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- CAT12.8.1 r2040: 1/1: ./sub-0027160/ses-1/sub-0027160_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 64s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 7s
- Initial correction 12s
- Refine background 4s
- Final correction 10s
- Final scaling 6s
- 54s
- Correct center-of-mass 5s
- Affine registration 15s
- SPM preprocessing 1 (estimate 1 - TPM registration): 101s
- SPM preprocessing 1 (estimate 2): 104s
- SPM preprocessing 2 (write):
- Write Segmentation 22s
- Update Segmentation 25s
- Update Skull-Stripping 51s
- Update probability maps 10s
- 109s
- Global intensity correction: 19s
- SANLM denoising after intensity normalization (medium): 37s
- Fast Optimized Shooting registration 41s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.07) 19s
- Estimate local tissue thresholds (WM) 25s
- Estimate local tissue thresholds (GM) 39s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 59s
- 153s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 4s
- Ventricle detection 21s
- Blood vessel detection 14s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 35s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 94s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 42s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 6s
- Level 1 cleanup (brain masking) 4s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 4s
- 15s
- 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 | 0.0906 0.0000 0.0906 | 32.0000
- 2 | 2.50 | 0.0861 0.0016 0.0877 | 29.4886
- 3 | 2.50 | 0.0845 0.0026 0.0871 | 26.9772
- 4 | 2.50 | 0.0837 0.0031 0.0868 | 24.6107
- 5 | 2.50 | 0.0830 0.0034 0.0864 | 22.6548
- 6 | 2.50 | 0.0825 0.0036 0.0861 | 20.6989
- 7 | 2.50 | 0.0820 0.0037 0.0857 | 18.9688
- 8 | 2.50 | 0.0815 0.0039 0.0854 | 17.4455
- 9 | 2.50 | 0.0809 0.0040 0.0850 | 15.9223
- 10 | 2.50 | 0.0804 0.0042 0.0846 | 14.6627
- 11 | 2.50 | 0.0799 0.0043 0.0842 | 13.4764
- 12 | 2.50 | 0.0793 0.0044 0.0837 | 12.3015
- 13 | 2.50 | 0.0788 0.0046 0.0833 | 11.3776
- 14 | 2.50 | 0.0783 0.0046 0.0829 | 10.4537
- 15 | 2.25 | 0.0787 0.0048 0.0835 | 9.5920
- 16 | 2.25 | 0.0751 0.0066 0.0817 | 8.8725
- 17 | 2.25 | 0.0736 0.0072 0.0808 | 8.1530
- 29 | 2.00 | 0.0753 0.0033 0.0787 | 3.3283
- 30 | 2.00 | 0.0687 0.0061 0.0748 | 3.1221
- 31 | 2.00 | 0.0663 0.0071 0.0734 | 2.9160
- 43 | 1.75 | 0.0652 0.0041 0.0693 | 1.5785
- 44 | 1.75 | 0.0606 0.0065 0.0671 | 1.5194
- 45 | 1.75 | 0.0590 0.0073 0.0663 | 1.4626
- 57 | 1.50 | 0.0576 0.0054 0.0630 | 1.0900
- 58 | 1.50 | 0.0544 0.0075 0.0619 | 1.0730
- 59 | 1.50 | 0.0534 0.0081 0.0615 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 217s
- Prepare output 15s
- 232s
- Jacobian determinant (RMS): 0.010 0.041 0.064 0.091 0.115 | 0.122411
- Template Matching: 0.091 0.221 0.199 0.177 0.160 | 0.160132
- Write result maps: 52s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 48s
- CSF distance: 21s
- PBT2x thickness: 63s
- 139s
- Create initial surface 105s
- Topology correction: 121s
- Surface refinement: 117s
- Reduction of surface collisions with optimization: 90s
- Spherical mapping with areal smoothing 109s
- Spherical registration 321s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 43s
- CSF distance: 21s
- PBT2x thickness: 63s
- 134s
- Create initial surface 102s
- Topology correction: 121s
- Surface refinement: 112s
- Reduction of surface collisions with optimization: 86s
- Spherical mapping with areal smoothing 111s
- Spherical registration 355s
- Final surface processing results:
- Average thickness (FS): 2.6618 0.6705 mm
- Surface intensity / position RMSE: 0.0711 / 0.0733
- Euler number / defect number / defect size: 20.0 / 9.0 / 0.50%
- Display thickness: /var/lib/condor/execute/dir_1727897/ds/SWU_3/sub-0027160/ses-1/surf/lh.thickness.sub-0027160_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1727897/ds/SWU_3/sub-0027160/ses-1/surf/rh.thickness.sub-0027160_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1727897/ds/SWU_3/sub-0027160/ses-1/sub-0027160_ses-1_run-1_T1w.nii
- Surface ROI estimation: 13s
- Surface and thickness estimation takes: 2148s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 13s
- ROI estimation of 'neuromorphometrics' atlas 46s
- ROI estimation of 'lpba40' atlas 14s
- ROI estimation of 'hammers' atlas 32s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 12s
- ROI estimation of 'aal3' atlas 20s
- ROI estimation of 'mori' atlas 25s
- ROI estimation of 'anatomy3' atlas 50s
- ROI estimation of 'julichbrain' atlas 59s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 20s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 32s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 78s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 111s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 9s
- Write results 11s
- 523s
- Quality check: 16s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1727897/ds/SWU_3/sub-0027160/ses-1/report/catreport_sub-0027160_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 65 minute(s) and 27 second(s).
- Image Quality Rating (IQR): 82.41% (B-)
- GM volume (GMV): 49.63% (776.63 / 1564.77 ml)
- GM thickness (GMT): 2.66 0.67 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1727897/ds/SWU_3/sub-0027160/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_1727897/ds/SWU_3/sub-0027160/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_1727897/ds/SWU_3/sub-0027160/ses-1/label
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