
- Prepare output 11s
- 215s
- Jacobian determinant (RMS): 0.010 0.035 0.053 0.076 0.098 | 0.104583
- Template Matching: 0.083 0.220 0.202 0.182 0.165 | 0.165168
- Write result maps: 16s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 62s
- CSF distance: 19s
- PBT2x thickness: 57s
- 146s
- Create initial surface 102s
- Topology correction: 110s
- Surface refinement: 88s
- Reduction of surface collisions with optimization: 77s
- Spherical mapping with areal smoothing 99s
- Spherical registration 369s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 68s
- CSF distance: 19s
- PBT2x thickness: 56s
- 149s
- Create initial surface 99s
- Topology correction: 108s
- Surface refinement: 112s
- Reduction of surface collisions with optimization: 90s
- Spherical mapping with areal smoothing 102s
- Spherical registration 367s
- Final surface processing results:
- Average thickness (FS): 2.5771 0.6301 mm
- Surface intensity / position RMSE: 0.0687 / 0.0702
- Euler number / defect number / defect size: 22.0 / 12.5 / 0.53%
- Display thickness: /var/lib/condor/execute/dir_60985/ds/sub-20/surf/lh.thickness.sub-20_T1w
- Display thickness: /var/lib/condor/execute/dir_60985/ds/sub-20/surf/rh.thickness.sub-20_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_60985/ds/sub-20/sub-20_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 2136s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 5s
- ROI estimation of 'neuromorphometrics' atlas 16s
- ROI estimation of 'lpba40' atlas 5s
- ROI estimation of 'hammers' atlas 10s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 4s
- ROI estimation of 'aal3' atlas 6s
- ROI estimation of 'mori' atlas 9s
- ROI estimation of 'anatomy3' atlas 12s
- ROI estimation of 'julichbrain' atlas 16s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 7s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 11s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 24s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 36s
- Write results 38s
- 162s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_60985/ds/sub-20/report/catreport_sub-20_T1w.pdf
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- CAT preprocessing takes 51 minute(s) and 48 second(s).
- Image Quality Rating (IQR): 82.78% (B-)
- GM volume (GMV): 47.87% (670.32 / 1400.42 ml)
- GM thickness (GMT): 2.58 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_60985/ds/sub-20/mri
- Reports are saved in /var/lib/condor/execute/dir_60985/ds/sub-20/report
- Labels are saved in /var/lib/condor/execute/dir_60985/ds/sub-20/label
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