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- CAT12.8.1 r2040: 1/1: ./sub-0025647/ses-1/sub-0025647_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 82s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 7s
- Initial correction 7s
- Refine background 3s
- Final correction 6s
- Final scaling 8s
- 45s
- Correct center-of-mass 5s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 64s
- SPM preprocessing 1 (estimate 2): 59s
- SPM preprocessing 2 (write):
- Write Segmentation 17s
- Update Segmentation 19s
- Update Skull-Stripping 41s
- Update probability maps 9s
- 86s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 24s
- Fast Optimized Shooting registration 33s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.03) 14s
- Estimate local tissue thresholds (WM) 19s
- Estimate local tissue thresholds (GM) 28s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 45s
- 115s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 17s
- Blood vessel detection 9s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.02) 25s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 3s
- Final corrections 4s
- 71s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 33s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- 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 | 0.0814 0.0000 0.0814 | 32.0000
- 2 | 2.50 | 0.0794 0.0010 0.0803 | 29.4886
- 3 | 2.50 | 0.0788 0.0015 0.0802 | 26.9772
- 4 | 2.50 | 0.0785 0.0016 0.0801 | 24.6107
- 5 | 2.50 | 0.0782 0.0018 0.0800 | 22.6548
- 6 | 2.50 | 0.0780 0.0018 0.0799 | 20.6989
- 7 | 2.50 | 0.0778 0.0019 0.0797 | 18.9688
- 8 | 2.50 | 0.0776 0.0020 0.0796 | 17.4455
- 9 | 2.50 | 0.0774 0.0021 0.0794 | 15.9223
- 10 | 2.50 | 0.0771 0.0022 0.0793 | 14.6627
- 11 | 2.50 | 0.0769 0.0022 0.0791 | 13.4764
- 12 | 2.50 | 0.0766 0.0023 0.0789 | 12.3015
- 13 | 2.50 | 0.0763 0.0024 0.0787 | 11.3776
- 14 | 2.50 | 0.0761 0.0024 0.0785 | 10.4537
- 15 | 2.25 | 0.0748 0.0025 0.0773 | 9.5920
- 16 | 2.25 | 0.0724 0.0038 0.0762 | 8.8725
- 29 | 2.00 | 0.0743 0.0017 0.0760 | 3.3283
- 30 | 2.00 | 0.0688 0.0039 0.0728 | 3.1221
- 31 | 2.00 | 0.0670 0.0048 0.0719 | 2.9160
- 43 | 1.75 | 0.0665 0.0027 0.0692 | 1.5785
- 44 | 1.75 | 0.0623 0.0050 0.0673 | 1.5194
- 45 | 1.75 | 0.0609 0.0058 0.0667 | 1.4626
- 57 | 1.50 | 0.0599 0.0042 0.0640 | 1.0900
- 58 | 1.50 | 0.0566 0.0063 0.0629 | 1.0730
- 59 | 1.50 | 0.0556 0.0070 0.0625 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 169s
- Prepare output 10s
- 179s
- Jacobian determinant (RMS): 0.010 0.036 0.055 0.080 0.106 | 0.113709
- Template Matching: 0.081 0.217 0.201 0.183 0.167 | 0.166690
- Write result maps: 34s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 32s
- CSF distance: 16s
- PBT2x thickness: 47s
- 101s
- Create initial surface 84s
- Topology correction: 95s
- Surface refinement: 92s
- Reduction of surface collisions with optimization: 75s
- Spherical mapping with areal smoothing 84s
- Spherical registration 300s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 27s
- CSF distance: 16s
- PBT2x thickness: 46s
- 95s
- Create initial surface 85s
- Topology correction: 104s
- Surface refinement: 84s
- Reduction of surface collisions with optimization: 78s
- Spherical mapping with areal smoothing 92s
- Spherical registration 310s
- Final surface processing results:
- Average thickness (FS): 2.5910 0.6739 mm
- Surface intensity / position RMSE: 0.0796 / 0.1012
- Euler number / defect number / defect size: 26.0 / 11.5 / 1.29%
- Display thickness: /var/lib/condor/execute/dir_3209399/ds/SWU_4/sub-0025647/ses-1/surf/lh.thickness.sub-0025647_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3209399/ds/SWU_4/sub-0025647/ses-1/surf/rh.thickness.sub-0025647_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3209399/ds/SWU_4/sub-0025647/ses-1/sub-0025647_ses-1_run-1_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 1780s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 41s
- ROI estimation of 'lpba40' atlas 11s
- ROI estimation of 'hammers' atlas 29s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 9s
- ROI estimation of 'aal3' atlas 16s
- ROI estimation of 'mori' atlas 20s
- ROI estimation of 'anatomy3' atlas 31s
- ROI estimation of 'julichbrain' atlas 40s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 32s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 67s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 100s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 9s
- Write results 10s
- 436s
- Quality check: 12s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3209399/ds/SWU_4/sub-0025647/ses-1/report/catreport_sub-0025647_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 53 minute(s) and 34 second(s).
- Image Quality Rating (IQR): 82.49% (B-)
- GM volume (GMV): 52.51% (760.71 / 1448.59 ml)
- GM thickness (GMT): 2.59 0.67 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3209399/ds/SWU_4/sub-0025647/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_3209399/ds/SWU_4/sub-0025647/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_3209399/ds/SWU_4/sub-0025647/ses-1/label
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