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- CAT12.8.1 r2040: 1/1: ./sub-0025991/ses-1/sub-0025991_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 42s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 5s
- Initial correction 4s
- Refine background 2s
- Final correction 4s
- Final scaling 4s
- 29s
- Correct center-of-mass 3s
- Affine registration 7s
- SPM preprocessing 1 (estimate 1 - TPM registration): 53s
- SPM preprocessing 1 (estimate 2): 49s
- SPM preprocessing 2 (write):
- Write Segmentation 13s
- Update Segmentation 15s
- Update Skull-Stripping 34s
- Update probability maps 7s
- 69s
- Global intensity correction: 14s
- SANLM denoising after intensity normalization (medium): 19s
- Fast Optimized Shooting registration 26s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 11s
- Estimate local tissue thresholds (WM) 15s
- Estimate local tissue thresholds (GM) 20s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 36s
- 90s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 3s
- Ventricle detection 9s
- Blood vessel detection 7s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.04) 18s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 50s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 28s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 3s
- Level 1 cleanup (brain masking) 2s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 9s
- 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 | 0.0837 0.0000 0.0837 | 32.0000
- 2 | 2.50 | 0.0809 0.0012 0.0821 | 29.4886
- 3 | 2.50 | 0.0800 0.0019 0.0818 | 26.9772
- 4 | 2.50 | 0.0796 0.0021 0.0817 | 24.6107
- 5 | 2.50 | 0.0792 0.0023 0.0815 | 22.6548
- 6 | 2.50 | 0.0789 0.0024 0.0813 | 20.6989
- 7 | 2.50 | 0.0786 0.0025 0.0811 | 18.9688
- 8 | 2.50 | 0.0783 0.0026 0.0809 | 17.4455
- 9 | 2.50 | 0.0780 0.0027 0.0806 | 15.9223
- 10 | 2.50 | 0.0776 0.0028 0.0804 | 14.6627
- 11 | 2.50 | 0.0773 0.0029 0.0802 | 13.4764
- 12 | 2.50 | 0.0769 0.0029 0.0799 | 12.3015
- 13 | 2.50 | 0.0766 0.0030 0.0796 | 11.3776
- 14 | 2.50 | 0.0762 0.0031 0.0793 | 10.4537
- 15 | 2.25 | 0.0754 0.0032 0.0786 | 9.5920
- 16 | 2.25 | 0.0724 0.0047 0.0771 | 8.8725
- 29 | 2.00 | 0.0734 0.0021 0.0755 | 3.3283
- 30 | 2.00 | 0.0673 0.0046 0.0719 | 3.1221
- 31 | 2.00 | 0.0652 0.0056 0.0708 | 2.9160
- 43 | 1.75 | 0.0640 0.0032 0.0672 | 1.5785
- 44 | 1.75 | 0.0597 0.0054 0.0652 | 1.5194
- 45 | 1.75 | 0.0583 0.0062 0.0645 | 1.4626
- 57 | 1.50 | 0.0567 0.0045 0.0612 | 1.0900
- 58 | 1.50 | 0.0537 0.0065 0.0602 | 1.0730
- 59 | 1.50 | 0.0527 0.0071 0.0598 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 133s
- Prepare output 8s
- 142s
- Jacobian determinant (RMS): 0.011 0.042 0.062 0.086 0.108 | 0.115219
- Template Matching: 0.084 0.217 0.196 0.175 0.158 | 0.158167
- Write result maps: 27s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 28s
- CSF distance: 11s
- PBT2x thickness: 33s
- 77s
- Create initial surface 66s
- Topology correction: 74s
- Surface refinement: 51s
- Reduction of surface collisions with optimization: 53s
- Spherical mapping with areal smoothing 62s
- Spherical registration 248s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 21s
- CSF distance: 12s
- PBT2x thickness: 33s
- 70s
- Create initial surface 64s
- Topology correction: 73s
- Surface refinement: 80s
- Reduction of surface collisions with optimization: 52s
- Spherical mapping with areal smoothing 61s
- Spherical registration 252s
- Final surface processing results:
- Average thickness (FS): 2.3973 0.6019 mm
- Surface intensity / position RMSE: 0.0608 / 0.0633
- Euler number / defect number / defect size: 12.0 / 7.0 / 0.27%
- Display thickness: /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-1/surf/lh.thickness.sub-0025991_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-1/surf/rh.thickness.sub-0025991_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-1/sub-0025991_ses-1_run-1_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1357s
- 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 19s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 10s
- ROI estimation of 'mori' atlas 15s
- ROI estimation of 'anatomy3' atlas 21s
- ROI estimation of 'julichbrain' atlas 28s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 20s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 45s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 67s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s
- Write results 7s
- 294s
- Quality check: 9s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-1/report/catreport_sub-0025991_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 39 minute(s) and 47 second(s).
- Image Quality Rating (IQR): 82.19% (B-)
- GM volume (GMV): 45.37% (613.12 / 1351.51 ml)
- GM thickness (GMT): 2.40 0.60 mm
- Segmentations are saved in /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-1/label
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