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- CAT12.8.1 r1980: 1/1: ./dir_59705/ds/sub-1043/sub-1043_ses-01_T1w.n
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- SANLM denoising (medium): 177s
- APP: Rough bias correction:
- Initialize 11s
- Estimate background 14s
- Initial correction 23s
- Refine background 5s
- Final correction 12s
- Final scaling 8s
- 85s
- Correct center-of-mass 6s
- Affine registration 28s
- SPM preprocessing 1 (estimate 1 - TPM registration): 12s
- Use initial fine affine registration. 95s
- SPM preprocessing 1 (estimate 2): 88s
- SPM preprocessing 2 (write):
- Write Segmentation 29s
- Update Segmentation 30s
- Update Skull-Stripping 70s
- Update probability maps 15s
- 144s
- Global intensity correction: 27s
- SANLM denoising after intensity normalization (medium): 20s
- Fast Optimized Shooting registration 48s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 6s
- Prepare partitions 10s
- Prepare segments (LASmod = 1.05) 23s
- Estimate local tissue thresholds (WM) 34s
- Estimate local tissue thresholds (GM) 51s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 59s
- 187s
- ROI segmentation (partitioning):
- Atlas -> subject space 12s
- Major structures 5s
- Ventricle detection 25s
- Blood vessel detection 16s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 41s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 5s
- Final corrections 8s
- 115s
- Blood vessel correction (BVCstr=0.50): 3s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 46s
- 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
- 17s
- 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 | 0.0860 0.0000 0.0860 | 32.0000
- 2 | 2.50 | 0.0827 0.0013 0.0839 | 29.4886
- 3 | 2.50 | 0.0819 0.0018 0.0837 | 26.9772
- 4 | 2.50 | 0.0815 0.0019 0.0835 | 24.6107
- 5 | 2.50 | 0.0813 0.0020 0.0833 | 22.6548
- 6 | 2.50 | 0.0811 0.0020 0.0831 | 20.6989
- 7 | 2.50 | 0.0809 0.0020 0.0829 | 18.9688
- 8 | 2.50 | 0.0807 0.0021 0.0828 | 17.4455
- 9 | 2.50 | 0.0805 0.0020 0.0826 | 15.9223
- 10 | 2.50 | 0.0803 0.0021 0.0824 | 14.6627
- 11 | 2.50 | 0.0801 0.0021 0.0822 | 13.4764
- 12 | 2.50 | 0.0799 0.0021 0.0820 | 12.3015
- 13 | 2.50 | 0.0797 0.0021 0.0818 | 11.3776
- 14 | 2.50 | 0.0795 0.0021 0.0816 | 10.4537
- 15 | 2.25 | 0.0789 0.0021 0.0810 | 9.5920
- 16 | 2.25 | 0.0761 0.0034 0.0795 | 8.8725
- 17 | 2.25 | 0.0753 0.0037 0.0791 | 8.1530
- 18 | 2.25 | 0.0748 0.0038 0.0787 | 7.5234
- 29 | 2.00 | 0.0779 0.0018 0.0798 | 3.3283
- 30 | 2.00 | 0.0728 0.0041 0.0769 | 3.1221
- 31 | 2.00 | 0.0714 0.0048 0.0762 | 2.9160
- 43 | 1.75 | 0.0714 0.0027 0.0741 | 1.5785
- 44 | 1.75 | 0.0668 0.0052 0.0720 | 1.5194
- 45 | 1.75 | 0.0654 0.0060 0.0714 | 1.4626
- 57 | 1.50 | 0.0646 0.0043 0.0689 | 1.0900
- 58 | 1.50 | 0.0611 0.0066 0.0678 | 1.0730
- 59 | 1.50 | 0.0600 0.0074 0.0674 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 210s
- Prepare output 17s
- 226s
- Jacobian determinant (RMS): 0.005 0.019 0.041 0.071 0.102 | 0.109380
- Template Matching: 0.086 0.225 0.214 0.196 0.180 | 0.180130
- Write result maps: 42s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 39s
- CSF distance: 22s
- PBT2x thickness: 62s
- 131s
- Create initial surface 112s
- Topology correction: 133s
- Surface refinement: 143s
- Reduction of surface collisions with optimization: 92s
- Spherical mapping with areal smoothing 116s
- Spherical registration 341s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 38s
- CSF distance: 20s
- PBT2x thickness: 61s
- 126s
- Create initial surface 106s
- Topology correction: 128s
- Surface refinement: 121s
- Reduction of surface collisions with optimization: 87s
- Spherical mapping with areal smoothing 103s
- Spherical registration 346s
- Final surface processing results:
- Average thickness (FS): 2.5213 0.7080 mm
- Surface intensity / position RMSE: 0.0954 / 0.1329
- Euler number / defect number / defect size: 212.0 / 73.0 / 6.65%
- Display thickness: /var/lib/condor/execute/dir_59705/ds/sub-1043/surf/lh.thickness.sub-1043_ses-01_T1w
- Display thickness: /var/lib/condor/execute/dir_59705/ds/sub-1043/surf/rh.thickness.sub-1043_ses-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_59705/ds/sub-1043/sub-1043_ses-01_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 2215s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 14s
- ROI estimation of 'neuromorphometrics' atlas 50s
- ROI estimation of 'lpba40' atlas 14s
- ROI estimation of 'hammers' atlas 36s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 12s
- ROI estimation of 'aal3' atlas 22s
- ROI estimation of 'mori' atlas 29s
- ROI estimation of 'anatomy3' atlas 42s
- ROI estimation of 'julichbrain' atlas 53s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 21s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 36s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 86s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 128s
- Write results 129s
- 546s
- Quality check: 7s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_59705/ds/sub-1043/report/catreport_sub-1043_ses-01_T1w.pdf
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- CAT preprocessing takes 71 minute(s) and 0 second(s).
- Image Quality Rating (IQR): 81.21% (B-)
- GM volume (GMV): 55.10% (798.39 / 1449.00 ml)
- GM thickness (GMT): 2.52 0.71 mm
- Segmentations are saved in /var/lib/condor/execute/dir_59705/ds/sub-1043/mri
- Reports are saved in /var/lib/condor/execute/dir_59705/ds/sub-1043/report
- Labels are saved in /var/lib/condor/execute/dir_59705/ds/sub-1043/label
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