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- CAT12.8.1 r1980: 1/1: ./dir_11908/ds/sub-026/sub-026_ses-t1_T1w.n
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- SANLM denoising (medium): 20s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 7s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 6s
- 40s
- Correct center-of-mass 6s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 77s
- SPM preprocessing 1 (estimate 2): 97s
- SPM preprocessing 2 (write):
- Write Segmentation 18s
- Update Segmentation 17s
- Update Skull-Stripping 40s
- Update probability maps 9s
- 85s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 8s
- Fast Optimized Shooting registration 34s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.10) 12s
- Estimate local tissue thresholds (WM) 16s
- Estimate local tissue thresholds (GM) 19s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 15s
- 72s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 10s
- Blood vessel detection 7s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 23s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 59s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 28s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 2s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 10s
- 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 | 0.0819 0.0000 0.0819 | 32.0000
- 2 | 2.50 | 0.0791 0.0013 0.0803 | 29.4886
- 3 | 2.50 | 0.0782 0.0019 0.0801 | 26.9772
- 4 | 2.50 | 0.0778 0.0022 0.0800 | 24.6107
- 5 | 2.50 | 0.0774 0.0024 0.0798 | 22.6548
- 6 | 2.50 | 0.0771 0.0025 0.0796 | 20.6989
- 7 | 2.50 | 0.0768 0.0026 0.0794 | 18.9688
- 8 | 2.50 | 0.0765 0.0027 0.0792 | 17.4455
- 9 | 2.50 | 0.0761 0.0028 0.0789 | 15.9223
- 10 | 2.50 | 0.0758 0.0029 0.0787 | 14.6627
- 11 | 2.50 | 0.0754 0.0030 0.0785 | 13.4764
- 12 | 2.50 | 0.0751 0.0031 0.0782 | 12.3015
- 13 | 2.50 | 0.0747 0.0033 0.0779 | 11.3776
- 14 | 2.50 | 0.0743 0.0033 0.0776 | 10.4537
- 15 | 2.25 | 0.0739 0.0034 0.0773 | 9.5920
- 16 | 2.25 | 0.0705 0.0051 0.0756 | 8.8725
- 29 | 2.00 | 0.0715 0.0023 0.0738 | 3.3283
- 30 | 2.00 | 0.0650 0.0049 0.0699 | 3.1221
- 31 | 2.00 | 0.0627 0.0060 0.0687 | 2.9160
- 43 | 1.75 | 0.0614 0.0035 0.0649 | 1.5785
- 44 | 1.75 | 0.0572 0.0057 0.0629 | 1.5194
- 45 | 1.75 | 0.0558 0.0065 0.0622 | 1.4626
- 57 | 1.50 | 0.0542 0.0048 0.0590 | 1.0900
- 58 | 1.50 | 0.0513 0.0066 0.0579 | 1.0730
- 59 | 1.50 | 0.0503 0.0073 0.0576 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 156s
- Prepare output 9s
- 165s
- Jacobian determinant (RMS): 0.012 0.045 0.068 0.095 0.119 | 0.128076
- Template Matching: 0.082 0.212 0.188 0.167 0.151 | 0.150935
- Write result maps: 20s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 22s
- CSF distance: 11s
- PBT2x thickness: 33s
- 70s
- Create initial surface 66s
- Topology correction: 63s
- Surface refinement: 69s
- Reduction of surface collisions with optimization: 46s
- Spherical mapping with areal smoothing 61s
- Spherical registration 284s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 25s
- CSF distance: 11s
- PBT2x thickness: 31s
- 71s
- Create initial surface 62s
- Topology correction: 59s
- Surface refinement: 71s
- Reduction of surface collisions with optimization: 43s
- Spherical mapping with areal smoothing 56s
- Spherical registration 277s
- Final surface processing results:
- Average thickness (FS): 2.4643 0.6314 mm
- Surface intensity / position RMSE: 0.0662 / 0.0679
- Euler number / defect number / defect size: 28.0 / 21.0 / 0.90%
- Display thickness: /var/lib/condor/execute/dir_11908/ds/sub-026/surf/lh.thickness.sub-026_ses-t1_T1w
- Display thickness: /var/lib/condor/execute/dir_11908/ds/sub-026/surf/rh.thickness.sub-026_ses-t1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_11908/ds/sub-026/sub-026_ses-t1_T1w.nii
- Surface ROI estimation: 6s
- Surface and thickness estimation takes: 1366s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 6s
- ROI estimation of 'neuromorphometrics' atlas 24s
- ROI estimation of 'lpba40' atlas 7s
- ROI estimation of 'hammers' atlas 17s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 6s
- ROI estimation of 'aal3' atlas 10s
- ROI estimation of 'mori' atlas 14s
- ROI estimation of 'anatomy3' atlas 21s
- ROI estimation of 'julichbrain' atlas 28s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 20s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 46s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 67s
- Write results 68s
- 278s
- Quality check: 4s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_11908/ds/sub-026/report/catreport_sub-026_ses-t1_T1w.pdf
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- CAT preprocessing takes 41 minute(s) and 22 second(s).
- Image Quality Rating (IQR): 84.38% (B)
- GM volume (GMV): 45.75% (543.43 / 1187.94 ml)
- GM thickness (GMT): 2.46 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_11908/ds/sub-026/mri
- Reports are saved in /var/lib/condor/execute/dir_11908/ds/sub-026/report
- Labels are saved in /var/lib/condor/execute/dir_11908/ds/sub-026/label
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