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- CAT12.8.1 r2040: 1/1: ./sub-0026032/ses-2/sub-0026032_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 354s
- Internal resampling (1.20x0.50x0.50mm > 0.80x0.80x0.80mm): 3s
- APP: Rough bias correction:
- Initialize 15s
- Estimate background 13s
- Initial correction 15s
- Refine background 7s
- Final correction 13s
- Final scaling 12s
- 90s
- Correct center-of-mass 5s
- Affine registration 20s
- SPM preprocessing 1 (estimate 1 - TPM registration): 178s
- SPM preprocessing 1 (estimate 2): 63s
- SPM preprocessing 2 (write):
- Write Segmentation 40s
- Update Segmentation 46s
- Update Skull-Stripping 107s
- Update probability maps 21s
- 215s
- Global intensity correction: 41s
- SANLM denoising after intensity normalization (medium): 79s
- Fast Optimized Shooting registration 60s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 11s
- Prepare partitions 6s
- Prepare segments (LASmod = 1.00) 41s
- Estimate local tissue thresholds (WM) 52s
- Estimate local tissue thresholds (GM) 78s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 110s
- 307s
- ROI segmentation (partitioning):
- Atlas -> subject space 20s
- Major structures 9s
- Ventricle detection 40s
- Blood vessel detection 30s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.03) 69s
- Manual stroke lesion detection 0s
- Closing of deep structures 5s
- Side alignment 10s
- Final corrections 11s
- 194s
- Blood vessel correction (BVCstr=0.50): 4s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 76s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 11s
- Level 1 cleanup (brain masking) 7s
- Level 2 cleanup (CSF correction) 4s
- Level 3 cleanup (CSF/WM PVE) 7s
- 30s
- 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 | 0.0858 0.0000 0.0858 | 32.0000
- 2 | 2.50 | 0.0827 0.0013 0.0840 | 29.4886
- 3 | 2.50 | 0.0818 0.0020 0.0838 | 26.9772
- 4 | 2.50 | 0.0813 0.0023 0.0836 | 24.6107
- 5 | 2.50 | 0.0809 0.0024 0.0834 | 22.6548
- 6 | 2.50 | 0.0806 0.0025 0.0832 | 20.6989
- 7 | 2.50 | 0.0803 0.0026 0.0830 | 18.9688
- 8 | 2.50 | 0.0800 0.0028 0.0827 | 17.4455
- 9 | 2.50 | 0.0796 0.0028 0.0825 | 15.9223
- 10 | 2.50 | 0.0793 0.0030 0.0822 | 14.6627
- 11 | 2.50 | 0.0789 0.0030 0.0820 | 13.4764
- 12 | 2.50 | 0.0785 0.0031 0.0817 | 12.3015
- 13 | 2.50 | 0.0782 0.0032 0.0814 | 11.3776
- 14 | 2.50 | 0.0778 0.0033 0.0811 | 10.4537
- 15 | 2.25 | 0.0778 0.0034 0.0812 | 9.5920
- 16 | 2.25 | 0.0746 0.0049 0.0795 | 8.8725
- 29 | 2.00 | 0.0759 0.0022 0.0781 | 3.3283
- 30 | 2.00 | 0.0695 0.0048 0.0743 | 3.1221
- 31 | 2.00 | 0.0672 0.0059 0.0731 | 2.9160
- 43 | 1.75 | 0.0663 0.0034 0.0697 | 1.5785
- 44 | 1.75 | 0.0617 0.0058 0.0675 | 1.5194
- 45 | 1.75 | 0.0601 0.0067 0.0668 | 1.4626
- 57 | 1.50 | 0.0586 0.0049 0.0634 | 1.0900
- 58 | 1.50 | 0.0553 0.0070 0.0623 | 1.0730
- 59 | 1.50 | 0.0541 0.0077 0.0619 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 207s
- Prepare output 22s
- 229s
- Jacobian determinant (RMS): 0.012 0.045 0.067 0.094 0.118 | 0.124591
- Template Matching: 0.086 0.224 0.202 0.180 0.162 | 0.162439
- Write result maps: 292s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 45s
- CSF distance: 23s
- PBT2x thickness: 67s
- 144s
- Create initial surface 122s
- Topology correction: 131s
- Surface refinement: 111s
- Reduction of surface collisions with optimization: 109s
- Spherical mapping with areal smoothing 137s
- Spherical registration 345s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 56s
- CSF distance: 22s
- PBT2x thickness: 67s
- 154s
- Create initial surface 118s
- Topology correction: 138s
- Surface refinement: 133s
- Reduction of surface collisions with optimization: 101s
- Spherical mapping with areal smoothing 131s
- Spherical registration 351s
- Final surface processing results:
- Average thickness (FS): 2.4836 0.6024 mm
- Surface intensity / position RMSE: 0.0698 / 0.0653
- Euler number / defect number / defect size: 14.0 / 10.5 / 0.23%
- Display thickness: /var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-2/surf/lh.thickness.sub-0026032_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-2/surf/rh.thickness.sub-0026032_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-2/sub-0026032_ses-2_run-1_T1w.nii
- Surface ROI estimation: 11s
- Surface and thickness estimation takes: 2439s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 19s
- ROI estimation of 'neuromorphometrics' atlas 71s
- ROI estimation of 'lpba40' atlas 20s
- ROI estimation of 'hammers' atlas 51s
- ROI estimation of 'thalamus' atlas 4s
- ROI estimation of 'ibsr' atlas 18s
- ROI estimation of 'aal3' atlas 29s
- ROI estimation of 'mori' atlas 43s
- ROI estimation of 'anatomy3' atlas 62s
- ROI estimation of 'julichbrain' atlas 81s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 33s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 56s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 125s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 189s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 16s
- Write results 17s
- 820s
- Quality check: 66s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-2/report/catreport_sub-0026032_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 95 minute(s) and 4 second(s).
- Image Quality Rating (IQR): 80.70% (B-)
- GM volume (GMV): 48.94% (798.73 / 1632.12 ml)
- GM thickness (GMT): 2.48 0.60 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-2/label
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