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- CAT12.8.1 r1980: 1/1: ./dir_2469/ds/sub-1181/sub-1181_ses-01_T1w.n
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- SANLM denoising (medium): 120s
- APP: Rough bias correction:
- Initialize 11s
- Estimate background 10s
- Initial correction 23s
- Refine background 5s
- Final correction 12s
- Final scaling 9s
- 82s
- Correct center-of-mass 6s
- Affine registration 22s
- SPM preprocessing 1 (estimate 1 - TPM registration): 12s
- Use initial fine affine registration. 89s
- SPM preprocessing 1 (estimate 2): 83s
- SPM preprocessing 2 (write):
- Write Segmentation 28s
- Update Segmentation 27s
- Update Skull-Stripping 67s
- Update probability maps 14s
- 135s
- Global intensity correction: 26s
- SANLM denoising after intensity normalization (medium): 13s
- Fast Optimized Shooting registration 47s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 5s
- Prepare segments (LASmod = 1.04) 21s
- Estimate local tissue thresholds (WM) 31s
- Estimate local tissue thresholds (GM) 47s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 52s
- 167s
- ROI segmentation (partitioning):
- Atlas -> subject space 11s
- Major structures 5s
- Ventricle detection 23s
- Blood vessel detection 14s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 34s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 7s
- 101s
- Blood vessel correction (BVCstr=0.50): 3s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 42s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 6s
- Level 1 cleanup (brain masking) 4s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 4s
- 15s
- 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 | 0.0852 0.0000 0.0852 | 32.0000
- 2 | 2.50 | 0.0818 0.0013 0.0830 | 29.4886
- 3 | 2.50 | 0.0809 0.0019 0.0827 | 26.9772
- 4 | 2.50 | 0.0805 0.0020 0.0825 | 24.6107
- 5 | 2.50 | 0.0802 0.0021 0.0823 | 22.6548
- 6 | 2.50 | 0.0800 0.0022 0.0821 | 20.6989
- 7 | 2.50 | 0.0797 0.0022 0.0820 | 18.9688
- 8 | 2.50 | 0.0795 0.0023 0.0818 | 17.4455
- 9 | 2.50 | 0.0792 0.0023 0.0815 | 15.9223
- 10 | 2.50 | 0.0790 0.0023 0.0813 | 14.6627
- 11 | 2.50 | 0.0788 0.0024 0.0811 | 13.4764
- 12 | 2.50 | 0.0785 0.0024 0.0809 | 12.3015
- 13 | 2.50 | 0.0783 0.0024 0.0807 | 11.3776
- 14 | 2.50 | 0.0780 0.0024 0.0804 | 10.4537
- 15 | 2.25 | 0.0773 0.0025 0.0798 | 9.5920
- 16 | 2.25 | 0.0747 0.0037 0.0784 | 8.8725
- 29 | 2.00 | 0.0770 0.0016 0.0787 | 3.3283
- 30 | 2.00 | 0.0714 0.0039 0.0754 | 3.1221
- 31 | 2.00 | 0.0697 0.0048 0.0745 | 2.9160
- 43 | 1.75 | 0.0696 0.0027 0.0723 | 1.5785
- 44 | 1.75 | 0.0651 0.0052 0.0702 | 1.5194
- 45 | 1.75 | 0.0637 0.0059 0.0696 | 1.4626
- 57 | 1.50 | 0.0629 0.0043 0.0671 | 1.0900
- 58 | 1.50 | 0.0595 0.0065 0.0660 | 1.0730
- 59 | 1.50 | 0.0584 0.0072 0.0656 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 200s
- Prepare output 16s
- 216s
- Jacobian determinant (RMS): 0.008 0.028 0.047 0.078 0.108 | 0.115207
- Template Matching: 0.085 0.224 0.209 0.191 0.175 | 0.175324
- Write result maps: 40s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 29s
- CSF distance: 19s
- PBT2x thickness: 55s
- 109s
- Create initial surface 95s
- Topology correction: 120s
- Surface refinement: 75s
- Reduction of surface collisions with optimization: 73s
- Spherical mapping with areal smoothing 98s
- Spherical registration 350s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 31s
- CSF distance: 19s
- PBT2x thickness: 54s
- 110s
- Create initial surface 92s
- Topology correction: 107s
- Surface refinement: 88s
- Reduction of surface collisions with optimization: 69s
- Spherical mapping with areal smoothing 95s
- Spherical registration 319s
- Final surface processing results:
- Average thickness (FS): 2.5838 0.6598 mm
- Surface intensity / position RMSE: 0.0883 / 0.1024
- Euler number / defect number / defect size: 64.0 / 44.5 / 2.27%
- Display thickness: /var/lib/condor/execute/dir_2469/ds/sub-1181/surf/lh.thickness.sub-1181_ses-01_T1w
- Display thickness: /var/lib/condor/execute/dir_2469/ds/sub-1181/surf/rh.thickness.sub-1181_ses-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2469/ds/sub-1181/sub-1181_ses-01_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 1917s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 14s
- ROI estimation of 'neuromorphometrics' atlas 47s
- ROI estimation of 'lpba40' atlas 14s
- ROI estimation of 'hammers' atlas 33s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 12s
- ROI estimation of 'aal3' atlas 19s
- ROI estimation of 'mori' atlas 28s
- ROI estimation of 'anatomy3' atlas 40s
- ROI estimation of 'julichbrain' atlas 54s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 21s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 37s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 85s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 128s
- Write results 129s
- 536s
- Quality check: 7s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2469/ds/sub-1181/report/catreport_sub-1181_ses-01_T1w.pdf
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- CAT preprocessing takes 63 minute(s) and 20 second(s).
- Image Quality Rating (IQR): 80.29% (B-)
- GM volume (GMV): 57.54% (723.95 / 1258.11 ml)
- GM thickness (GMT): 2.58 0.66 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2469/ds/sub-1181/mri
- Reports are saved in /var/lib/condor/execute/dir_2469/ds/sub-1181/report
- Labels are saved in /var/lib/condor/execute/dir_2469/ds/sub-1181/label
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