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- CAT12.8.1 r2040: 1/1: ./sub-0027274/ses-1/sub-0027274_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 61s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 6s
- Initial correction 5s
- Refine background 3s
- Final correction 4s
- Final scaling 5s
- 33s
- Correct center-of-mass 5s
- Affine registration 7s
- SPM preprocessing 1 (estimate 1 - TPM registration): 72s
- SPM preprocessing 1 (estimate 2): 59s
- SPM preprocessing 2 (write):
- Write Segmentation 16s
- Update Segmentation 20s
- Update Skull-Stripping 39s
- Update probability maps 8s
- 83s
- Global intensity correction: 14s
- SANLM denoising after intensity normalization (medium): 35s
- Fast Optimized Shooting registration 32s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.00) 16s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 28s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 40s
- 114s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 19s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 29s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 4s
- 82s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 38s
- 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) 3s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 3s
- 12s
- 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 | 0.0860 0.0000 0.0860 | 32.0000
- 2 | 2.50 | 0.0833 0.0012 0.0845 | 29.4886
- 3 | 2.50 | 0.0825 0.0018 0.0844 | 26.9772
- 4 | 2.50 | 0.0822 0.0020 0.0842 | 24.6107
- 5 | 2.50 | 0.0819 0.0022 0.0840 | 22.6548
- 6 | 2.50 | 0.0816 0.0023 0.0839 | 20.6989
- 7 | 2.50 | 0.0813 0.0024 0.0837 | 18.9688
- 8 | 2.50 | 0.0810 0.0025 0.0835 | 17.4455
- 9 | 2.50 | 0.0807 0.0025 0.0833 | 15.9223
- 10 | 2.50 | 0.0804 0.0026 0.0831 | 14.6627
- 11 | 2.50 | 0.0801 0.0027 0.0828 | 13.4764
- 12 | 2.50 | 0.0798 0.0027 0.0826 | 12.3015
- 13 | 2.50 | 0.0795 0.0028 0.0824 | 11.3776
- 14 | 2.50 | 0.0792 0.0029 0.0821 | 10.4537
- 15 | 2.25 | 0.0789 0.0030 0.0818 | 9.5920
- 16 | 2.25 | 0.0759 0.0044 0.0803 | 8.8725
- 17 | 2.25 | 0.0747 0.0049 0.0796 | 8.1530
- 29 | 2.00 | 0.0767 0.0022 0.0789 | 3.3283
- 30 | 2.00 | 0.0712 0.0045 0.0757 | 3.1221
- 31 | 2.00 | 0.0694 0.0054 0.0748 | 2.9160
- 43 | 1.75 | 0.0688 0.0031 0.0719 | 1.5785
- 44 | 1.75 | 0.0645 0.0054 0.0699 | 1.5194
- 45 | 1.75 | 0.0631 0.0061 0.0693 | 1.4626
- 57 | 1.50 | 0.0620 0.0044 0.0665 | 1.0900
- 58 | 1.50 | 0.0587 0.0066 0.0654 | 1.0730
- 59 | 1.50 | 0.0576 0.0073 0.0649 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 163s
- Prepare output 10s
- 174s
- Jacobian determinant (RMS): 0.010 0.035 0.054 0.077 0.103 | 0.108797
- Template Matching: 0.086 0.224 0.208 0.189 0.173 | 0.172939
- Write result maps: 30s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 51s
- CSF distance: 20s
- PBT2x thickness: 55s
- 134s
- Create initial surface 102s
- Topology correction: 112s
- Surface refinement: 106s
- Reduction of surface collisions with optimization: 95s
- Spherical mapping with areal smoothing 97s
- Spherical registration 283s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 33s
- CSF distance: 19s
- PBT2x thickness: 54s
- 113s
- Create initial surface 102s
- Topology correction: 115s
- Surface refinement: 149s
- Reduction of surface collisions with optimization: 107s
- Spherical mapping with areal smoothing 152s
- Spherical registration 315s
- Final surface processing results:
- Average thickness (FS): 2.6299 0.6323 mm
- Surface intensity / position RMSE: 0.0725 / 0.0691
- Euler number / defect number / defect size: 12.0 / 17.0 / 0.17%
- Display thickness: /var/lib/condor/execute/dir_2614931/ds/UWM/sub-0027274/ses-1/surf/lh.thickness.sub-0027274_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2614931/ds/UWM/sub-0027274/ses-1/surf/rh.thickness.sub-0027274_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2614931/ds/UWM/sub-0027274/ses-1/sub-0027274_ses-1_run-1_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 2090s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 8s
- ROI estimation of 'neuromorphometrics' atlas 29s
- ROI estimation of 'lpba40' atlas 9s
- ROI estimation of 'hammers' atlas 21s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 12s
- ROI estimation of 'mori' atlas 18s
- ROI estimation of 'anatomy3' atlas 25s
- ROI estimation of 'julichbrain' atlas 34s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 14s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 25s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 52s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 76s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s
- Write results 8s
- 339s
- Quality check: 12s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2614931/ds/UWM/sub-0027274/ses-1/report/catreport_sub-0027274_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 56 minute(s) and 11 second(s).
- Image Quality Rating (IQR): 81.05% (B-)
- GM volume (GMV): 50.69% (901.31 / 1778.10 ml)
- GM thickness (GMT): 2.63 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2614931/ds/UWM/sub-0027274/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_2614931/ds/UWM/sub-0027274/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_2614931/ds/UWM/sub-0027274/ses-1/label
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