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- CAT12.8.1 r2040: 1/1: ./sub-0025852/ses-1/sub-0025852_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 39s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 4s
- Initial correction 5s
- Refine background 2s
- Final correction 4s
- Final scaling 4s
- 30s
- Correct center-of-mass 3s
- Affine registration 7s
- SPM preprocessing 1 (estimate 1 - TPM registration): 62s
- SPM preprocessing 1 (estimate 2): 54s
- SPM preprocessing 2 (write):
- Write Segmentation 14s
- Update Segmentation 17s
- Update Skull-Stripping 34s
- Update probability maps 8s
- 73s
- Global intensity correction: 13s
- SANLM denoising after intensity normalization (medium): 24s
- Fast Optimized Shooting registration 27s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.12) 12s
- Estimate local tissue thresholds (WM) 15s
- Estimate local tissue thresholds (GM) 22s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 39s
- 97s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 9s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.10) 18s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 3s
- Final corrections 4s
- 53s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 29s
- 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
- 9s
- 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 | 0.0847 0.0000 0.0847 | 32.0000
- 2 | 2.50 | 0.0821 0.0012 0.0833 | 29.4886
- 3 | 2.50 | 0.0814 0.0018 0.0831 | 26.9772
- 4 | 2.50 | 0.0810 0.0020 0.0830 | 24.6107
- 5 | 2.50 | 0.0807 0.0021 0.0829 | 22.6548
- 6 | 2.50 | 0.0805 0.0022 0.0827 | 20.6989
- 7 | 2.50 | 0.0802 0.0023 0.0825 | 18.9688
- 8 | 2.50 | 0.0799 0.0024 0.0823 | 17.4455
- 9 | 2.50 | 0.0797 0.0024 0.0821 | 15.9223
- 10 | 2.50 | 0.0794 0.0025 0.0819 | 14.6627
- 11 | 2.50 | 0.0791 0.0026 0.0817 | 13.4764
- 12 | 2.50 | 0.0788 0.0026 0.0815 | 12.3015
- 13 | 2.50 | 0.0785 0.0027 0.0812 | 11.3776
- 14 | 2.50 | 0.0782 0.0028 0.0810 | 10.4537
- 15 | 2.25 | 0.0775 0.0028 0.0803 | 9.5920
- 16 | 2.25 | 0.0744 0.0043 0.0787 | 8.8725
- 29 | 2.00 | 0.0761 0.0019 0.0780 | 3.3283
- 30 | 2.00 | 0.0699 0.0044 0.0743 | 3.1221
- 31 | 2.00 | 0.0679 0.0054 0.0733 | 2.9160
- 43 | 1.75 | 0.0670 0.0031 0.0701 | 1.5785
- 44 | 1.75 | 0.0626 0.0054 0.0680 | 1.5194
- 45 | 1.75 | 0.0611 0.0062 0.0674 | 1.4626
- 57 | 1.50 | 0.0597 0.0045 0.0642 | 1.0900
- 58 | 1.50 | 0.0565 0.0066 0.0631 | 1.0730
- 59 | 1.50 | 0.0554 0.0073 0.0627 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 137s
- Prepare output 8s
- 146s
- Jacobian determinant (RMS): 0.009 0.032 0.049 0.072 0.095 | 0.101974
- Template Matching: 0.085 0.223 0.204 0.183 0.166 | 0.166243
- Write result maps: 29s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 39s
- CSF distance: 13s
- PBT2x thickness: 38s
- 96s
- Create initial surface 70s
- Topology correction: 84s
- Surface refinement: 69s
- Reduction of surface collisions with optimization: 64s
- Spherical mapping with areal smoothing 72s
- Spherical registration 210s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 36s
- CSF distance: 13s
- PBT2x thickness: 38s
- 93s
- Create initial surface 68s
- Topology correction: 84s
- Surface refinement: 92s
- Reduction of surface collisions with optimization: 62s
- Spherical mapping with areal smoothing 76s
- Spherical registration 252s
- Final surface processing results:
- Average thickness (FS): 2.5481 0.6412 mm
- Surface intensity / position RMSE: 0.0680 / 0.0722
- Euler number / defect number / defect size: 20.0 / 18.0 / 0.65%
- Display thickness: /var/lib/condor/execute/dir_2186923/ds/SWU_4/sub-0025852/ses-1/surf/lh.thickness.sub-0025852_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2186923/ds/SWU_4/sub-0025852/ses-1/surf/rh.thickness.sub-0025852_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2186923/ds/SWU_4/sub-0025852/ses-1/sub-0025852_ses-1_run-1_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1481s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 23s
- ROI estimation of 'neuromorphometrics' atlas 83s
- ROI estimation of 'lpba40' atlas 24s
- ROI estimation of 'hammers' atlas 59s
- ROI estimation of 'thalamus' atlas 5s
- ROI estimation of 'ibsr' atlas 20s
- ROI estimation of 'aal3' atlas 36s
- ROI estimation of 'mori' atlas 52s
- ROI estimation of 'anatomy3' atlas 72s
- ROI estimation of 'julichbrain' atlas 97s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 38s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 67s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 110s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 102s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s
- Write results 7s
- 796s
- Quality check: 10s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2186923/ds/SWU_4/sub-0025852/ses-1/report/catreport_sub-0025852_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 51 minute(s) and 2 second(s).
- Image Quality Rating (IQR): 83.61% (B)
- GM volume (GMV): 45.83% (794.44 / 1733.54 ml)
- GM thickness (GMT): 2.55 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2186923/ds/SWU_4/sub-0025852/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_2186923/ds/SWU_4/sub-0025852/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_2186923/ds/SWU_4/sub-0025852/ses-1/label
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