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- CAT12.8.1 r2040: 1/1: ./sub-0025254/ses-1/sub-0025254_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 58s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 7s
- Initial correction 7s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 40s
- Correct center-of-mass 3s
- Affine registration 11s
- SPM preprocessing 1 (estimate 1 - TPM registration): 85s
- SPM preprocessing 1 (estimate 2): 72s
- SPM preprocessing 2 (write):
- Write Segmentation 17s
- Update Segmentation 19s
- Update Skull-Stripping 40s
- Update probability maps 8s
- 84s
- Global intensity correction: 15s
- SANLM denoising after intensity normalization (medium): 28s
- Fast Optimized Shooting registration 37s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 15s
- Estimate local tissue thresholds (WM) 20s
- Estimate local tissue thresholds (GM) 31s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 42s
- 116s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 4s
- Ventricle detection 15s
- Blood vessel detection 10s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 25s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 3s
- Final corrections 4s
- 71s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 34s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.07,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 3s
- 12s
- 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 | 0.0837 0.0000 0.0837 | 32.0000
- 2 | 2.50 | 0.0808 0.0013 0.0821 | 29.4886
- 3 | 2.50 | 0.0800 0.0019 0.0819 | 26.9772
- 4 | 2.50 | 0.0795 0.0022 0.0817 | 24.6107
- 5 | 2.50 | 0.0792 0.0023 0.0815 | 22.6548
- 6 | 2.50 | 0.0789 0.0024 0.0813 | 20.6989
- 7 | 2.50 | 0.0786 0.0025 0.0811 | 18.9688
- 8 | 2.50 | 0.0783 0.0027 0.0809 | 17.4455
- 9 | 2.50 | 0.0780 0.0027 0.0807 | 15.9223
- 10 | 2.50 | 0.0776 0.0029 0.0805 | 14.6627
- 11 | 2.50 | 0.0773 0.0030 0.0802 | 13.4764
- 12 | 2.50 | 0.0769 0.0030 0.0800 | 12.3015
- 13 | 2.50 | 0.0766 0.0031 0.0797 | 11.3776
- 14 | 2.50 | 0.0762 0.0032 0.0794 | 10.4537
- 15 | 2.25 | 0.0759 0.0033 0.0792 | 9.5920
- 16 | 2.25 | 0.0726 0.0049 0.0775 | 8.8725
- 29 | 2.00 | 0.0734 0.0022 0.0756 | 3.3283
- 30 | 2.00 | 0.0671 0.0048 0.0718 | 3.1221
- 31 | 2.00 | 0.0649 0.0058 0.0707 | 2.9160
- 43 | 1.75 | 0.0638 0.0034 0.0671 | 1.5785
- 44 | 1.75 | 0.0596 0.0056 0.0652 | 1.5194
- 45 | 1.75 | 0.0582 0.0064 0.0645 | 1.4626
- 57 | 1.50 | 0.0567 0.0047 0.0614 | 1.0900
- 58 | 1.50 | 0.0537 0.0066 0.0603 | 1.0730
- 59 | 1.50 | 0.0527 0.0073 0.0600 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 190s
- Prepare output 12s
- 202s
- Jacobian determinant (RMS): 0.012 0.043 0.064 0.089 0.113 | 0.120170
- Template Matching: 0.084 0.218 0.195 0.174 0.158 | 0.158118
- Write result maps: 42s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 50s
- CSF distance: 18s
- PBT2x thickness: 53s
- 127s
- Create initial surface 95s
- Topology correction: 105s
- Surface refinement: 99s
- Reduction of surface collisions with optimization: 73s
- Spherical mapping with areal smoothing 100s
- Spherical registration 353s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 34s
- CSF distance: 19s
- PBT2x thickness: 55s
- 114s
- Create initial surface 94s
- Topology correction: 103s
- Surface refinement: 84s
- Reduction of surface collisions with optimization: 68s
- Spherical mapping with areal smoothing 96s
- Spherical registration 346s
- Final surface processing results:
- Average thickness (FS): 2.6383 0.6373 mm
- Surface intensity / position RMSE: 0.0691 / 0.0650
- Euler number / defect number / defect size: 6.0 / 10.0 / 0.11%
- Display thickness: /var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-1/surf/lh.thickness.sub-0025254_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-1/surf/rh.thickness.sub-0025254_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-1/sub-0025254_ses-1_run-1_T1w.nii
- Surface ROI estimation: 12s
- Surface and thickness estimation takes: 1963s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 8s
- ROI estimation of 'neuromorphometrics' atlas 29s
- ROI estimation of 'lpba40' atlas 9s
- ROI estimation of 'hammers' atlas 22s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 14s
- ROI estimation of 'mori' atlas 20s
- ROI estimation of 'anatomy3' atlas 30s
- ROI estimation of 'julichbrain' atlas 37s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 14s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 25s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 60s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 83s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s
- Write results 9s
- 370s
- Quality check: 13s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-1/report/catreport_sub-0025254_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 55 minute(s) and 44 second(s).
- Image Quality Rating (IQR): 82.22% (B-)
- GM volume (GMV): 51.38% (677.51 / 1318.57 ml)
- GM thickness (GMT): 2.64 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-1/label
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