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- CAT12.8.1 r2040: 1/1: ./sub-0025140/ses-1/sub-0025140_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 55s
- Internal resampling (1.33x1.00x1.00mm > 1.00x1.00x1.00mm): 1s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 6s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 4s
- 35s
- Correct center-of-mass 4s
- Affine registration 9s
- SPM preprocessing 1 (estimate 1 - TPM registration): 75s
- SPM preprocessing 1 (estimate 2): 54s
- SPM preprocessing 2 (write):
- Write Segmentation 16s
- Update Segmentation 19s
- Update Skull-Stripping 39s
- Update probability maps 8s
- 81s
- Global intensity correction: 15s
- SANLM denoising after intensity normalization (medium): 29s
- Fast Optimized Shooting registration 30s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.08) 14s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 25s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 39s
- 105s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 10s
- Blood vessel detection 9s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 26s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 3s
- Final corrections 4s
- 63s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 32s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 3s
- 11s
- 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 | 0.0790 0.0000 0.0790 | 32.0000
- 2 | 2.50 | 0.0767 0.0011 0.0778 | 29.4886
- 3 | 2.50 | 0.0761 0.0016 0.0777 | 26.9772
- 4 | 2.50 | 0.0758 0.0017 0.0775 | 24.6107
- 5 | 2.50 | 0.0755 0.0019 0.0774 | 22.6548
- 6 | 2.50 | 0.0753 0.0019 0.0772 | 20.6989
- 7 | 2.50 | 0.0751 0.0020 0.0771 | 18.9688
- 8 | 2.50 | 0.0749 0.0021 0.0769 | 17.4455
- 9 | 2.50 | 0.0746 0.0021 0.0768 | 15.9223
- 10 | 2.50 | 0.0744 0.0022 0.0766 | 14.6627
- 11 | 2.50 | 0.0741 0.0023 0.0764 | 13.4764
- 12 | 2.50 | 0.0739 0.0023 0.0762 | 12.3015
- 13 | 2.50 | 0.0736 0.0024 0.0760 | 11.3776
- 14 | 2.50 | 0.0734 0.0024 0.0758 | 10.4537
- 15 | 2.25 | 0.0724 0.0025 0.0748 | 9.5920
- 16 | 2.25 | 0.0698 0.0037 0.0735 | 8.8725
- 29 | 2.00 | 0.0717 0.0017 0.0734 | 3.3283
- 30 | 2.00 | 0.0661 0.0039 0.0701 | 3.1221
- 31 | 2.00 | 0.0643 0.0049 0.0691 | 2.9160
- 43 | 1.75 | 0.0636 0.0028 0.0664 | 1.5785
- 44 | 1.75 | 0.0593 0.0051 0.0644 | 1.5194
- 45 | 1.75 | 0.0579 0.0059 0.0638 | 1.4626
- 57 | 1.50 | 0.0567 0.0043 0.0609 | 1.0900
- 58 | 1.50 | 0.0535 0.0064 0.0598 | 1.0730
- 59 | 1.50 | 0.0524 0.0070 0.0594 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 151s
- Prepare output 9s
- 160s
- Jacobian determinant (RMS): 0.010 0.034 0.052 0.076 0.100 | 0.108211
- Template Matching: 0.079 0.209 0.193 0.174 0.157 | 0.157205
- Write result maps: 49s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 29s
- CSF distance: 15s
- PBT2x thickness: 45s
- 95s
- Create initial surface 89s
- Topology correction: 104s
- Surface refinement: 117s
- Reduction of surface collisions with optimization: 78s
- Spherical mapping with areal smoothing 81s
- Spherical registration 258s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 26s
- CSF distance: 14s
- PBT2x thickness: 43s
- 90s
- Create initial surface 81s
- Topology correction: 101s
- Surface refinement: 79s
- Reduction of surface collisions with optimization: 76s
- Spherical mapping with areal smoothing 78s
- Spherical registration 252s
- Final surface processing results:
- Average thickness (FS): 2.5830 0.7101 mm
- Surface intensity / position RMSE: 0.0850 / 0.1112
- Euler number / defect number / defect size: 238.0 / 67.0 / 6.88%
- Display thickness: /var/lib/condor/execute/dir_3126748/ds/NYU_2/sub-0025140/ses-1/surf/lh.thickness.sub-0025140_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3126748/ds/NYU_2/sub-0025140/ses-1/surf/rh.thickness.sub-0025140_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3126748/ds/NYU_2/sub-0025140/ses-1/sub-0025140_ses-1_run-1_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1672s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 26s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 18s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 11s
- ROI estimation of 'mori' atlas 15s
- ROI estimation of 'anatomy3' atlas 22s
- ROI estimation of 'julichbrain' atlas 29s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 46s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 69s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s
- Write results 7s
- 299s
- Quality check: 10s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3126748/ds/NYU_2/sub-0025140/ses-1/report/catreport_sub-0025140_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 47 minute(s) and 38 second(s).
- Image Quality Rating (IQR): 76.03% (C)
- GM volume (GMV): 50.45% (819.78 / 1624.86 ml)
- GM thickness (GMT): 2.58 0.71 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3126748/ds/NYU_2/sub-0025140/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_3126748/ds/NYU_2/sub-0025140/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_3126748/ds/NYU_2/sub-0025140/ses-1/label
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