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- CAT12.8.1 r1980: 1/1: ./dir_13776/ds/sub-001/sub-001_ses-t1_T1w.n
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- SANLM denoising (medium): 13s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 8s
- Initial correction 7s
- Refine background 4s
- Final correction 6s
- Final scaling 7s
- 45s
- Correct center-of-mass 5s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 84s
- SPM preprocessing 1 (estimate 2): 93s
- SPM preprocessing 2 (write):
- Write Segmentation 18s
- Update Segmentation 21s
- Update Skull-Stripping 45s
- Update probability maps 9s
- 93s
- Global intensity correction: 17s
- SANLM denoising after intensity normalization (medium): 7s
- Fast Optimized Shooting registration 39s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.02) 17s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 23s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 13s
- 84s
- ROI segmentation (partitioning):
- Atlas -> subject space 10s
- Major structures 4s
- Ventricle detection 13s
- Blood vessel detection 10s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 29s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 77s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 45s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 5s
- Level 1 cleanup (brain masking) 4s
- 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 | 0.0831 0.0000 0.0831 | 32.0000
- 2 | 2.50 | 0.0801 0.0013 0.0814 | 29.4886
- 3 | 2.50 | 0.0792 0.0020 0.0812 | 26.9772
- 4 | 2.50 | 0.0787 0.0022 0.0810 | 24.6107
- 5 | 2.50 | 0.0784 0.0024 0.0808 | 22.6548
- 6 | 2.50 | 0.0781 0.0025 0.0806 | 20.6989
- 7 | 2.50 | 0.0777 0.0026 0.0804 | 18.9688
- 8 | 2.50 | 0.0774 0.0028 0.0801 | 17.4455
- 9 | 2.50 | 0.0770 0.0028 0.0799 | 15.9223
- 10 | 2.50 | 0.0766 0.0030 0.0796 | 14.6627
- 11 | 2.50 | 0.0763 0.0031 0.0794 | 13.4764
- 12 | 2.50 | 0.0759 0.0032 0.0791 | 12.3015
- 13 | 2.50 | 0.0755 0.0033 0.0788 | 11.3776
- 14 | 2.50 | 0.0751 0.0034 0.0785 | 10.4537
- 15 | 2.25 | 0.0750 0.0035 0.0785 | 9.5920
- 16 | 2.25 | 0.0719 0.0051 0.0769 | 8.8725
- 29 | 2.00 | 0.0731 0.0023 0.0754 | 3.3283
- 30 | 2.00 | 0.0666 0.0049 0.0715 | 3.1221
- 31 | 2.00 | 0.0643 0.0060 0.0703 | 2.9160
- 43 | 1.75 | 0.0633 0.0035 0.0668 | 1.5785
- 44 | 1.75 | 0.0591 0.0057 0.0648 | 1.5194
- 45 | 1.75 | 0.0576 0.0065 0.0641 | 1.4626
- 57 | 1.50 | 0.0563 0.0048 0.0611 | 1.0900
- 58 | 1.50 | 0.0532 0.0068 0.0600 | 1.0730
- 59 | 1.50 | 0.0521 0.0075 0.0596 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 208s
- Prepare output 11s
- 218s
- Jacobian determinant (RMS): 0.012 0.046 0.069 0.096 0.120 | 0.127617
- Template Matching: 0.083 0.216 0.193 0.173 0.156 | 0.156303
- Write result maps: 29s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 36s
- CSF distance: 18s
- PBT2x thickness: 54s
- 114s
- Create initial surface 91s
- Topology correction: 107s
- Surface refinement: 127s
- Reduction of surface collisions with optimization: 92s
- Spherical mapping with areal smoothing 94s
- Spherical registration 249s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 36s
- CSF distance: 17s
- PBT2x thickness: 54s
- 114s
- Create initial surface 93s
- Topology correction: 108s
- Surface refinement: 97s
- Reduction of surface collisions with optimization: 90s
- Spherical mapping with areal smoothing 93s
- Spherical registration 243s
- Final surface processing results:
- Average thickness (FS): 2.5738 0.6695 mm
- Surface intensity / position RMSE: 0.0750 / 0.0860
- Euler number / defect number / defect size: 22.0 / 16.5 / 1.01%
- Display thickness: /var/lib/condor/execute/dir_13776/ds/sub-001/surf/lh.thickness.sub-001_ses-t1_T1w
- Display thickness: /var/lib/condor/execute/dir_13776/ds/sub-001/surf/rh.thickness.sub-001_ses-t1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_13776/ds/sub-001/sub-001_ses-t1_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1811s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 13s
- ROI estimation of 'neuromorphometrics' atlas 47s
- ROI estimation of 'lpba40' atlas 14s
- ROI estimation of 'hammers' atlas 33s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 12s
- ROI estimation of 'aal3' atlas 19s
- ROI estimation of 'mori' atlas 29s
- ROI estimation of 'anatomy3' atlas 41s
- ROI estimation of 'julichbrain' atlas 55s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 20s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 27s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 88s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 132s
- Write results 133s
- 533s
- Quality check: 5s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_13776/ds/sub-001/report/catreport_sub-001_ses-t1_T1w.pdf
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- CAT preprocessing takes 55 minute(s) and 37 second(s).
- Image Quality Rating (IQR): 84.40% (B)
- GM volume (GMV): 49.95% (735.58 / 1472.76 ml)
- GM thickness (GMT): 2.57 0.67 mm
- Segmentations are saved in /var/lib/condor/execute/dir_13776/ds/sub-001/mri
- Reports are saved in /var/lib/condor/execute/dir_13776/ds/sub-001/report
- Labels are saved in /var/lib/condor/execute/dir_13776/ds/sub-001/label
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