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- CAT12.8.1 r2040: 1/1: ./sub-0026036/ses-1/sub-0026036_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 232s
- Internal resampling (1.20x0.50x0.50mm > 0.80x0.80x0.80mm): 2s
- APP: Rough bias correction:
- Initialize 10s
- Estimate background 8s
- Initial correction 8s
- Refine background 5s
- Final correction 8s
- Final scaling 7s
- 55s
- Correct center-of-mass 3s
- Affine registration 27s
- SPM preprocessing 1 (estimate 1 - TPM registration): 107s
- SPM preprocessing 1 (estimate 2): 39s
- SPM preprocessing 2 (write):
- Write Segmentation 26s
- Update Segmentation 29s
- Update Skull-Stripping 67s
- Update probability maps 14s
- 135s
- Global intensity correction: 23s
- SANLM denoising after intensity normalization (medium): 48s
- Fast Optimized Shooting registration 36s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 6s
- Prepare partitions 4s
- Prepare segments (LASmod = 1.00) 22s
- Estimate local tissue thresholds (WM) 30s
- Estimate local tissue thresholds (GM) 45s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 63s
- 176s
- ROI segmentation (partitioning):
- Atlas -> subject space 16s
- Major structures 7s
- Ventricle detection 43s
- Blood vessel detection 18s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 56s
- Manual stroke lesion detection 0s
- Closing of deep structures 3s
- Side alignment 6s
- Final corrections 10s
- 159s
- Blood vessel correction (BVCstr=0.50): 3s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 49s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 7s
- Level 1 cleanup (brain masking) 6s
- Level 2 cleanup (CSF correction) 3s
- Level 3 cleanup (CSF/WM PVE) 5s
- 22s
- 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 | 0.0814 0.0000 0.0814 | 32.0000
- 2 | 2.50 | 0.0796 0.0009 0.0805 | 29.4886
- 3 | 2.50 | 0.0791 0.0014 0.0805 | 26.9772
- 4 | 2.50 | 0.0788 0.0016 0.0804 | 24.6107
- 5 | 2.50 | 0.0786 0.0017 0.0803 | 22.6548
- 6 | 2.50 | 0.0784 0.0017 0.0801 | 20.6989
- 7 | 2.50 | 0.0782 0.0018 0.0800 | 18.9688
- 8 | 2.50 | 0.0780 0.0019 0.0798 | 17.4455
- 9 | 2.50 | 0.0778 0.0019 0.0797 | 15.9223
- 10 | 2.50 | 0.0775 0.0020 0.0795 | 14.6627
- 11 | 2.50 | 0.0773 0.0020 0.0794 | 13.4764
- 12 | 2.50 | 0.0771 0.0021 0.0792 | 12.3015
- 13 | 2.50 | 0.0768 0.0022 0.0790 | 11.3776
- 14 | 2.50 | 0.0766 0.0022 0.0788 | 10.4537
- 15 | 2.25 | 0.0757 0.0023 0.0780 | 9.5920
- 16 | 2.25 | 0.0732 0.0035 0.0767 | 8.8725
- 29 | 2.00 | 0.0752 0.0016 0.0768 | 3.3283
- 30 | 2.00 | 0.0697 0.0039 0.0736 | 3.1221
- 31 | 2.00 | 0.0680 0.0048 0.0727 | 2.9160
- 43 | 1.75 | 0.0677 0.0027 0.0704 | 1.5785
- 44 | 1.75 | 0.0632 0.0052 0.0683 | 1.5194
- 45 | 1.75 | 0.0617 0.0060 0.0677 | 1.4626
- 57 | 1.50 | 0.0606 0.0043 0.0649 | 1.0900
- 58 | 1.50 | 0.0571 0.0066 0.0637 | 1.0730
- 59 | 1.50 | 0.0560 0.0073 0.0633 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 180s
- Prepare output 12s
- 193s
- Jacobian determinant (RMS): 0.010 0.034 0.053 0.081 0.111 | 0.118010
- Template Matching: 0.081 0.220 0.204 0.185 0.168 | 0.168030
- Write result maps: 233s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 24s
- CSF distance: 15s
- PBT2x thickness: 39s
- 83s
- Create initial surface 71s
- Topology correction: 84s
- Surface refinement: 71s
- Reduction of surface collisions with optimization: 70s
- Spherical mapping with areal smoothing 79s
- Spherical registration 224s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 29s
- CSF distance: 15s
- PBT2x thickness: 40s
- 88s
- Create initial surface 67s
- Topology correction: 81s
- Surface refinement: 75s
- Reduction of surface collisions with optimization: 66s
- Spherical mapping with areal smoothing 76s
- Spherical registration 219s
- Final surface processing results:
- Average thickness (FS): 2.7177 0.6136 mm
- Surface intensity / position RMSE: 0.0796 / 0.0747
- Euler number / defect number / defect size: 30.0 / 19.0 / 0.74%
- Display thickness: /var/lib/condor/execute/dir_3274552/ds/Utah_1/sub-0026036/ses-1/surf/lh.thickness.sub-0026036_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3274552/ds/Utah_1/sub-0026036/ses-1/surf/rh.thickness.sub-0026036_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3274552/ds/Utah_1/sub-0026036/ses-1/sub-0026036_ses-1_run-1_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1483s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 15s
- ROI estimation of 'neuromorphometrics' atlas 52s
- ROI estimation of 'lpba40' atlas 15s
- ROI estimation of 'hammers' atlas 36s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 13s
- ROI estimation of 'aal3' atlas 21s
- ROI estimation of 'mori' atlas 31s
- ROI estimation of 'anatomy3' atlas 42s
- ROI estimation of 'julichbrain' atlas 56s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 23s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 43s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 99s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 152s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 12s
- Write results 13s
- 615s
- Quality check: 41s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3274552/ds/Utah_1/sub-0026036/ses-1/report/catreport_sub-0026036_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 62 minute(s) and 50 second(s).
- Image Quality Rating (IQR): 81.13% (B-)
- GM volume (GMV): 54.28% (880.36 / 1621.79 ml)
- GM thickness (GMT): 2.72 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3274552/ds/Utah_1/sub-0026036/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_3274552/ds/Utah_1/sub-0026036/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_3274552/ds/Utah_1/sub-0026036/ses-1/label
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