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- CAT12.8.1 r2040: 1/1: ./sub-0025472/ses-1/sub-0025472_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 25s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 4s
- Initial correction 4s
- Refine background 2s
- Final correction 4s
- Final scaling 4s
- 28s
- Correct center-of-mass 2s
- Affine registration 8s
- SPM preprocessing 1 (estimate 1 - TPM registration): 26s
- Use previous fine affine registration. 51s
- SPM preprocessing 1 (estimate 2): 65s
- SPM preprocessing 2 (write):
- Write Segmentation 15s
- Update Segmentation 18s
- Update Skull-Stripping 36s
- Update probability maps 8s
- 77s
- Global intensity correction: 13s
- SANLM denoising after intensity normalization (medium): 20s
- Fast Optimized Shooting registration 26s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 11s
- Estimate local tissue thresholds (WM) 15s
- Estimate local tissue thresholds (GM) 21s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 35s
- 90s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 3s
- Ventricle detection 10s
- Blood vessel detection 7s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.04) 19s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 52s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 27s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 3s
- Level 1 cleanup (brain masking) 2s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 9s
- 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 | 0.0854 0.0000 0.0854 | 32.0000
- 2 | 2.50 | 0.0826 0.0012 0.0838 | 29.4886
- 3 | 2.50 | 0.0817 0.0019 0.0836 | 26.9772
- 4 | 2.50 | 0.0813 0.0021 0.0834 | 24.6107
- 5 | 2.50 | 0.0809 0.0023 0.0832 | 22.6548
- 6 | 2.50 | 0.0807 0.0024 0.0830 | 20.6989
- 7 | 2.50 | 0.0804 0.0025 0.0828 | 18.9688
- 8 | 2.50 | 0.0800 0.0026 0.0826 | 17.4455
- 9 | 2.50 | 0.0797 0.0027 0.0824 | 15.9223
- 10 | 2.50 | 0.0794 0.0028 0.0822 | 14.6627
- 11 | 2.50 | 0.0791 0.0029 0.0819 | 13.4764
- 12 | 2.50 | 0.0787 0.0029 0.0816 | 12.3015
- 13 | 2.50 | 0.0784 0.0030 0.0814 | 11.3776
- 14 | 2.50 | 0.0780 0.0031 0.0811 | 10.4537
- 15 | 2.25 | 0.0781 0.0032 0.0813 | 9.5920
- 16 | 2.25 | 0.0752 0.0046 0.0799 | 8.8725
- 17 | 2.25 | 0.0740 0.0052 0.0792 | 8.1530
- 29 | 2.00 | 0.0758 0.0024 0.0782 | 3.3283
- 30 | 2.00 | 0.0700 0.0048 0.0748 | 3.1221
- 31 | 2.00 | 0.0680 0.0058 0.0737 | 2.9160
- 43 | 1.75 | 0.0670 0.0033 0.0703 | 1.5785
- 44 | 1.75 | 0.0625 0.0056 0.0682 | 1.5194
- 45 | 1.75 | 0.0610 0.0065 0.0675 | 1.4626
- 57 | 1.50 | 0.0598 0.0047 0.0645 | 1.0900
- 58 | 1.50 | 0.0566 0.0068 0.0634 | 1.0730
- 59 | 1.50 | 0.0555 0.0076 0.0630 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 137s
- Prepare output 8s
- 146s
- Jacobian determinant (RMS): 0.011 0.042 0.063 0.086 0.109 | 0.116953
- Template Matching: 0.085 0.222 0.204 0.183 0.166 | 0.166452
- Write result maps: 31s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 34s
- CSF distance: 11s
- PBT2x thickness: 34s
- 84s
- Create initial surface 65s
- Topology correction: 79s
- Surface refinement: 83s
- Reduction of surface collisions with optimization: 60s
- Spherical mapping with areal smoothing 68s
- Spherical registration 200s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 30s
- CSF distance: 12s
- PBT2x thickness: 34s
- 81s
- Create initial surface 67s
- Topology correction: 79s
- Surface refinement: 75s
- Reduction of surface collisions with optimization: 55s
- Spherical mapping with areal smoothing 74s
- Spherical registration 237s
- Final surface processing results:
- Average thickness (FS): 2.3520 0.6623 mm
- Surface intensity / position RMSE: 0.0725 / 0.0759
- Euler number / defect number / defect size: 36.0 / 24.0 / 1.15%
- Display thickness: /var/lib/condor/execute/dir_578211/ds/IACAS/sub-0025472/ses-1/surf/lh.thickness.sub-0025472_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_578211/ds/IACAS/sub-0025472/ses-1/surf/rh.thickness.sub-0025472_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_578211/ds/IACAS/sub-0025472/ses-1/sub-0025472_ses-1_run-1_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1391s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 21s
- ROI estimation of 'neuromorphometrics' atlas 86s
- ROI estimation of 'lpba40' atlas 26s
- ROI estimation of 'hammers' atlas 60s
- ROI estimation of 'thalamus' atlas 5s
- ROI estimation of 'ibsr' atlas 23s
- ROI estimation of 'aal3' atlas 38s
- ROI estimation of 'mori' atlas 52s
- ROI estimation of 'anatomy3' atlas 70s
- ROI estimation of 'julichbrain' atlas 90s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 36s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 61s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 116s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 133s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 11s
- Write results 12s
- 830s
- Quality check: 10s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_578211/ds/IACAS/sub-0025472/ses-1/report/catreport_sub-0025472_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 50 minute(s) and 43 second(s).
- Image Quality Rating (IQR): 77.84% (C+)
- GM volume (GMV): 44.71% (721.03 / 1612.62 ml)
- GM thickness (GMT): 2.35 0.66 mm
- Segmentations are saved in /var/lib/condor/execute/dir_578211/ds/IACAS/sub-0025472/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_578211/ds/IACAS/sub-0025472/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_578211/ds/IACAS/sub-0025472/ses-1/label
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