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- CAT12.8.1 r1980: 1/1: ./dir_32090/ds/sub-1000/sub-1000_ses-01_T1w.n
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- SANLM denoising (medium): 188s
- APP: Rough bias correction:
- Initialize 9s
- Estimate background 8s
- Initial correction 15s
- Refine background 4s
- Final correction 9s
- Final scaling 7s
- 60s
- Correct center-of-mass 4s
- Affine registration 21s
- SPM preprocessing 1 (estimate 1 - TPM registration): 85s
- SPM preprocessing 1 (estimate 2): 59s
- SPM preprocessing 2 (write):
- Write Segmentation 21s
- Update Segmentation 23s
- Update Skull-Stripping 53s
- Update probability maps 11s
- 109s
- Global intensity correction: 21s
- SANLM denoising after intensity normalization (medium): 17s
- Fast Optimized Shooting registration 34s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 4s
- Prepare segments (LASmod = 1.27) 16s
- Estimate local tissue thresholds (WM) 23s
- Estimate local tissue thresholds (GM) 32s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 42s
- 127s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 4s
- Ventricle detection 17s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 34s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 6s
- 86s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 36s
- 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) 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 | 0.0833 0.0000 0.0833 | 32.0000
- 2 | 2.50 | 0.0806 0.0011 0.0817 | 29.4886
- 3 | 2.50 | 0.0798 0.0017 0.0815 | 26.9772
- 4 | 2.50 | 0.0794 0.0019 0.0814 | 24.6107
- 5 | 2.50 | 0.0791 0.0021 0.0812 | 22.6548
- 6 | 2.50 | 0.0789 0.0021 0.0810 | 20.6989
- 7 | 2.50 | 0.0786 0.0022 0.0808 | 18.9688
- 8 | 2.50 | 0.0784 0.0023 0.0807 | 17.4455
- 9 | 2.50 | 0.0781 0.0023 0.0804 | 15.9223
- 10 | 2.50 | 0.0778 0.0024 0.0802 | 14.6627
- 11 | 2.50 | 0.0775 0.0025 0.0800 | 13.4764
- 12 | 2.50 | 0.0773 0.0025 0.0798 | 12.3015
- 13 | 2.50 | 0.0770 0.0026 0.0796 | 11.3776
- 14 | 2.50 | 0.0767 0.0026 0.0793 | 10.4537
- 15 | 2.25 | 0.0771 0.0027 0.0798 | 9.5920
- 16 | 2.25 | 0.0744 0.0040 0.0784 | 8.8725
- 29 | 2.00 | 0.0767 0.0018 0.0785 | 3.3283
- 30 | 2.00 | 0.0708 0.0042 0.0750 | 3.1221
- 31 | 2.00 | 0.0687 0.0052 0.0739 | 2.9160
- 43 | 1.75 | 0.0682 0.0030 0.0712 | 1.5785
- 44 | 1.75 | 0.0636 0.0054 0.0690 | 1.5194
- 45 | 1.75 | 0.0620 0.0063 0.0683 | 1.4626
- 57 | 1.50 | 0.0611 0.0046 0.0657 | 1.0900
- 58 | 1.50 | 0.0576 0.0068 0.0644 | 1.0730
- 59 | 1.50 | 0.0564 0.0076 0.0640 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 151s
- Prepare output 12s
- 163s
- Jacobian determinant (RMS): 0.010 0.035 0.055 0.084 0.113 | 0.120419
- Template Matching: 0.083 0.223 0.206 0.186 0.169 | 0.169282
- Write result maps: 31s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 28s
- CSF distance: 15s
- PBT2x thickness: 45s
- 94s
- Create initial surface 88s
- Topology correction: 106s
- Surface refinement: 89s
- Reduction of surface collisions with optimization: 74s
- Spherical mapping with areal smoothing 86s
- Spherical registration 291s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 29s
- CSF distance: 15s
- PBT2x thickness: 43s
- 92s
- Create initial surface 82s
- Topology correction: 107s
- Surface refinement: 113s
- Reduction of surface collisions with optimization: 72s
- Spherical mapping with areal smoothing 80s
- Spherical registration 275s
- Final surface processing results:
- Average thickness (FS): 2.4252 0.6462 mm
- Surface intensity / position RMSE: 0.0852 / 0.1090
- Euler number / defect number / defect size: 104.0 / 47.0 / 3.45%
- Display thickness: /var/lib/condor/execute/dir_32090/ds/sub-1000/surf/lh.thickness.sub-1000_ses-01_T1w
- Display thickness: /var/lib/condor/execute/dir_32090/ds/sub-1000/surf/rh.thickness.sub-1000_ses-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_32090/ds/sub-1000/sub-1000_ses-01_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1751s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 11s
- ROI estimation of 'neuromorphometrics' atlas 42s
- ROI estimation of 'lpba40' atlas 12s
- ROI estimation of 'hammers' atlas 31s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 11s
- ROI estimation of 'aal3' atlas 17s
- ROI estimation of 'mori' atlas 24s
- ROI estimation of 'anatomy3' atlas 34s
- ROI estimation of 'julichbrain' atlas 46s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 18s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 32s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 74s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 112s
- Write results 113s
- 469s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_32090/ds/sub-1000/report/catreport_sub-1000_ses-01_T1w.pdf
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- CAT preprocessing takes 56 minute(s) and 23 second(s).
- Image Quality Rating (IQR): 80.37% (B-)
- GM volume (GMV): 50.53% (716.32 / 1417.54 ml)
- GM thickness (GMT): 2.43 0.65 mm
- Segmentations are saved in /var/lib/condor/execute/dir_32090/ds/sub-1000/mri
- Reports are saved in /var/lib/condor/execute/dir_32090/ds/sub-1000/report
- Labels are saved in /var/lib/condor/execute/dir_32090/ds/sub-1000/label
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