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- CAT12.8.1 r2040: 1/1: ./sub-0025467/ses-1/sub-0025467_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 21s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 4s
- Initial correction 4s
- Refine background 2s
- Final correction 3s
- Final scaling 4s
- 26s
- Correct center-of-mass 2s
- Affine registration 6s
- SPM preprocessing 1 (estimate 1 - TPM registration): 9s
- Use initial fine affine registration. 47s
- SPM preprocessing 1 (estimate 2): 50s
- SPM preprocessing 2 (write):
- Write Segmentation 14s
- Update Segmentation 15s
- Update Skull-Stripping 36s
- Update probability maps 8s
- 72s
- Global intensity correction: 14s
- SANLM denoising after intensity normalization (medium): 17s
- Fast Optimized Shooting registration 27s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 2s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 10s
- Estimate local tissue thresholds (WM) 14s
- Estimate local tissue thresholds (GM) 19s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 34s
- 86s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 2s
- Ventricle detection 7s
- Blood vessel detection 6s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.08) 14s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 4s
- 43s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 26s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 3s
- Level 1 cleanup (brain masking) 2s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 8s
- 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 | 0.0890 0.0000 0.0890 | 32.0000
- 2 | 2.50 | 0.0855 0.0015 0.0869 | 29.4886
- 3 | 2.50 | 0.0844 0.0023 0.0866 | 26.9772
- 4 | 2.50 | 0.0838 0.0026 0.0864 | 24.6107
- 5 | 2.50 | 0.0834 0.0028 0.0862 | 22.6548
- 6 | 2.50 | 0.0830 0.0029 0.0859 | 20.6989
- 7 | 2.50 | 0.0826 0.0031 0.0857 | 18.9688
- 8 | 2.50 | 0.0822 0.0032 0.0854 | 17.4455
- 9 | 2.50 | 0.0818 0.0033 0.0851 | 15.9223
- 10 | 2.50 | 0.0813 0.0035 0.0848 | 14.6627
- 11 | 2.50 | 0.0809 0.0036 0.0845 | 13.4764
- 12 | 2.50 | 0.0804 0.0037 0.0841 | 12.3015
- 13 | 2.50 | 0.0799 0.0039 0.0838 | 11.3776
- 14 | 2.50 | 0.0795 0.0040 0.0834 | 10.4537
- 15 | 2.25 | 0.0807 0.0041 0.0848 | 9.5920
- 16 | 2.25 | 0.0768 0.0061 0.0828 | 8.8725
- 17 | 2.25 | 0.0751 0.0068 0.0819 | 8.1530
- 18 | 2.25 | 0.0741 0.0071 0.0812 | 7.5234
- 29 | 2.00 | 0.0762 0.0034 0.0796 | 3.3283
- 30 | 2.00 | 0.0698 0.0062 0.0760 | 3.1221
- 31 | 2.00 | 0.0675 0.0073 0.0748 | 2.9160
- 43 | 1.75 | 0.0662 0.0042 0.0704 | 1.5785
- 44 | 1.75 | 0.0614 0.0067 0.0682 | 1.5194
- 45 | 1.75 | 0.0598 0.0076 0.0674 | 1.4626
- 57 | 1.50 | 0.0584 0.0056 0.0640 | 1.0900
- 58 | 1.50 | 0.0550 0.0078 0.0628 | 1.0730
- 59 | 1.50 | 0.0539 0.0085 0.0624 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 146s
- Prepare output 8s
- 154s
- Jacobian determinant (RMS): 0.013 0.051 0.079 0.106 0.130 | 0.137396
- Template Matching: 0.089 0.222 0.203 0.179 0.162 | 0.161629
- Write result maps: 32s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 37s
- CSF distance: 11s
- PBT2x thickness: 29s
- 81s
- Create initial surface 59s
- Topology correction: 67s
- Surface refinement: 53s
- Reduction of surface collisions with optimization: 41s
- Spherical mapping with areal smoothing 56s
- Spherical registration 221s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 26s
- CSF distance: 9s
- PBT2x thickness: 28s
- 67s
- Create initial surface 54s
- Topology correction: 65s
- Surface refinement: 50s
- Reduction of surface collisions with optimization: 43s
- Spherical mapping with areal smoothing 58s
- Spherical registration 211s
- Final surface processing results:
- Average thickness (FS): 2.3176 0.6647 mm
- Surface intensity / position RMSE: 0.0663 / 0.0723
- Euler number / defect number / defect size: 28.0 / 17.0 / 0.97%
- Display thickness: /var/lib/condor/execute/dir_3515445/ds/IACAS/sub-0025467/ses-1/surf/lh.thickness.sub-0025467_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3515445/ds/IACAS/sub-0025467/ses-1/surf/rh.thickness.sub-0025467_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3515445/ds/IACAS/sub-0025467/ses-1/sub-0025467_ses-1_run-1_T1w.nii
- Surface ROI estimation: 6s
- Surface and thickness estimation takes: 1196s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 27s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 19s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 12s
- ROI estimation of 'mori' atlas 19s
- ROI estimation of 'anatomy3' atlas 33s
- ROI estimation of 'julichbrain' atlas 50s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 27s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 78s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 189s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 254s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 18s
- Write results 19s
- 751s
- Quality check: 11s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3515445/ds/IACAS/sub-0025467/ses-1/report/catreport_sub-0025467_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 46 minute(s) and 21 second(s).
- Image Quality Rating (IQR): 80.67% (B-)
- GM volume (GMV): 43.08% (560.61 / 1301.27 ml)
- GM thickness (GMT): 2.32 0.67 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3515445/ds/IACAS/sub-0025467/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_3515445/ds/IACAS/sub-0025467/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_3515445/ds/IACAS/sub-0025467/ses-1/label
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