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- CAT12.8.1 r2040: 1/1: ./sub-0026031/ses-1/sub-0026031_ses-1_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 16s
- Estimate background 12s
- Initial correction 14s
- Refine background 7s
- Final correction 12s
- Final scaling 10s
- 86s
- Correct center-of-mass 9s
- Affine registration 59s
- SPM preprocessing 1 (estimate 1 - TPM registration): 7s
- Use initial fine affine registration. 146s
- SPM preprocessing 1 (estimate 2): 68s
- SPM preprocessing 2 (write):
- Write Segmentation 41s
- Update Segmentation 43s
- Update Skull-Stripping 107s
- Update probability maps 23s
- 214s
- Global intensity correction: 43s
- SANLM denoising after intensity normalization (medium): 82s
- Fast Optimized Shooting registration 59s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 10s
- Prepare partitions 7s
- Prepare segments (LASmod = 1.00) 39s
- Estimate local tissue thresholds (WM) 55s
- Estimate local tissue thresholds (GM) 86s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 106s
- 314s
- ROI segmentation (partitioning):
- Atlas -> subject space 20s
- Major structures 9s
- Ventricle detection 41s
- Blood vessel detection 31s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 73s
- Manual stroke lesion detection 0s
- Closing of deep structures 4s
- Side alignment 10s
- Final corrections 12s
- 201s
- Blood vessel correction (BVCstr=0.50): 4s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 75s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- 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
- 28s
- 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 | 0.0867 0.0000 0.0867 | 32.0000
- 2 | 2.50 | 0.0844 0.0011 0.0855 | 29.4886
- 3 | 2.50 | 0.0837 0.0017 0.0854 | 26.9772
- 4 | 2.50 | 0.0834 0.0018 0.0853 | 24.6107
- 5 | 2.50 | 0.0832 0.0020 0.0851 | 22.6548
- 6 | 2.50 | 0.0829 0.0020 0.0849 | 20.6989
- 7 | 2.50 | 0.0827 0.0021 0.0848 | 18.9688
- 8 | 2.50 | 0.0824 0.0022 0.0846 | 17.4455
- 9 | 2.50 | 0.0822 0.0022 0.0844 | 15.9223
- 10 | 2.50 | 0.0819 0.0023 0.0842 | 14.6627
- 11 | 2.50 | 0.0817 0.0024 0.0840 | 13.4764
- 12 | 2.50 | 0.0814 0.0024 0.0838 | 12.3015
- 13 | 2.50 | 0.0811 0.0025 0.0836 | 11.3776
- 14 | 2.50 | 0.0808 0.0025 0.0834 | 10.4537
- 15 | 2.25 | 0.0816 0.0026 0.0841 | 9.5920
- 16 | 2.25 | 0.0782 0.0042 0.0824 | 8.8725
- 17 | 2.25 | 0.0770 0.0048 0.0817 | 8.1530
- 18 | 2.25 | 0.0762 0.0050 0.0812 | 7.5234
- 19 | 2.25 | 0.0756 0.0051 0.0808 | 6.9630
- 20 | 2.25 | 0.0751 0.0051 0.0803 | 6.4027
- 21 | 2.25 | 0.0746 0.0052 0.0798 | 5.9447
- 29 | 2.00 | 0.0776 0.0031 0.0807 | 3.3283
- 30 | 2.00 | 0.0727 0.0053 0.0781 | 3.1221
- 31 | 2.00 | 0.0711 0.0061 0.0772 | 2.9160
- 43 | 1.75 | 0.0711 0.0034 0.0745 | 1.5785
- 44 | 1.75 | 0.0659 0.0063 0.0722 | 1.5194
- 45 | 1.75 | 0.0643 0.0071 0.0715 | 1.4626
- 57 | 1.50 | 0.0632 0.0052 0.0683 | 1.0900
- 58 | 1.50 | 0.0593 0.0078 0.0671 | 1.0730
- 59 | 1.50 | 0.0582 0.0085 0.0666 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 215s
- Prepare output 24s
- 239s
- Jacobian determinant (RMS): 0.009 0.034 0.063 0.100 0.140 | 0.146758
- Template Matching: 0.087 0.224 0.213 0.193 0.175 | 0.174529
- Write result maps: 369s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 59s
- CSF distance: 25s
- PBT2x thickness: 72s
- 163s
- Create initial surface 116s
- Topology correction: 137s
- Surface refinement: 118s
- Reduction of surface collisions with optimization: 109s
- Spherical mapping with areal smoothing 141s
- Spherical registration 367s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 50s
- CSF distance: 25s
- PBT2x thickness: 71s
- 155s
- Create initial surface 114s
- Topology correction: 130s
- Surface refinement: 140s
- Reduction of surface collisions with optimization: 103s
- Spherical mapping with areal smoothing 123s
- Spherical registration 343s
- Final surface processing results:
- Average thickness (FS): 2.7573 0.6483 mm
- Surface intensity / position RMSE: 0.0810 / 0.0751
- Euler number / defect number / defect size: 32.0 / 17.0 / 0.76%
- Display thickness: /var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-1/surf/lh.thickness.sub-0026031_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-1/surf/rh.thickness.sub-0026031_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-1/sub-0026031_ses-1_run-1_T1w.nii
- Surface ROI estimation: 11s
- Surface and thickness estimation takes: 2474s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 19s
- ROI estimation of 'neuromorphometrics' atlas 70s
- 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 30s
- ROI estimation of 'mori' atlas 45s
- ROI estimation of 'anatomy3' atlas 69s
- ROI estimation of 'julichbrain' atlas 85s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 39s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 75s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 164s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 249s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 22s
- Write results 24s
- 961s
- Quality check: 71s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-1/report/catreport_sub-0026031_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 100 minute(s) and 17 second(s).
- Image Quality Rating (IQR): 72.87% (C-)
- GM volume (GMV): 55.15% (892.86 / 1618.87 ml)
- GM thickness (GMT): 2.76 0.65 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-1/label
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