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- CAT12.8.1 r2040: 1/1: ./sub-0027428/ses-2/sub-0027428_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 37s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 7s
- Initial correction 8s
- Refine background 4s
- Final correction 6s
- Final scaling 5s
- 45s
- Correct center-of-mass 3s
- Affine registration 13s
- SPM preprocessing 1 (estimate 1 - TPM registration): 13s
- Use initial fine affine registration. 5s
- Use previous fine affine registration. 67s
- SPM preprocessing 1 (estimate 2): 79s
- SPM preprocessing 2 (write):
- Write Segmentation 20s
- Update Segmentation 19s
- Update Skull-Stripping 48s
- Update probability maps 11s
- 97s
- Global intensity correction: 20s
- SANLM denoising after intensity normalization (medium): 23s
- Fast Optimized Shooting registration 34s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 5s
- Prepare segments (LASmod = 1.00) 13s
- Estimate local tissue thresholds (WM) 21s
- Estimate local tissue thresholds (GM) 29s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 46s
- 122s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 3s
- Ventricle detection 10s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 23s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 5s
- 62s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 31s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 3s
- 11s
- 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 | 0.0827 0.0000 0.0827 | 32.0000
- 2 | 2.50 | 0.0796 0.0013 0.0809 | 29.4886
- 3 | 2.50 | 0.0788 0.0020 0.0807 | 26.9772
- 4 | 2.50 | 0.0783 0.0022 0.0805 | 24.6107
- 5 | 2.50 | 0.0780 0.0024 0.0804 | 22.6548
- 6 | 2.50 | 0.0777 0.0025 0.0801 | 20.6989
- 7 | 2.50 | 0.0774 0.0026 0.0799 | 18.9688
- 8 | 2.50 | 0.0770 0.0027 0.0797 | 17.4455
- 9 | 2.50 | 0.0767 0.0027 0.0795 | 15.9223
- 10 | 2.50 | 0.0764 0.0029 0.0792 | 14.6627
- 11 | 2.50 | 0.0760 0.0029 0.0790 | 13.4764
- 12 | 2.50 | 0.0757 0.0030 0.0787 | 12.3015
- 13 | 2.50 | 0.0753 0.0031 0.0784 | 11.3776
- 14 | 2.50 | 0.0750 0.0032 0.0782 | 10.4537
- 15 | 2.25 | 0.0747 0.0033 0.0779 | 9.5920
- 16 | 2.25 | 0.0715 0.0048 0.0763 | 8.8725
- 29 | 2.00 | 0.0723 0.0022 0.0745 | 3.3283
- 30 | 2.00 | 0.0663 0.0046 0.0709 | 3.1221
- 31 | 2.00 | 0.0642 0.0056 0.0698 | 2.9160
- 43 | 1.75 | 0.0633 0.0032 0.0665 | 1.5785
- 44 | 1.75 | 0.0591 0.0054 0.0645 | 1.5194
- 45 | 1.75 | 0.0578 0.0062 0.0639 | 1.4626
- 57 | 1.50 | 0.0566 0.0045 0.0611 | 1.0900
- 58 | 1.50 | 0.0535 0.0065 0.0600 | 1.0730
- 59 | 1.50 | 0.0525 0.0072 0.0597 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 171s
- Prepare output 11s
- 183s
- Jacobian determinant (RMS): 0.012 0.043 0.065 0.092 0.119 | 0.126860
- Template Matching: 0.083 0.214 0.193 0.173 0.158 | 0.157641
- Write result maps: 45s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 24s
- CSF distance: 14s
- PBT2x thickness: 40s
- 83s
- Create initial surface 75s
- Topology correction: 77s
- Surface refinement: 79s
- Reduction of surface collisions with optimization: 58s
- Spherical mapping with areal smoothing 71s
- Spherical registration 292s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 22s
- CSF distance: 12s
- PBT2x thickness: 37s
- 76s
- Create initial surface 72s
- Topology correction: 71s
- Surface refinement: 61s
- Reduction of surface collisions with optimization: 59s
- Spherical mapping with areal smoothing 72s
- Spherical registration 290s
- Final surface processing results:
- Average thickness (FS): 2.5809 0.6616 mm
- Surface intensity / position RMSE: 0.0785 / 0.0866
- Euler number / defect number / defect size: 52.0 / 20.0 / 1.86%
- Display thickness: /var/lib/condor/execute/dir_1015018/ds/DC_1/sub-0027428/ses-2/surf/lh.thickness.sub-0027428_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1015018/ds/DC_1/sub-0027428/ses-2/surf/rh.thickness.sub-0027428_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1015018/ds/DC_1/sub-0027428/ses-2/sub-0027428_ses-2_run-1_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1531s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 10s
- ROI estimation of 'neuromorphometrics' atlas 36s
- 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 33s
- ROI estimation of 'julichbrain' atlas 48s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 20s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 36s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 80s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 139s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 16s
- Write results 18s
- 505s
- Quality check: 17s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1015018/ds/DC_1/sub-0027428/ses-2/report/catreport_sub-0027428_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 51 minute(s) and 14 second(s).
- Image Quality Rating (IQR): 75.32% (C)
- GM volume (GMV): 54.27% (637.50 / 1174.70 ml)
- GM thickness (GMT): 2.58 0.66 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1015018/ds/DC_1/sub-0027428/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_1015018/ds/DC_1/sub-0027428/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_1015018/ds/DC_1/sub-0027428/ses-2/label
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