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- CAT12.8.1 r1980: 1/1: ./dir_22635/ds/sub-1270/sub-1270_ses-02_T1w.n
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- SANLM denoising (medium): 85s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 8s
- Initial correction 15s
- Refine background 4s
- Final correction 8s
- Final scaling 7s
- 57s
- Correct center-of-mass 4s
- Affine registration 20s
- SPM preprocessing 1 (estimate 1 - TPM registration): 83s
- SPM preprocessing 1 (estimate 2): 70s
- SPM preprocessing 2 (write):
- Write Segmentation 21s
- Update Segmentation 22s
- Update Skull-Stripping 51s
- Update probability maps 11s
- 105s
- Global intensity correction: 21s
- SANLM denoising after intensity normalization (medium): 18s
- Fast Optimized Shooting registration 34s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.14) 17s
- Estimate local tissue thresholds (WM) 22s
- Estimate local tissue thresholds (GM) 33s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 55s
- 140s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 4s
- Ventricle detection 20s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 32s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 87s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 37s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- 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 | 0.0886 0.0000 0.0886 | 32.0000
- 2 | 2.50 | 0.0853 0.0013 0.0866 | 29.4886
- 3 | 2.50 | 0.0843 0.0021 0.0864 | 26.9772
- 4 | 2.50 | 0.0838 0.0023 0.0862 | 24.6107
- 5 | 2.50 | 0.0835 0.0025 0.0860 | 22.6548
- 6 | 2.50 | 0.0831 0.0026 0.0857 | 20.6989
- 7 | 2.50 | 0.0828 0.0027 0.0855 | 18.9688
- 8 | 2.50 | 0.0825 0.0028 0.0853 | 17.4455
- 9 | 2.50 | 0.0821 0.0029 0.0850 | 15.9223
- 10 | 2.50 | 0.0817 0.0030 0.0847 | 14.6627
- 11 | 2.50 | 0.0814 0.0031 0.0844 | 13.4764
- 12 | 2.50 | 0.0810 0.0032 0.0841 | 12.3015
- 13 | 2.50 | 0.0806 0.0033 0.0838 | 11.3776
- 14 | 2.50 | 0.0802 0.0033 0.0835 | 10.4537
- 15 | 2.25 | 0.0821 0.0034 0.0855 | 9.5920
- 16 | 2.25 | 0.0786 0.0051 0.0837 | 8.8725
- 17 | 2.25 | 0.0771 0.0057 0.0829 | 8.1530
- 18 | 2.25 | 0.0762 0.0060 0.0822 | 7.5234
- 19 | 2.25 | 0.0755 0.0062 0.0816 | 6.9630
- 20 | 2.25 | 0.0748 0.0062 0.0810 | 6.4027
- 29 | 2.00 | 0.0774 0.0034 0.0809 | 3.3283
- 30 | 2.00 | 0.0726 0.0057 0.0783 | 3.1221
- 31 | 2.00 | 0.0708 0.0065 0.0773 | 2.9160
- 43 | 1.75 | 0.0704 0.0037 0.0741 | 1.5785
- 44 | 1.75 | 0.0658 0.0062 0.0719 | 1.5194
- 45 | 1.75 | 0.0642 0.0070 0.0712 | 1.4626
- 57 | 1.50 | 0.0636 0.0052 0.0687 | 1.0900
- 58 | 1.50 | 0.0600 0.0075 0.0675 | 1.0730
- 59 | 1.50 | 0.0588 0.0082 0.0670 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 165s
- Prepare output 11s
- 176s
- Jacobian determinant (RMS): 0.011 0.042 0.068 0.095 0.122 | 0.129832
- Template Matching: 0.089 0.224 0.212 0.193 0.176 | 0.176474
- Write result maps: 29s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 29s
- CSF distance: 15s
- PBT2x thickness: 43s
- 93s
- Create initial surface 81s
- Topology correction: 91s
- Surface refinement: 87s
- Reduction of surface collisions with optimization: 65s
- Spherical mapping with areal smoothing 79s
- Spherical registration 296s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 24s
- CSF distance: 15s
- PBT2x thickness: 45s
- 91s
- Create initial surface 82s
- Topology correction: 93s
- Surface refinement: 77s
- Reduction of surface collisions with optimization: 71s
- Spherical mapping with areal smoothing 86s
- Spherical registration 299s
- Final surface processing results:
- Average thickness (FS): 2.5989 0.6644 mm
- Surface intensity / position RMSE: 0.0828 / 0.0886
- Euler number / defect number / defect size: 40.0 / 19.5 / 1.04%
- Display thickness: /var/lib/condor/execute/dir_22635/ds/sub-1270/surf/lh.thickness.sub-1270_ses-02_T1w
- Display thickness: /var/lib/condor/execute/dir_22635/ds/sub-1270/surf/rh.thickness.sub-1270_ses-02_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_22635/ds/sub-1270/sub-1270_ses-02_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1690s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 10s
- ROI estimation of 'neuromorphometrics' atlas 38s
- ROI estimation of 'lpba40' atlas 11s
- ROI estimation of 'hammers' atlas 26s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 9s
- ROI estimation of 'aal3' atlas 15s
- ROI estimation of 'mori' atlas 22s
- ROI estimation of 'anatomy3' atlas 32s
- ROI estimation of 'julichbrain' atlas 43s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 30s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 69s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 106s
- Write results 107s
- 433s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_22635/ds/sub-1270/report/catreport_sub-1270_ses-02_T1w.pdf
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- CAT preprocessing takes 54 minute(s) and 3 second(s).
- Image Quality Rating (IQR): 80.17% (B-)
- GM volume (GMV): 52.91% (737.72 / 1394.37 ml)
- GM thickness (GMT): 2.60 0.66 mm
- Segmentations are saved in /var/lib/condor/execute/dir_22635/ds/sub-1270/mri
- Reports are saved in /var/lib/condor/execute/dir_22635/ds/sub-1270/report
- Labels are saved in /var/lib/condor/execute/dir_22635/ds/sub-1270/label
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