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- CAT12.8.1 r1980: 1/1: ./execute/dir_374794/ds/sub-01/sub-01_T1w.n
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- SANLM denoising (medium): 92s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 10s
- Initial correction 11s
- Refine background 4s
- Final correction 9s
- Final scaling 10s
- 62s
- Correct center-of-mass 4s
- Affine registration 17s
- SPM preprocessing 1 (estimate 1 - TPM registration): 108s
- SPM preprocessing 1 (estimate 2): 112s
- SPM preprocessing 2 (write):
- Write Segmentation 22s
- Update Segmentation 28s
- Update Skull-Stripping 60s
- Update probability maps 11s
- 122s
- Global intensity correction: 21s
- SANLM denoising after intensity normalization (medium): 19s
- Fast Optimized Shooting registration 41s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 6s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.05) 23s
- Estimate local tissue thresholds (WM) 28s
- Estimate local tissue thresholds (GM) 43s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 38s
- 146s
- ROI segmentation (partitioning):
- Atlas -> subject space 11s
- Major structures 6s
- Ventricle detection 26s
- Blood vessel detection 17s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.09) 41s
- Manual stroke lesion detection 0s
- Closing of deep structures 3s
- Side alignment 6s
- Final corrections 6s
- 115s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 49s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.990.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 7s
- Level 1 cleanup (brain masking) 5s
- Level 2 cleanup (CSF correction) 3s
- Level 3 cleanup (CSF/WM PVE) 5s
- 19s
- 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 | 0.0846 0.0000 0.0846 | 32.0000
- 2 | 2.50 | 0.0815 0.0013 0.0828 | 29.4886
- 3 | 2.50 | 0.0805 0.0020 0.0825 | 26.9772
- 4 | 2.50 | 0.0801 0.0023 0.0823 | 24.6107
- 5 | 2.50 | 0.0797 0.0024 0.0821 | 22.6548
- 6 | 2.50 | 0.0794 0.0025 0.0819 | 20.6989
- 7 | 2.50 | 0.0791 0.0026 0.0817 | 18.9688
- 8 | 2.50 | 0.0788 0.0027 0.0815 | 17.4455
- 9 | 2.50 | 0.0784 0.0028 0.0812 | 15.9223
- 10 | 2.50 | 0.0781 0.0029 0.0810 | 14.6627
- 11 | 2.50 | 0.0777 0.0030 0.0807 | 13.4764
- 12 | 2.50 | 0.0774 0.0030 0.0804 | 12.3015
- 13 | 2.50 | 0.0770 0.0032 0.0801 | 11.3776
- 14 | 2.50 | 0.0766 0.0032 0.0798 | 10.4537
- 15 | 2.25 | 0.0762 0.0033 0.0795 | 9.5920
- 16 | 2.25 | 0.0729 0.0049 0.0779 | 8.8725
- 29 | 2.00 | 0.0739 0.0022 0.0761 | 3.3283
- 30 | 2.00 | 0.0673 0.0049 0.0722 | 3.1221
- 31 | 2.00 | 0.0651 0.0059 0.0711 | 2.9160
- 43 | 1.75 | 0.0640 0.0034 0.0675 | 1.5785
- 44 | 1.75 | 0.0597 0.0057 0.0655 | 1.5194
- 45 | 1.75 | 0.0583 0.0065 0.0648 | 1.4626
- 57 | 1.50 | 0.0569 0.0048 0.0617 | 1.0900
- 58 | 1.50 | 0.0538 0.0068 0.0606 | 1.0730
- 59 | 1.50 | 0.0528 0.0074 0.0602 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 216s
- Prepare output 16s
- 232s
- Jacobian determinant (RMS): 0.011 0.042 0.066 0.095 0.121 | 0.128457
- Template Matching: 0.085 0.219 0.195 0.175 0.158 | 0.158275
- Write result maps: 76s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 48s
- CSF distance: 23s
- PBT2x thickness: 66s
- 146s
- Create initial surface 115s
- Topology correction: 123s
- Surface refinement: 176s
- Reduction of surface collisions with optimization: 95s
- Spherical mapping with areal smoothing 121s
- Spherical registration 342s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 49s
- CSF distance: 24s
- PBT2x thickness: 67s
- 148s
- Create initial surface 115s
- Topology correction: 131s
- Surface refinement: 127s
- Reduction of surface collisions with optimization: 88s
- Spherical mapping with areal smoothing 135s
- Spherical registration 337s
- Final surface processing results:
- Average thickness (FS): 2.5384 0.5940 mm
- Surface intensity / position RMSE: 0.0637 / 0.0622
- Euler number / defect number / defect size: 12.0 / 12.5 / 0.18%
- Display thickness: /var/lib/condor/execute/dir_374794/ds/sub-01/surf/lh.thickness.sub-01_T1w
- Display thickness: /var/lib/condor/execute/dir_374794/ds/sub-01/surf/rh.thickness.sub-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_374794/ds/sub-01/sub-01_T1w.nii
- Surface ROI estimation: 12s
- Surface and thickness estimation takes: 2328s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 11s
- ROI estimation of 'neuromorphometrics' atlas 40s
- ROI estimation of 'lpba40' atlas 11s
- ROI estimation of 'hammers' atlas 26s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 10s
- ROI estimation of 'aal3' atlas 15s
- ROI estimation of 'mori' atlas 22s
- ROI estimation of 'anatomy3' atlas 32s
- ROI estimation of 'julichbrain' atlas 44s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 29s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 69s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 102s
- Write results 104s
- 432s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_374794/ds/sub-01/report/catreport_sub-01_T1w.pdf
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- CAT preprocessing takes 68 minute(s) and 39 second(s).
- Image Quality Rating (IQR): 87.12% (B+)
- GM volume (GMV): 47.54% (774.15 / 1628.48 ml)
- GM thickness (GMT): 2.54 0.59 mm
- Segmentations are saved in /var/lib/condor/execute/dir_374794/ds/sub-01/mri
- Reports are saved in /var/lib/condor/execute/dir_374794/ds/sub-01/report
- Labels are saved in /var/lib/condor/execute/dir_374794/ds/sub-01/label
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