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- CAT12.8.1 r2040: 1/1: ./sub-0025736/ses-1/sub-0025736_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 43s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 4s
- Initial correction 4s
- Refine background 2s
- Final correction 3s
- Final scaling 4s
- 27s
- Correct center-of-mass 5s
- Affine registration 6s
- SPM preprocessing 1 (estimate 1 - TPM registration): 5s
- Use initial fine affine registration. 39s
- SPM preprocessing 1 (estimate 2): 39s
- SPM preprocessing 2 (write):
- Write Segmentation 12s
- Update Segmentation 12s
- Update Skull-Stripping 27s
- Update probability maps 6s
- 57s
- Global intensity correction: 10s
- SANLM denoising after intensity normalization (medium): 16s
- Fast Optimized Shooting registration 23s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 2s
- Prepare partitions 1s
- Prepare segments (LASmod = 1.19) 9s
- Estimate local tissue thresholds (WM) 12s
- Estimate local tissue thresholds (GM) 17s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 29s
- 73s
- ROI segmentation (partitioning):
- Atlas -> subject space 5s
- Major structures 2s
- Ventricle detection 7s
- Blood vessel detection 5s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 12s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 3s
- 37s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 22s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 2s
- Level 1 cleanup (brain masking) 2s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 7s
- 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 | 0.0828 0.0000 0.0828 | 32.0000
- 2 | 2.50 | 0.0804 0.0011 0.0815 | 29.4886
- 3 | 2.50 | 0.0797 0.0017 0.0814 | 26.9772
- 4 | 2.50 | 0.0794 0.0019 0.0812 | 24.6107
- 5 | 2.50 | 0.0791 0.0020 0.0811 | 22.6548
- 6 | 2.50 | 0.0788 0.0021 0.0809 | 20.6989
- 7 | 2.50 | 0.0785 0.0022 0.0808 | 18.9688
- 8 | 2.50 | 0.0783 0.0023 0.0806 | 17.4455
- 9 | 2.50 | 0.0780 0.0024 0.0804 | 15.9223
- 10 | 2.50 | 0.0777 0.0025 0.0802 | 14.6627
- 11 | 2.50 | 0.0774 0.0026 0.0800 | 13.4764
- 12 | 2.50 | 0.0771 0.0026 0.0797 | 12.3015
- 13 | 2.50 | 0.0767 0.0028 0.0795 | 11.3776
- 14 | 2.50 | 0.0764 0.0028 0.0792 | 10.4537
- 15 | 2.25 | 0.0763 0.0029 0.0792 | 9.5920
- 16 | 2.25 | 0.0732 0.0044 0.0776 | 8.8725
- 29 | 2.00 | 0.0747 0.0020 0.0767 | 3.3283
- 30 | 2.00 | 0.0684 0.0045 0.0729 | 3.1221
- 31 | 2.00 | 0.0662 0.0055 0.0717 | 2.9160
- 43 | 1.75 | 0.0652 0.0032 0.0684 | 1.5785
- 44 | 1.75 | 0.0608 0.0055 0.0662 | 1.5194
- 45 | 1.75 | 0.0593 0.0063 0.0656 | 1.4626
- 57 | 1.50 | 0.0578 0.0046 0.0623 | 1.0900
- 58 | 1.50 | 0.0546 0.0066 0.0612 | 1.0730
- 59 | 1.50 | 0.0536 0.0072 0.0609 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 108s
- Prepare output 7s
- 114s
- Jacobian determinant (RMS): 0.011 0.039 0.059 0.083 0.106 | 0.112145
- Template Matching: 0.083 0.220 0.199 0.178 0.161 | 0.160818
- Write result maps: 22s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 18s
- CSF distance: 9s
- PBT2x thickness: 26s
- 57s
- Create initial surface 46s
- Topology correction: 62s
- Surface refinement: 50s
- Reduction of surface collisions with optimization: 40s
- Spherical mapping with areal smoothing 51s
- Spherical registration 180s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 16s
- CSF distance: 8s
- PBT2x thickness: 26s
- 54s
- Create initial surface 46s
- Topology correction: 61s
- Surface refinement: 52s
- Reduction of surface collisions with optimization: 43s
- Spherical mapping with areal smoothing 65s
- Spherical registration 203s
- Final surface processing results:
- Average thickness (FS): 2.5193 0.6502 mm
- Surface intensity / position RMSE: 0.0701 / 0.0751
- Euler number / defect number / defect size: 22.0 / 9.5 / 1.33%
- Display thickness: /var/lib/condor/execute/dir_2985964/ds/SWU_4/sub-0025736/ses-1/surf/lh.thickness.sub-0025736_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2985964/ds/SWU_4/sub-0025736/ses-1/surf/rh.thickness.sub-0025736_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2985964/ds/SWU_4/sub-0025736/ses-1/sub-0025736_ses-1_run-1_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1070s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 24s
- ROI estimation of 'lpba40' atlas 7s
- ROI estimation of 'hammers' atlas 17s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 6s
- ROI estimation of 'aal3' atlas 9s
- ROI estimation of 'mori' atlas 14s
- ROI estimation of 'anatomy3' atlas 20s
- ROI estimation of 'julichbrain' atlas 28s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 19s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 42s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 63s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 5s
- Write results 6s
- 272s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2985964/ds/SWU_4/sub-0025736/ses-1/report/catreport_sub-0025736_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 32 minute(s) and 30 second(s).
- Image Quality Rating (IQR): 82.79% (B-)
- GM volume (GMV): 49.40% (652.06 / 1319.85 ml)
- GM thickness (GMT): 2.52 0.65 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2985964/ds/SWU_4/sub-0025736/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_2985964/ds/SWU_4/sub-0025736/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_2985964/ds/SWU_4/sub-0025736/ses-1/label
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