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- CAT12.8.1 r2040: 1/1: ./sub-0025254/ses-2/sub-0025254_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 54s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 7s
- Initial correction 7s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 39s
- Correct center-of-mass 5s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 89s
- SPM preprocessing 1 (estimate 2): 72s
- SPM preprocessing 2 (write):
- Write Segmentation 18s
- Update Segmentation 20s
- Update Skull-Stripping 42s
- Update probability maps 9s
- 89s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 28s
- Fast Optimized Shooting registration 38s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 16s
- Estimate local tissue thresholds (WM) 20s
- Estimate local tissue thresholds (GM) 32s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 43s
- 120s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 4s
- Ventricle detection 17s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 27s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 4s
- 75s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 35s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.07,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 5s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 3s
- 13s
- 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 | 0.0841 0.0000 0.0841 | 32.0000
- 2 | 2.50 | 0.0810 0.0013 0.0823 | 29.4886
- 3 | 2.50 | 0.0801 0.0020 0.0821 | 26.9772
- 4 | 2.50 | 0.0797 0.0022 0.0819 | 24.6107
- 5 | 2.50 | 0.0793 0.0024 0.0818 | 22.6548
- 6 | 2.50 | 0.0790 0.0025 0.0815 | 20.6989
- 7 | 2.50 | 0.0787 0.0026 0.0813 | 18.9688
- 8 | 2.50 | 0.0784 0.0028 0.0811 | 17.4455
- 9 | 2.50 | 0.0780 0.0028 0.0809 | 15.9223
- 10 | 2.50 | 0.0777 0.0030 0.0806 | 14.6627
- 11 | 2.50 | 0.0773 0.0031 0.0804 | 13.4764
- 12 | 2.50 | 0.0769 0.0031 0.0801 | 12.3015
- 13 | 2.50 | 0.0766 0.0033 0.0798 | 11.3776
- 14 | 2.50 | 0.0762 0.0033 0.0795 | 10.4537
- 15 | 2.25 | 0.0758 0.0034 0.0792 | 9.5920
- 16 | 2.25 | 0.0724 0.0051 0.0775 | 8.8725
- 29 | 2.00 | 0.0732 0.0023 0.0755 | 3.3283
- 30 | 2.00 | 0.0668 0.0049 0.0716 | 3.1221
- 31 | 2.00 | 0.0646 0.0059 0.0705 | 2.9160
- 43 | 1.75 | 0.0633 0.0034 0.0668 | 1.5785
- 44 | 1.75 | 0.0592 0.0056 0.0648 | 1.5194
- 45 | 1.75 | 0.0578 0.0064 0.0642 | 1.4626
- 57 | 1.50 | 0.0563 0.0047 0.0610 | 1.0900
- 58 | 1.50 | 0.0533 0.0066 0.0599 | 1.0730
- 59 | 1.50 | 0.0523 0.0073 0.0595 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 206s
- Prepare output 13s
- 219s
- Jacobian determinant (RMS): 0.012 0.044 0.065 0.091 0.113 | 0.120811
- Template Matching: 0.084 0.217 0.194 0.173 0.157 | 0.156837
- Write result maps: 38s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 45s
- CSF distance: 18s
- PBT2x thickness: 55s
- 125s
- Create initial surface 97s
- Topology correction: 88s
- Surface refinement: 110s
- Reduction of surface collisions with optimization: 71s
- Spherical mapping with areal smoothing 97s
- Spherical registration 344s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 32s
- CSF distance: 17s
- PBT2x thickness: 52s
- 107s
- Create initial surface 91s
- Topology correction: 88s
- Surface refinement: 80s
- Reduction of surface collisions with optimization: 69s
- Spherical mapping with areal smoothing 95s
- Spherical registration 339s
- Final surface processing results:
- Average thickness (FS): 2.6188 0.6316 mm
- Surface intensity / position RMSE: 0.0678 / 0.0640
- Euler number / defect number / defect size: 8.0 / 11.0 / 0.22%
- Display thickness: /var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-2/surf/lh.thickness.sub-0025254_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-2/surf/rh.thickness.sub-0025254_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-2/sub-0025254_ses-2_run-1_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 1905s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 29s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 20s
- 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 27s
- ROI estimation of 'julichbrain' atlas 37s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 26s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 61s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 92s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s
- Write results 10s
- 372s
- Quality check: 14s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-2/report/catreport_sub-0025254_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 55 minute(s) and 32 second(s).
- Image Quality Rating (IQR): 82.47% (B-)
- GM volume (GMV): 50.31% (658.89 / 1309.58 ml)
- GM thickness (GMT): 2.62 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-2/label
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