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- CAT12.8.1 r2040: 1/1: ./sub-0027269/ses-2/sub-0027269_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 58s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 5s
- Initial correction 5s
- Refine background 3s
- Final correction 4s
- Final scaling 4s
- 33s
- Correct center-of-mass 5s
- Affine registration 8s
- SPM preprocessing 1 (estimate 1 - TPM registration): 78s
- SPM preprocessing 1 (estimate 2): 58s
- SPM preprocessing 2 (write):
- Write Segmentation 15s
- Update Segmentation 18s
- Update Skull-Stripping 41s
- Update probability maps 9s
- 83s
- Global intensity correction: 15s
- SANLM denoising after intensity normalization (medium): 28s
- Fast Optimized Shooting registration 31s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 14s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 26s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 37s
- 104s
- 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) 24s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 3s
- Final corrections 4s
- 66s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 34s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.04]
- 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 | 0.0874 0.0000 0.0874 | 32.0000
- 2 | 2.50 | 0.0844 0.0013 0.0857 | 29.4886
- 3 | 2.50 | 0.0836 0.0019 0.0855 | 26.9772
- 4 | 2.50 | 0.0831 0.0022 0.0853 | 24.6107
- 5 | 2.50 | 0.0828 0.0024 0.0852 | 22.6548
- 6 | 2.50 | 0.0825 0.0025 0.0849 | 20.6989
- 7 | 2.50 | 0.0822 0.0026 0.0847 | 18.9688
- 8 | 2.50 | 0.0818 0.0027 0.0845 | 17.4455
- 9 | 2.50 | 0.0815 0.0028 0.0843 | 15.9223
- 10 | 2.50 | 0.0812 0.0029 0.0840 | 14.6627
- 11 | 2.50 | 0.0808 0.0030 0.0838 | 13.4764
- 12 | 2.50 | 0.0804 0.0030 0.0835 | 12.3015
- 13 | 2.50 | 0.0801 0.0032 0.0832 | 11.3776
- 14 | 2.50 | 0.0797 0.0032 0.0829 | 10.4537
- 15 | 2.25 | 0.0792 0.0033 0.0825 | 9.5920
- 16 | 2.25 | 0.0759 0.0049 0.0808 | 8.8725
- 17 | 2.25 | 0.0745 0.0055 0.0800 | 8.1530
- 29 | 2.00 | 0.0758 0.0025 0.0783 | 3.3283
- 30 | 2.00 | 0.0698 0.0050 0.0748 | 3.1221
- 31 | 2.00 | 0.0677 0.0060 0.0737 | 2.9160
- 43 | 1.75 | 0.0665 0.0035 0.0700 | 1.5785
- 44 | 1.75 | 0.0622 0.0057 0.0679 | 1.5194
- 45 | 1.75 | 0.0608 0.0065 0.0673 | 1.4626
- 57 | 1.50 | 0.0591 0.0048 0.0639 | 1.0900
- 58 | 1.50 | 0.0561 0.0067 0.0628 | 1.0730
- 59 | 1.50 | 0.0551 0.0074 0.0625 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 176s
- Prepare output 10s
- 186s
- Jacobian determinant (RMS): 0.012 0.043 0.064 0.088 0.111 | 0.117536
- Template Matching: 0.087 0.223 0.203 0.182 0.165 | 0.165354
- Write result maps: 52s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 56s
- CSF distance: 16s
- PBT2x thickness: 47s
- 126s
- Create initial surface 93s
- Topology correction: 92s
- Surface refinement: 76s
- Reduction of surface collisions with optimization: 71s
- Spherical mapping with areal smoothing 80s
- Spherical registration 267s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 35s
- CSF distance: 16s
- PBT2x thickness: 45s
- 101s
- Create initial surface 88s
- Topology correction: 91s
- Surface refinement: 80s
- Reduction of surface collisions with optimization: 68s
- Spherical mapping with areal smoothing 78s
- Spherical registration 285s
- Final surface processing results:
- Average thickness (FS): 2.5356 0.6425 mm
- Surface intensity / position RMSE: 0.0680 / 0.0715
- Euler number / defect number / defect size: 16.0 / 15.0 / 0.83%
- Display thickness: /var/lib/condor/execute/dir_611862/ds/UWM/sub-0027269/ses-2/surf/lh.thickness.sub-0027269_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_611862/ds/UWM/sub-0027269/ses-2/surf/rh.thickness.sub-0027269_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_611862/ds/UWM/sub-0027269/ses-2/sub-0027269_ses-2_run-1_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1694s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 8s
- ROI estimation of 'neuromorphometrics' atlas 28s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 20s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 8s
- ROI estimation of 'aal3' atlas 12s
- ROI estimation of 'mori' atlas 18s
- ROI estimation of 'anatomy3' atlas 28s
- ROI estimation of 'julichbrain' atlas 47s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 19s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 34s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 71s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 99s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s
- Write results 9s
- 410s
- Quality check: 13s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_611862/ds/UWM/sub-0027269/ses-2/report/catreport_sub-0027269_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 50 minute(s) and 52 second(s).
- Image Quality Rating (IQR): 81.92% (B-)
- GM volume (GMV): 48.32% (710.36 / 1470.15 ml)
- GM thickness (GMT): 2.54 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_611862/ds/UWM/sub-0027269/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_611862/ds/UWM/sub-0027269/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_611862/ds/UWM/sub-0027269/ses-2/label
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