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- CAT12.8.1 r2040: 1/1: ./sub-0025725/ses-2/sub-0025725_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 55s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 5s
- Initial correction 5s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 33s
- Correct center-of-mass 5s
- Affine registration 8s
- SPM preprocessing 1 (estimate 1 - TPM registration): 63s
- SPM preprocessing 1 (estimate 2): 53s
- SPM preprocessing 2 (write):
- Write Segmentation 14s
- Update Segmentation 16s
- Update Skull-Stripping 35s
- Update probability maps 8s
- 72s
- Global intensity correction: 13s
- SANLM denoising after intensity normalization (medium): 21s
- Fast Optimized Shooting registration 26s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 12s
- Estimate local tissue thresholds (WM) 15s
- Estimate local tissue thresholds (GM) 20s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 36s
- 91s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 3s
- Ventricle detection 10s
- Blood vessel detection 7s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.03) 19s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 53s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 28s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- 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 | 0.0825 0.0000 0.0825 | 32.0000
- 2 | 2.50 | 0.0801 0.0011 0.0812 | 29.4886
- 3 | 2.50 | 0.0794 0.0017 0.0811 | 26.9772
- 4 | 2.50 | 0.0790 0.0019 0.0809 | 24.6107
- 5 | 2.50 | 0.0787 0.0021 0.0808 | 22.6548
- 6 | 2.50 | 0.0784 0.0021 0.0806 | 20.6989
- 7 | 2.50 | 0.0782 0.0022 0.0804 | 18.9688
- 8 | 2.50 | 0.0779 0.0023 0.0802 | 17.4455
- 9 | 2.50 | 0.0776 0.0024 0.0800 | 15.9223
- 10 | 2.50 | 0.0773 0.0025 0.0798 | 14.6627
- 11 | 2.50 | 0.0770 0.0026 0.0796 | 13.4764
- 12 | 2.50 | 0.0767 0.0027 0.0793 | 12.3015
- 13 | 2.50 | 0.0764 0.0028 0.0791 | 11.3776
- 14 | 2.50 | 0.0760 0.0028 0.0789 | 10.4537
- 15 | 2.25 | 0.0746 0.0029 0.0775 | 9.5920
- 16 | 2.25 | 0.0718 0.0043 0.0761 | 8.8725
- 29 | 2.00 | 0.0725 0.0019 0.0745 | 3.3283
- 30 | 2.00 | 0.0668 0.0042 0.0710 | 3.1221
- 31 | 2.00 | 0.0649 0.0051 0.0701 | 2.9160
- 43 | 1.75 | 0.0639 0.0029 0.0669 | 1.5785
- 44 | 1.75 | 0.0600 0.0050 0.0650 | 1.5194
- 45 | 1.75 | 0.0587 0.0057 0.0645 | 1.4626
- 57 | 1.50 | 0.0573 0.0042 0.0615 | 1.0900
- 58 | 1.50 | 0.0544 0.0061 0.0605 | 1.0730
- Shooting registration with 2.50:-0.25:1.50 mm takes: 117s
- Prepare output 8s
- 125s
- Jacobian determinant (RMS): 0.010 0.037 0.055 0.077 0.098 | 0.102352
- Template Matching: 0.083 0.215 0.195 0.176 0.163 | 0.163264
- Write result maps: 30s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 35s
- CSF distance: 13s
- PBT2x thickness: 35s
- 89s
- Create initial surface 64s
- Topology correction: 84s
- Surface refinement: 82s
- Reduction of surface collisions with optimization: 57s
- Spherical mapping with areal smoothing 69s
- Spherical registration 219s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 22s
- CSF distance: 12s
- PBT2x thickness: 34s
- 74s
- Create initial surface 63s
- Topology correction: 84s
- Surface refinement: 95s
- Reduction of surface collisions with optimization: 62s
- Spherical mapping with areal smoothing 74s
- Spherical registration 241s
- Final surface processing results:
- Average thickness (FS): 2.3935 0.6742 mm
- Surface intensity / position RMSE: 0.0797 / 0.1085
- Euler number / defect number / defect size: 48.0 / 24.5 / 2.83%
- Display thickness: /var/lib/condor/execute/dir_3490517/ds/SWU_4/sub-0025725/ses-2/surf/lh.thickness.sub-0025725_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3490517/ds/SWU_4/sub-0025725/ses-2/surf/rh.thickness.sub-0025725_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3490517/ds/SWU_4/sub-0025725/ses-2/sub-0025725_ses-2_run-1_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 1441s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 12s
- ROI estimation of 'neuromorphometrics' atlas 45s
- ROI estimation of 'lpba40' atlas 13s
- ROI estimation of 'hammers' atlas 36s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 11s
- ROI estimation of 'aal3' atlas 21s
- ROI estimation of 'mori' atlas 33s
- ROI estimation of 'anatomy3' atlas 52s
- ROI estimation of 'julichbrain' atlas 67s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 30s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 62s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 112s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 136s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 9s
- Write results 10s
- 644s
- Quality check: 9s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3490517/ds/SWU_4/sub-0025725/ses-2/report/catreport_sub-0025725_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 48 minute(s) and 28 second(s).
- Image Quality Rating (IQR): 79.80% (C+)
- GM volume (GMV): 47.19% (742.56 / 1573.67 ml)
- GM thickness (GMT): 2.39 0.67 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3490517/ds/SWU_4/sub-0025725/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_3490517/ds/SWU_4/sub-0025725/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_3490517/ds/SWU_4/sub-0025725/ses-2/label
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