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- CAT12.8.1 r2040: 1/1: ./sub-0026128/ses-2/sub-0026128_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 36s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 4s
- Initial correction 4s
- Refine background 2s
- Final correction 3s
- Final scaling 3s
- 26s
- Correct center-of-mass 3s
- Affine registration 6s
- SPM preprocessing 1 (estimate 1 - TPM registration): 59s
- SPM preprocessing 1 (estimate 2): 60s
- SPM preprocessing 2 (write):
- Write Segmentation 13s
- Update Segmentation 14s
- Update Skull-Stripping 30s
- Update probability maps 7s
- 63s
- Global intensity correction: 11s
- 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 = 1.11) 10s
- Estimate local tissue thresholds (WM) 13s
- Estimate local tissue thresholds (GM) 19s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 28s
- 77s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 2s
- Ventricle detection 8s
- Blood vessel detection 6s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.08) 15s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 3s
- 44s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 25s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.04]
- 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
- 8s
- 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 | 0.0888 0.0000 0.0888 | 32.0000
- 2 | 2.50 | 0.0852 0.0015 0.0867 | 29.4886
- 3 | 2.50 | 0.0841 0.0023 0.0864 | 26.9772
- 4 | 2.50 | 0.0836 0.0026 0.0862 | 24.6107
- 5 | 2.50 | 0.0831 0.0028 0.0860 | 22.6548
- 6 | 2.50 | 0.0827 0.0030 0.0857 | 20.6989
- 7 | 2.50 | 0.0823 0.0031 0.0854 | 18.9688
- 8 | 2.50 | 0.0819 0.0033 0.0852 | 17.4455
- 9 | 2.50 | 0.0815 0.0034 0.0849 | 15.9223
- 10 | 2.50 | 0.0810 0.0036 0.0846 | 14.6627
- 11 | 2.50 | 0.0806 0.0037 0.0843 | 13.4764
- 12 | 2.50 | 0.0801 0.0038 0.0839 | 12.3015
- 13 | 2.50 | 0.0796 0.0039 0.0836 | 11.3776
- 14 | 2.50 | 0.0792 0.0040 0.0832 | 10.4537
- 15 | 2.25 | 0.0797 0.0042 0.0839 | 9.5920
- 16 | 2.25 | 0.0761 0.0060 0.0821 | 8.8725
- 17 | 2.25 | 0.0746 0.0066 0.0813 | 8.1530
- 29 | 2.00 | 0.0758 0.0030 0.0789 | 3.3283
- 30 | 2.00 | 0.0693 0.0058 0.0751 | 3.1221
- 31 | 2.00 | 0.0670 0.0069 0.0739 | 2.9160
- 43 | 1.75 | 0.0656 0.0040 0.0696 | 1.5785
- 44 | 1.75 | 0.0611 0.0064 0.0675 | 1.5194
- 45 | 1.75 | 0.0596 0.0072 0.0668 | 1.4626
- 57 | 1.50 | 0.0581 0.0053 0.0634 | 1.0900
- 58 | 1.50 | 0.0549 0.0074 0.0623 | 1.0730
- 59 | 1.50 | 0.0538 0.0081 0.0619 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 130s
- Prepare output 7s
- 137s
- Jacobian determinant (RMS): 0.014 0.053 0.081 0.110 0.136 | 0.143210
- Template Matching: 0.089 0.224 0.201 0.179 0.161 | 0.161421
- Write result maps: 29s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 26s
- CSF distance: 11s
- PBT2x thickness: 30s
- 71s
- Create initial surface 55s
- Topology correction: 69s
- Surface refinement: 75s
- Reduction of surface collisions with optimization: 46s
- Spherical mapping with areal smoothing 89s
- Spherical registration 207s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 19s
- CSF distance: 11s
- PBT2x thickness: 30s
- 64s
- Create initial surface 53s
- Topology correction: 66s
- Surface refinement: 50s
- Reduction of surface collisions with optimization: 44s
- Spherical mapping with areal smoothing 62s
- Spherical registration 211s
- Final surface processing results:
- Average thickness (FS): 2.5187 0.6104 mm
- Surface intensity / position RMSE: 0.0633 / 0.0615
- Euler number / defect number / defect size: 12.0 / 10.0 / 0.35%
- Display thickness: /var/lib/condor/execute/dir_2298364/ds/UM/sub-0026128/ses-2/surf/lh.thickness.sub-0026128_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2298364/ds/UM/sub-0026128/ses-2/surf/rh.thickness.sub-0026128_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2298364/ds/UM/sub-0026128/ses-2/sub-0026128_ses-2_run-1_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1231s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 26s
- ROI estimation of 'lpba40' atlas 7s
- ROI estimation of 'hammers' atlas 18s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 6s
- ROI estimation of 'aal3' atlas 10s
- ROI estimation of 'mori' atlas 15s
- ROI estimation of 'anatomy3' atlas 22s
- ROI estimation of 'julichbrain' atlas 30s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 22s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 48s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 75s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s
- Write results 7s
- 308s
- Quality check: 9s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2298364/ds/UM/sub-0026128/ses-2/report/catreport_sub-0026128_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 37 minute(s) and 32 second(s).
- Image Quality Rating (IQR): 79.08% (C+)
- GM volume (GMV): 46.14% (631.19 / 1367.89 ml)
- GM thickness (GMT): 2.52 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2298364/ds/UM/sub-0026128/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_2298364/ds/UM/sub-0026128/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_2298364/ds/UM/sub-0026128/ses-2/label
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