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- CAT12.8.1 r1980: 1/1: ./dir_13479/ds/sub-0405/sub-0405_ses-01_T1w.n
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- SANLM denoising (medium): 140s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 5s
- Initial correction 12s
- Refine background 4s
- Final correction 7s
- Final scaling 7s
- 49s
- Correct center-of-mass 3s
- Affine registration 15s
- SPM preprocessing 1 (estimate 1 - TPM registration): 75s
- SPM preprocessing 1 (estimate 2): 48s
- SPM preprocessing 2 (write):
- Write Segmentation 18s
- Update Segmentation 18s
- Update Skull-Stripping 43s
- Update probability maps 9s
- 89s
- Global intensity correction: 17s
- SANLM denoising after intensity normalization (medium): 20s
- Fast Optimized Shooting registration 31s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.23) 12s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 24s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 39s
- 104s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 3s
- Ventricle detection 12s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 24s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 5s
- 64s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 23s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- 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
- 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 | 0.0851 0.0000 0.0851 | 32.0000
- 2 | 2.50 | 0.0823 0.0012 0.0835 | 29.4886
- 3 | 2.50 | 0.0815 0.0019 0.0834 | 26.9772
- 4 | 2.50 | 0.0811 0.0021 0.0832 | 24.6107
- 5 | 2.50 | 0.0808 0.0023 0.0830 | 22.6548
- 6 | 2.50 | 0.0805 0.0023 0.0828 | 20.6989
- 7 | 2.50 | 0.0802 0.0024 0.0827 | 18.9688
- 8 | 2.50 | 0.0800 0.0025 0.0825 | 17.4455
- 9 | 2.50 | 0.0797 0.0026 0.0823 | 15.9223
- 10 | 2.50 | 0.0793 0.0027 0.0820 | 14.6627
- 11 | 2.50 | 0.0790 0.0028 0.0818 | 13.4764
- 12 | 2.50 | 0.0787 0.0028 0.0815 | 12.3015
- 13 | 2.50 | 0.0784 0.0029 0.0813 | 11.3776
- 14 | 2.50 | 0.0781 0.0030 0.0810 | 10.4537
- 15 | 2.25 | 0.0778 0.0030 0.0808 | 9.5920
- 16 | 2.25 | 0.0746 0.0045 0.0791 | 8.8725
- 29 | 2.00 | 0.0760 0.0021 0.0780 | 3.3283
- 30 | 2.00 | 0.0698 0.0045 0.0742 | 3.1221
- 31 | 2.00 | 0.0676 0.0055 0.0731 | 2.9160
- 43 | 1.75 | 0.0667 0.0032 0.0699 | 1.5785
- 44 | 1.75 | 0.0625 0.0054 0.0678 | 1.5194
- 45 | 1.75 | 0.0610 0.0061 0.0672 | 1.4626
- 57 | 1.50 | 0.0597 0.0045 0.0642 | 1.0900
- 58 | 1.50 | 0.0566 0.0065 0.0631 | 1.0730
- 59 | 1.50 | 0.0556 0.0071 0.0627 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 131s
- Prepare output 8s
- 139s
- Jacobian determinant (RMS): 0.010 0.037 0.056 0.080 0.102 | 0.108434
- Template Matching: 0.085 0.224 0.203 0.183 0.167 | 0.166739
- Write result maps: 27s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 31s
- CSF distance: 12s
- PBT2x thickness: 35s
- 82s
- Create initial surface 57s
- Topology correction: 64s
- Surface refinement: 69s
- Reduction of surface collisions with optimization: 42s
- Spherical mapping with areal smoothing 59s
- Spherical registration 183s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 28s
- CSF distance: 11s
- PBT2x thickness: 35s
- 79s
- Create initial surface 58s
- Topology correction: 64s
- Surface refinement: 55s
- Reduction of surface collisions with optimization: 42s
- Spherical mapping with areal smoothing 59s
- Spherical registration 185s
- Final surface processing results:
- Average thickness (FS): 2.5527 0.6456 mm
- Surface intensity / position RMSE: 0.0721 / 0.0733
- Euler number / defect number / defect size: 30.0 / 19.0 / 0.83%
- Display thickness: /var/lib/condor/execute/dir_13479/ds/sub-0405/surf/lh.thickness.sub-0405_ses-01_T1w
- Display thickness: /var/lib/condor/execute/dir_13479/ds/sub-0405/surf/rh.thickness.sub-0405_ses-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_13479/ds/sub-0405/sub-0405_ses-01_T1w.nii
- Surface ROI estimation: 5s
- Surface and thickness estimation takes: 1176s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 15s
- ROI estimation of 'neuromorphometrics' atlas 55s
- ROI estimation of 'lpba40' atlas 16s
- ROI estimation of 'hammers' atlas 39s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 13s
- ROI estimation of 'aal3' atlas 22s
- ROI estimation of 'mori' atlas 32s
- ROI estimation of 'anatomy3' atlas 46s
- ROI estimation of 'julichbrain' atlas 62s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 22s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 25s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 99s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 147s
- Write results 148s
- 599s
- Quality check: 4s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_13479/ds/sub-0405/report/catreport_sub-0405_ses-01_T1w.pdf
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- CAT preprocessing takes 45 minute(s) and 32 second(s).
- Image Quality Rating (IQR): 82.37% (B-)
- GM volume (GMV): 50.05% (690.05 / 1378.67 ml)
- GM thickness (GMT): 2.55 0.65 mm
- Segmentations are saved in /var/lib/condor/execute/dir_13479/ds/sub-0405/mri
- Reports are saved in /var/lib/condor/execute/dir_13479/ds/sub-0405/report
- Labels are saved in /var/lib/condor/execute/dir_13479/ds/sub-0405/label
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