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- CAT12.8.1 r2040: 1/1: ./sub-0025846/ses-1/sub-0025846_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 48s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 5s
- Initial correction 5s
- Refine background 3s
- Final correction 5s
- Final scaling 4s
- 34s
- Correct center-of-mass 3s
- Affine registration 8s
- SPM preprocessing 1 (estimate 1 - TPM registration): 7s
- Use initial fine affine registration. 5s
- Use previous fine affine registration. 52s
- SPM preprocessing 1 (estimate 2): 52s
- SPM preprocessing 2 (write):
- Write Segmentation 16s
- Update Segmentation 18s
- Update Skull-Stripping 40s
- Update probability maps 8s
- 82s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 27s
- Fast Optimized Shooting registration 32s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.13) 13s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 25s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 47s
- 112s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 13s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 22s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 63s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 31s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- 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
- 10s
- 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 | 0.0819 0.0000 0.0819 | 32.0000
- 2 | 2.50 | 0.0796 0.0011 0.0807 | 29.4886
- 3 | 2.50 | 0.0789 0.0016 0.0806 | 26.9772
- 4 | 2.50 | 0.0786 0.0018 0.0804 | 24.6107
- 5 | 2.50 | 0.0784 0.0019 0.0803 | 22.6548
- 6 | 2.50 | 0.0781 0.0020 0.0801 | 20.6989
- 7 | 2.50 | 0.0779 0.0021 0.0800 | 18.9688
- 8 | 2.50 | 0.0776 0.0022 0.0798 | 17.4455
- 9 | 2.50 | 0.0774 0.0022 0.0796 | 15.9223
- 10 | 2.50 | 0.0771 0.0023 0.0794 | 14.6627
- 11 | 2.50 | 0.0769 0.0023 0.0792 | 13.4764
- 12 | 2.50 | 0.0766 0.0024 0.0790 | 12.3015
- 13 | 2.50 | 0.0763 0.0025 0.0788 | 11.3776
- 14 | 2.50 | 0.0761 0.0025 0.0786 | 10.4537
- 15 | 2.25 | 0.0747 0.0026 0.0773 | 9.5920
- 16 | 2.25 | 0.0719 0.0039 0.0758 | 8.8725
- 29 | 2.00 | 0.0734 0.0018 0.0752 | 3.3283
- 30 | 2.00 | 0.0676 0.0041 0.0717 | 3.1221
- 31 | 2.00 | 0.0658 0.0050 0.0708 | 2.9160
- 43 | 1.75 | 0.0649 0.0028 0.0677 | 1.5785
- 44 | 1.75 | 0.0606 0.0051 0.0657 | 1.5194
- 45 | 1.75 | 0.0592 0.0059 0.0651 | 1.4626
- 57 | 1.50 | 0.0576 0.0043 0.0619 | 1.0900
- 58 | 1.50 | 0.0545 0.0063 0.0608 | 1.0730
- 59 | 1.50 | 0.0534 0.0069 0.0604 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 161s
- Prepare output 10s
- 171s
- Jacobian determinant (RMS): 0.010 0.033 0.050 0.074 0.100 | 0.107008
- Template Matching: 0.082 0.216 0.197 0.177 0.160 | 0.160324
- Write result maps: 34s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 35s
- CSF distance: 14s
- PBT2x thickness: 43s
- 99s
- Create initial surface 83s
- Topology correction: 88s
- Surface refinement: 67s
- Reduction of surface collisions with optimization: 64s
- Spherical mapping with areal smoothing 77s
- Spherical registration 300s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 28s
- CSF distance: 14s
- PBT2x thickness: 42s
- 91s
- Create initial surface 80s
- Topology correction: 86s
- Surface refinement: 70s
- Reduction of surface collisions with optimization: 63s
- Spherical mapping with areal smoothing 74s
- Spherical registration 282s
- Final surface processing results:
- Average thickness (FS): 2.6621 0.6520 mm
- Surface intensity / position RMSE: 0.0640 / 0.0631
- Euler number / defect number / defect size: 8.0 / 8.0 / 0.20%
- Display thickness: /var/lib/condor/execute/dir_2847052/ds/SWU_4/sub-0025846/ses-1/surf/lh.thickness.sub-0025846_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2847052/ds/SWU_4/sub-0025846/ses-1/surf/rh.thickness.sub-0025846_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2847052/ds/SWU_4/sub-0025846/ses-1/sub-0025846_ses-1_run-1_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1617s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 32s
- ROI estimation of 'lpba40' atlas 9s
- ROI estimation of 'hammers' atlas 23s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 8s
- ROI estimation of 'aal3' atlas 13s
- ROI estimation of 'mori' atlas 21s
- ROI estimation of 'anatomy3' atlas 30s
- ROI estimation of 'julichbrain' atlas 41s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 16s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 32s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 66s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 100s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s
- Write results 10s
- 412s
- Quality check: 12s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2847052/ds/SWU_4/sub-0025846/ses-1/report/catreport_sub-0025846_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 48 minute(s) and 41 second(s).
- Image Quality Rating (IQR): 82.91% (B-)
- GM volume (GMV): 48.23% (673.09 / 1395.59 ml)
- GM thickness (GMT): 2.66 0.65 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2847052/ds/SWU_4/sub-0025846/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_2847052/ds/SWU_4/sub-0025846/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_2847052/ds/SWU_4/sub-0025846/ses-1/label
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