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- CAT12.8.1 r1980: 1/1: ./condor/execute/dir_19516/ds/sub-29/sub-29_T1w.n
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- SANLM denoising (medium): 81s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 15s
- Initial correction 10s
- Refine background 5s
- Final correction 8s
- Final scaling 8s
- 61s
- Correct center-of-mass 4s
- Affine registration 11s
- SPM preprocessing 1 (estimate 1 - TPM registration): 70s
- SPM preprocessing 1 (estimate 2): 53s
- SPM preprocessing 2 (write):
- Write Segmentation 20s
- Update Segmentation 21s
- Update Skull-Stripping 46s
- Update probability maps 11s
- 98s
- Global intensity correction: 18s
- SANLM denoising after intensity normalization (medium): 9s
- Fast Optimized Shooting registration 41s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 16s
- Estimate local tissue thresholds (WM) 25s
- Estimate local tissue thresholds (GM) 37s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 36s
- 125s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 19s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.48 > WMHCstr'=0.00) 26s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 78s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 36s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.990.05]
- Final cleanup (gcutstr=0.24):
- Level 1 cleanup (ROI estimation) 5s
- 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 | 0.0836 0.0000 0.0836 | 32.0000
- 2 | 2.50 | 0.0813 0.0011 0.0824 | 29.4886
- 3 | 2.50 | 0.0806 0.0017 0.0823 | 26.9772
- 4 | 2.50 | 0.0803 0.0019 0.0821 | 24.6107
- 5 | 2.50 | 0.0800 0.0020 0.0820 | 22.6548
- 6 | 2.50 | 0.0798 0.0021 0.0818 | 20.6989
- 7 | 2.50 | 0.0795 0.0022 0.0817 | 18.9688
- 8 | 2.50 | 0.0792 0.0023 0.0815 | 17.4455
- 9 | 2.50 | 0.0790 0.0023 0.0813 | 15.9223
- 10 | 2.50 | 0.0787 0.0024 0.0811 | 14.6627
- 11 | 2.50 | 0.0784 0.0025 0.0809 | 13.4764
- 12 | 2.50 | 0.0781 0.0026 0.0807 | 12.3015
- 13 | 2.50 | 0.0778 0.0027 0.0805 | 11.3776
- 14 | 2.50 | 0.0775 0.0027 0.0802 | 10.4537
- 15 | 2.25 | 0.0767 0.0028 0.0795 | 9.5920
- 16 | 2.25 | 0.0737 0.0043 0.0779 | 8.8725
- 29 | 2.00 | 0.0749 0.0019 0.0768 | 3.3283
- 30 | 2.00 | 0.0690 0.0043 0.0732 | 3.1221
- 31 | 2.00 | 0.0670 0.0052 0.0722 | 2.9160
- 43 | 1.75 | 0.0660 0.0030 0.0690 | 1.5785
- 44 | 1.75 | 0.0618 0.0052 0.0670 | 1.5194
- 45 | 1.75 | 0.0605 0.0059 0.0664 | 1.4626
- 57 | 1.50 | 0.0591 0.0043 0.0634 | 1.0900
- 58 | 1.50 | 0.0561 0.0062 0.0624 | 1.0730
- Shooting registration with 2.50:-0.25:1.50 mm takes: 171s
- Prepare output 13s
- 184s
- Jacobian determinant (RMS): 0.011 0.041 0.060 0.085 0.108 | 0.113219
- Template Matching: 0.084 0.221 0.201 0.181 0.168 | 0.168381
- Write result maps: 27s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 34s
- CSF distance: 18s
- PBT2x thickness: 56s
- 115s
- Create initial surface 99s
- Topology correction: 115s
- Surface refinement: 96s
- Reduction of surface collisions with optimization: 80s
- Spherical mapping with areal smoothing 102s
- Spherical registration 334s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 37s
- CSF distance: 19s
- PBT2x thickness: 55s
- 117s
- Create initial surface 95s
- Topology correction: 109s
- Surface refinement: 112s
- Reduction of surface collisions with optimization: 81s
- Spherical mapping with areal smoothing 97s
- Spherical registration 334s
- Final surface processing results:
- Average thickness (FS): 2.5385 0.6256 mm
- Surface intensity / position RMSE: 0.0680 / 0.0750
- Euler number / defect number / defect size: 40.0 / 23.5 / 1.46%
- Display thickness: /var/lib/condor/execute/dir_19516/ds/sub-29/surf/lh.thickness.sub-29_T1w
- Display thickness: /var/lib/condor/execute/dir_19516/ds/sub-29/surf/rh.thickness.sub-29_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_19516/ds/sub-29/sub-29_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 1993s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 11s
- ROI estimation of 'neuromorphometrics' atlas 39s
- ROI estimation of 'lpba40' atlas 10s
- ROI estimation of 'hammers' atlas 22s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 8s
- ROI estimation of 'aal3' atlas 14s
- ROI estimation of 'mori' atlas 20s
- ROI estimation of 'anatomy3' atlas 29s
- ROI estimation of 'julichbrain' atlas 37s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 25s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 59s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 89s
- Write results 90s
- 380s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_19516/ds/sub-29/report/catreport_sub-29_T1w.pdf
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- CAT preprocessing takes 56 minute(s) and 31 second(s).
- Image Quality Rating (IQR): 81.26% (B-)
- GM volume (GMV): 48.99% (696.49 / 1421.81 ml)
- GM thickness (GMT): 2.54 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_19516/ds/sub-29/mri
- Reports are saved in /var/lib/condor/execute/dir_19516/ds/sub-29/report
- Labels are saved in /var/lib/condor/execute/dir_19516/ds/sub-29/label
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