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- CAT12.8.1 r2040: 1/1: ./sub-0025736/ses-2/sub-0025736_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 29s
- APP: Rough bias correction:
- Initialize 4s
- Estimate background 3s
- Initial correction 3s
- Refine background 2s
- Final correction 3s
- Final scaling 3s
- 23s
- Correct center-of-mass 2s
- Affine registration 5s
- SPM preprocessing 1 (estimate 1 - TPM registration): 6s
- Use initial fine affine registration. 38s
- SPM preprocessing 1 (estimate 2): 38s
- SPM preprocessing 2 (write):
- Write Segmentation 11s
- Update Segmentation 12s
- Update Skull-Stripping 27s
- Update probability maps 6s
- 57s
- Global intensity correction: 11s
- SANLM denoising after intensity normalization (medium): 15s
- Fast Optimized Shooting registration 22s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 2s
- Prepare partitions 1s
- Prepare segments (LASmod = 1.19) 8s
- Estimate local tissue thresholds (WM) 12s
- Estimate local tissue thresholds (GM) 17s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 29s
- 72s
- ROI segmentation (partitioning):
- Atlas -> subject space 4s
- Major structures 2s
- Ventricle detection 5s
- Blood vessel detection 5s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 12s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 3s
- 34s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 21s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 2s
- Level 1 cleanup (brain masking) 2s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 7s
- 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 | 0.0816 0.0000 0.0816 | 32.0000
- 2 | 2.50 | 0.0792 0.0011 0.0803 | 29.4886
- 3 | 2.50 | 0.0785 0.0017 0.0802 | 26.9772
- 4 | 2.50 | 0.0781 0.0019 0.0800 | 24.6107
- 5 | 2.50 | 0.0779 0.0020 0.0799 | 22.6548
- 6 | 2.50 | 0.0776 0.0021 0.0797 | 20.6989
- 7 | 2.50 | 0.0774 0.0022 0.0795 | 18.9688
- 8 | 2.50 | 0.0771 0.0023 0.0794 | 17.4455
- 9 | 2.50 | 0.0768 0.0023 0.0792 | 15.9223
- 10 | 2.50 | 0.0765 0.0024 0.0790 | 14.6627
- 11 | 2.50 | 0.0762 0.0025 0.0788 | 13.4764
- 12 | 2.50 | 0.0759 0.0026 0.0785 | 12.3015
- 13 | 2.50 | 0.0756 0.0027 0.0783 | 11.3776
- 14 | 2.50 | 0.0753 0.0027 0.0781 | 10.4537
- 15 | 2.25 | 0.0753 0.0028 0.0781 | 9.5920
- 16 | 2.25 | 0.0723 0.0043 0.0766 | 8.8725
- 29 | 2.00 | 0.0740 0.0019 0.0760 | 3.3283
- 30 | 2.00 | 0.0678 0.0044 0.0722 | 3.1221
- 31 | 2.00 | 0.0656 0.0054 0.0710 | 2.9160
- 43 | 1.75 | 0.0646 0.0031 0.0677 | 1.5785
- 44 | 1.75 | 0.0601 0.0054 0.0655 | 1.5194
- 45 | 1.75 | 0.0586 0.0063 0.0648 | 1.4626
- 57 | 1.50 | 0.0572 0.0046 0.0617 | 1.0900
- 58 | 1.50 | 0.0541 0.0066 0.0607 | 1.0730
- 59 | 1.50 | 0.0530 0.0073 0.0602 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 108s
- Prepare output 7s
- 115s
- Jacobian determinant (RMS): 0.011 0.038 0.058 0.083 0.108 | 0.113440
- Template Matching: 0.082 0.217 0.197 0.176 0.159 | 0.158882
- Write result maps: 23s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 21s
- CSF distance: 9s
- PBT2x thickness: 26s
- 60s
- Create initial surface 46s
- Topology correction: 61s
- Surface refinement: 62s
- Reduction of surface collisions with optimization: 39s
- Spherical mapping with areal smoothing 52s
- Spherical registration 170s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 16s
- CSF distance: 9s
- PBT2x thickness: 26s
- 54s
- Create initial surface 46s
- Topology correction: 60s
- Surface refinement: 65s
- Reduction of surface collisions with optimization: 42s
- Spherical mapping with areal smoothing 61s
- Spherical registration 203s
- Final surface processing results:
- Average thickness (FS): 2.5251 0.6498 mm
- Surface intensity / position RMSE: 0.0749 / 0.0874
- Euler number / defect number / defect size: 32.0 / 17.5 / 1.71%
- Display thickness: /var/lib/condor/execute/dir_2985964/ds/SWU_4/sub-0025736/ses-2/surf/lh.thickness.sub-0025736_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2985964/ds/SWU_4/sub-0025736/ses-2/surf/rh.thickness.sub-0025736_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2985964/ds/SWU_4/sub-0025736/ses-2/sub-0025736_ses-2_run-1_T1w.nii
- Surface ROI estimation: 6s
- Surface and thickness estimation takes: 1083s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 23s
- ROI estimation of 'lpba40' atlas 6s
- ROI estimation of 'hammers' atlas 16s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 6s
- ROI estimation of 'aal3' atlas 9s
- ROI estimation of 'mori' atlas 14s
- ROI estimation of 'anatomy3' atlas 19s
- ROI estimation of 'julichbrain' atlas 26s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 10s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 19s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 42s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 64s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 5s
- Write results 6s
- 268s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2985964/ds/SWU_4/sub-0025736/ses-2/report/catreport_sub-0025736_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 32 minute(s) and 16 second(s).
- Image Quality Rating (IQR): 82.88% (B-)
- GM volume (GMV): 50.73% (659.51 / 1300.04 ml)
- GM thickness (GMT): 2.52 0.65 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2985964/ds/SWU_4/sub-0025736/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_2985964/ds/SWU_4/sub-0025736/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_2985964/ds/SWU_4/sub-0025736/ses-2/label
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