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- CAT12.8.1 r1980: 1/1: ./condor/execute/dir_9269/ds/sub-46/sub-46_T1w.n
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- SANLM denoising (medium): 71s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 14s
- Initial correction 9s
- Refine background 6s
- Final correction 7s
- Final scaling 13s
- 64s
- Correct center-of-mass 3s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 74s
- SPM preprocessing 1 (estimate 2): 72s
- SPM preprocessing 2 (write):
- Write Segmentation 19s
- Update Segmentation 22s
- Update Skull-Stripping 47s
- Update probability maps 11s
- 99s
- Global intensity correction: 20s
- SANLM denoising after intensity normalization (medium): 11s
- Fast Optimized Shooting registration 43s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.10) 17s
- Estimate local tissue thresholds (WM) 22s
- Estimate local tissue thresholds (GM) 29s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 31s
- 109s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 4s
- Ventricle detection 15s
- Blood vessel detection 10s
- WMH detection (WMHCstr=0.48 > WMHCstr'=0.06) 26s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 75s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 43s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.04]
- 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 | 0.0863 0.0000 0.0863 | 32.0000
- 2 | 2.50 | 0.0833 0.0013 0.0846 | 29.4886
- 3 | 2.50 | 0.0824 0.0019 0.0843 | 26.9772
- 4 | 2.50 | 0.0820 0.0022 0.0841 | 24.6107
- 5 | 2.50 | 0.0816 0.0023 0.0839 | 22.6548
- 6 | 2.50 | 0.0813 0.0024 0.0837 | 20.6989
- 7 | 2.50 | 0.0810 0.0025 0.0835 | 18.9688
- 8 | 2.50 | 0.0807 0.0026 0.0833 | 17.4455
- 9 | 2.50 | 0.0804 0.0027 0.0830 | 15.9223
- 10 | 2.50 | 0.0800 0.0028 0.0828 | 14.6627
- 11 | 2.50 | 0.0797 0.0029 0.0826 | 13.4764
- 12 | 2.50 | 0.0793 0.0029 0.0823 | 12.3015
- 13 | 2.50 | 0.0790 0.0030 0.0820 | 11.3776
- 14 | 2.50 | 0.0786 0.0031 0.0817 | 10.4537
- 15 | 2.25 | 0.0781 0.0032 0.0813 | 9.5920
- 16 | 2.25 | 0.0749 0.0047 0.0796 | 8.8725
- 29 | 2.00 | 0.0760 0.0021 0.0782 | 3.3283
- 30 | 2.00 | 0.0699 0.0045 0.0744 | 3.1221
- 31 | 2.00 | 0.0678 0.0055 0.0733 | 2.9160
- 43 | 1.75 | 0.0666 0.0032 0.0699 | 1.5785
- 44 | 1.75 | 0.0625 0.0053 0.0679 | 1.5194
- 45 | 1.75 | 0.0611 0.0061 0.0672 | 1.4626
- 57 | 1.50 | 0.0596 0.0045 0.0641 | 1.0900
- 58 | 1.50 | 0.0566 0.0064 0.0630 | 1.0730
- Shooting registration with 2.50:-0.25:1.50 mm takes: 193s
- Prepare output 11s
- 203s
- Jacobian determinant (RMS): 0.011 0.041 0.060 0.082 0.103 | 0.108048
- Template Matching: 0.086 0.225 0.203 0.183 0.170 | 0.169821
- Write result maps: 29s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 44s
- CSF distance: 19s
- PBT2x thickness: 57s
- 128s
- Create initial surface 99s
- Topology correction: 114s
- Surface refinement: 137s
- Reduction of surface collisions with optimization: 91s
- Spherical mapping with areal smoothing 102s
- Spherical registration 269s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 54s
- CSF distance: 19s
- PBT2x thickness: 57s
- 138s
- Create initial surface 100s
- Topology correction: 114s
- Surface refinement: 102s
- Reduction of surface collisions with optimization: 88s
- Spherical mapping with areal smoothing 97s
- Spherical registration 265s
- Final surface processing results:
- Average thickness (FS): 2.4898 0.5790 mm
- Surface intensity / position RMSE: 0.0625 / 0.0617
- Euler number / defect number / defect size: 16.0 / 18.0 / 0.45%
- Display thickness: /var/lib/condor/execute/dir_9269/ds/sub-46/surf/lh.thickness.sub-46_T1w
- Display thickness: /var/lib/condor/execute/dir_9269/ds/sub-46/surf/rh.thickness.sub-46_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_9269/ds/sub-46/sub-46_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1947s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 13s
- ROI estimation of 'neuromorphometrics' atlas 50s
- ROI estimation of 'lpba40' atlas 14s
- ROI estimation of 'hammers' atlas 35s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 12s
- ROI estimation of 'aal3' atlas 20s
- ROI estimation of 'mori' atlas 30s
- ROI estimation of 'anatomy3' atlas 43s
- ROI estimation of 'julichbrain' atlas 57s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 21s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 27s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 92s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 138s
- Write results 139s
- 558s
- Quality check: 5s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_9269/ds/sub-46/report/catreport_sub-46_T1w.pdf
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- CAT preprocessing takes 59 minute(s) and 8 second(s).
- Image Quality Rating (IQR): 84.22% (B)
- GM volume (GMV): 46.54% (697.71 / 1499.07 ml)
- GM thickness (GMT): 2.49 0.58 mm
- Segmentations are saved in /var/lib/condor/execute/dir_9269/ds/sub-46/mri
- Reports are saved in /var/lib/condor/execute/dir_9269/ds/sub-46/report
- Labels are saved in /var/lib/condor/execute/dir_9269/ds/sub-46/label
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