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- CAT12.8.1 r1980: 1/1: ./dir_2068184/ds/sub-1103/sub-1103_ses-02_T1w.n
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- SANLM denoising (medium): 196s
- APP: Rough bias correction:
- Initialize 10s
- Estimate background 13s
- Initial correction 26s
- Refine background 5s
- Final correction 12s
- Final scaling 11s
- 88s
- Correct center-of-mass 4s
- Affine registration 26s
- SPM preprocessing 1 (estimate 1 - TPM registration): 113s
- SPM preprocessing 1 (estimate 2): 102s
- SPM preprocessing 2 (write):
- Write Segmentation 27s
- Update Segmentation 30s
- Update Skull-Stripping 67s
- Update probability maps 14s
- 138s
- Global intensity correction: 26s
- SANLM denoising after intensity normalization (medium): 28s
- Fast Optimized Shooting registration 46s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 6s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.17) 24s
- Estimate local tissue thresholds (WM) 33s
- Estimate local tissue thresholds (GM) 51s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 61s
- 184s
- ROI segmentation (partitioning):
- Atlas -> subject space 12s
- Major structures 6s
- Ventricle detection 22s
- Blood vessel detection 18s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 48s
- Manual stroke lesion detection 0s
- Closing of deep structures 3s
- Side alignment 6s
- Final corrections 7s
- 121s
- Blood vessel correction (BVCstr=0.50): 3s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 52s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 7s
- Level 1 cleanup (brain masking) 4s
- Level 2 cleanup (CSF correction) 2s
- 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 | 0.0818 0.0000 0.0818 | 32.0000
- 2 | 2.50 | 0.0801 0.0009 0.0810 | 29.4886
- 3 | 2.50 | 0.0796 0.0013 0.0810 | 26.9772
- 4 | 2.50 | 0.0794 0.0015 0.0809 | 24.6107
- 5 | 2.50 | 0.0792 0.0016 0.0808 | 22.6548
- 6 | 2.50 | 0.0791 0.0016 0.0807 | 20.6989
- 7 | 2.50 | 0.0789 0.0017 0.0806 | 18.9688
- 8 | 2.50 | 0.0787 0.0017 0.0804 | 17.4455
- 9 | 2.50 | 0.0785 0.0018 0.0803 | 15.9223
- 10 | 2.50 | 0.0783 0.0018 0.0801 | 14.6627
- 11 | 2.50 | 0.0781 0.0019 0.0800 | 13.4764
- 12 | 2.50 | 0.0779 0.0019 0.0798 | 12.3015
- 13 | 2.50 | 0.0777 0.0019 0.0797 | 11.3776
- 14 | 2.50 | 0.0775 0.0020 0.0795 | 10.4537
- 15 | 2.25 | 0.0766 0.0020 0.0786 | 9.5920
- 16 | 2.25 | 0.0740 0.0033 0.0773 | 8.8725
- 29 | 2.00 | 0.0758 0.0015 0.0773 | 3.3283
- 30 | 2.00 | 0.0702 0.0037 0.0739 | 3.1221
- 31 | 2.00 | 0.0684 0.0046 0.0730 | 2.9160
- 43 | 1.75 | 0.0678 0.0026 0.0704 | 1.5785
- 44 | 1.75 | 0.0635 0.0049 0.0684 | 1.5194
- 45 | 1.75 | 0.0621 0.0057 0.0678 | 1.4626
- 57 | 1.50 | 0.0610 0.0041 0.0651 | 1.0900
- 58 | 1.50 | 0.0578 0.0062 0.0640 | 1.0730
- 59 | 1.50 | 0.0568 0.0069 0.0636 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 195s
- Prepare output 17s
- 211s
- Jacobian determinant (RMS): 0.007 0.026 0.043 0.071 0.098 | 0.105778
- Template Matching: 0.082 0.222 0.205 0.186 0.170 | 0.170306
- Write result maps: 37s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 50s
- CSF distance: 23s
- PBT2x thickness: 74s
- 156s
- Create initial surface 120s
- Topology correction: 146s
- Surface refinement: 133s
- Reduction of surface collisions with optimization: 109s
- Spherical mapping with areal smoothing 120s
- Spherical registration 332s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 44s
- CSF distance: 22s
- PBT2x thickness: 68s
- 142s
- Create initial surface 117s
- Topology correction: 130s
- Surface refinement: 114s
- Reduction of surface collisions with optimization: 99s
- Spherical mapping with areal smoothing 117s
- Spherical registration 358s
- Final surface processing results:
- Average thickness (FS): 2.5503 0.6072 mm
- Surface intensity / position RMSE: 0.0800 / 0.0836
- Euler number / defect number / defect size: 40.0 / 30.5 / 1.57%
- Display thickness: /var/lib/condor/execute/dir_2068184/ds/sub-1103/surf/lh.thickness.sub-1103_ses-02_T1w
- Display thickness: /var/lib/condor/execute/dir_2068184/ds/sub-1103/surf/rh.thickness.sub-1103_ses-02_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2068184/ds/sub-1103/sub-1103_ses-02_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 2327s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 13s
- ROI estimation of 'neuromorphometrics' atlas 46s
- ROI estimation of 'lpba40' atlas 13s
- ROI estimation of 'hammers' atlas 32s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 11s
- ROI estimation of 'aal3' atlas 18s
- ROI estimation of 'mori' atlas 27s
- ROI estimation of 'anatomy3' atlas 39s
- ROI estimation of 'julichbrain' atlas 52s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 21s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 35s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 82s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 122s
- Write results 124s
- 516s
- Quality check: 9s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2068184/ds/sub-1103/report/catreport_sub-1103_ses-02_T1w.pdf
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- CAT preprocessing takes 73 minute(s) and 24 second(s).
- Image Quality Rating (IQR): 81.78% (B-)
- GM volume (GMV): 49.93% (834.93 / 1672.26 ml)
- GM thickness (GMT): 2.55 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2068184/ds/sub-1103/mri
- Reports are saved in /var/lib/condor/execute/dir_2068184/ds/sub-1103/report
- Labels are saved in /var/lib/condor/execute/dir_2068184/ds/sub-1103/label
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