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- CAT12.8.1 r1980: 1/1: ./condor/execute/dir_19926/ds/sub-32/sub-32_T1w.n
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- SANLM denoising (medium): 35s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 7s
- Initial correction 7s
- Refine background 3s
- Final correction 6s
- Final scaling 7s
- 39s
- Correct center-of-mass 2s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 74s
- SPM preprocessing 1 (estimate 2): 61s
- SPM preprocessing 2 (write):
- Write Segmentation 15s
- Update Segmentation 19s
- Update Skull-Stripping 39s
- Update probability maps 8s
- 81s
- Global intensity correction: 14s
- SANLM denoising after intensity normalization (medium): 11s
- Fast Optimized Shooting registration 31s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 17s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 24s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 37s
- 106s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 20s
- Blood vessel detection 12s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.11) 36s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 5s
- Final corrections 4s
- 91s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 37s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 5s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 3s
- 14s
- 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 | 0.0849 0.0000 0.0849 | 32.0000
- 2 | 2.50 | 0.0819 0.0013 0.0832 | 29.4886
- 3 | 2.50 | 0.0811 0.0019 0.0830 | 26.9772
- 4 | 2.50 | 0.0807 0.0021 0.0828 | 24.6107
- 5 | 2.50 | 0.0803 0.0023 0.0826 | 22.6548
- 6 | 2.50 | 0.0801 0.0023 0.0824 | 20.6989
- 7 | 2.50 | 0.0798 0.0024 0.0822 | 18.9688
- 8 | 2.50 | 0.0795 0.0025 0.0820 | 17.4455
- 9 | 2.50 | 0.0792 0.0026 0.0818 | 15.9223
- 10 | 2.50 | 0.0789 0.0027 0.0816 | 14.6627
- 11 | 2.50 | 0.0785 0.0028 0.0813 | 13.4764
- 12 | 2.50 | 0.0782 0.0028 0.0810 | 12.3015
- 13 | 2.50 | 0.0779 0.0029 0.0808 | 11.3776
- 14 | 2.50 | 0.0775 0.0030 0.0805 | 10.4537
- 15 | 2.25 | 0.0772 0.0031 0.0802 | 9.5920
- 16 | 2.25 | 0.0742 0.0045 0.0787 | 8.8725
- 29 | 2.00 | 0.0755 0.0020 0.0776 | 3.3283
- 30 | 2.00 | 0.0692 0.0046 0.0738 | 3.1221
- 31 | 2.00 | 0.0670 0.0057 0.0727 | 2.9160
- 43 | 1.75 | 0.0659 0.0033 0.0692 | 1.5785
- 44 | 1.75 | 0.0613 0.0057 0.0670 | 1.5194
- 45 | 1.75 | 0.0598 0.0066 0.0664 | 1.4626
- 57 | 1.50 | 0.0582 0.0048 0.0630 | 1.0900
- 58 | 1.50 | 0.0549 0.0069 0.0618 | 1.0730
- 59 | 1.50 | 0.0538 0.0076 0.0614 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 166s
- Prepare output 11s
- 177s
- Jacobian determinant (RMS): 0.010 0.040 0.063 0.092 0.118 | 0.126898
- Template Matching: 0.085 0.223 0.201 0.179 0.161 | 0.161420
- Write result maps: 23s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 58s
- CSF distance: 18s
- PBT2x thickness: 48s
- 132s
- Create initial surface 107s
- Topology correction: 112s
- Surface refinement: 134s
- Reduction of surface collisions with optimization: 90s
- Spherical mapping with areal smoothing 96s
- Spherical registration 291s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 45s
- CSF distance: 18s
- PBT2x thickness: 51s
- 121s
- Create initial surface 106s
- Topology correction: 114s
- Surface refinement: 125s
- Reduction of surface collisions with optimization: 89s
- Spherical mapping with areal smoothing 96s
- Spherical registration 300s
- Final surface processing results:
- Average thickness (FS): 2.3621 0.5730 mm
- Surface intensity / position RMSE: 0.0604 / 0.0684
- Euler number / defect number / defect size: 24.0 / 8.5 / 1.02%
- Display thickness: /var/lib/condor/execute/dir_19926/ds/sub-32/surf/lh.thickness.sub-32_T1w
- Display thickness: /var/lib/condor/execute/dir_19926/ds/sub-32/surf/rh.thickness.sub-32_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_19926/ds/sub-32/sub-32_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 2012s
- 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 11s
- ROI estimation of 'mori' atlas 16s
- ROI estimation of 'anatomy3' atlas 23s
- 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 50s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 73s
- Write results 74s
- 307s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_19926/ds/sub-32/report/catreport_sub-32_T1w.pdf
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- CAT preprocessing takes 54 minute(s) and 8 second(s).
- Image Quality Rating (IQR): 85.00% (B)
- GM volume (GMV): 42.32% (779.89 / 1842.87 ml)
- GM thickness (GMT): 2.36 0.57 mm
- Segmentations are saved in /var/lib/condor/execute/dir_19926/ds/sub-32/mri
- Reports are saved in /var/lib/condor/execute/dir_19926/ds/sub-32/report
- Labels are saved in /var/lib/condor/execute/dir_19926/ds/sub-32/label
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