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- CAT12.8.1 r2040: 1/1: ./sub-0025905/ses-2/sub-0025905_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 35s
- Internal resampling (1.33x1.00x1.00mm > 1.00x1.00x1.00mm): 1s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 6s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 6s
- 41s
- Correct center-of-mass 4s
- Affine registration 11s
- SPM preprocessing 1 (estimate 1 - TPM registration): 86s
- SPM preprocessing 1 (estimate 2): 71s
- SPM preprocessing 2 (write):
- Write Segmentation 18s
- Update Segmentation 20s
- Update Skull-Stripping 46s
- Update probability maps 10s
- 93s
- Global intensity correction: 18s
- SANLM denoising after intensity normalization (medium): 27s
- Fast Optimized Shooting registration 33s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 4s
- Prepare segments (LASmod = 1.07) 14s
- Estimate local tissue thresholds (WM) 20s
- Estimate local tissue thresholds (GM) 27s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 42s
- 115s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 17s
- Blood vessel detection 9s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 24s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 3s
- Final corrections 5s
- 72s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 32s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.670.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 3s
- 12s
- 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 | 0.0815 0.0000 0.0815 | 32.0000
- 2 | 2.50 | 0.0789 0.0012 0.0800 | 29.4886
- 3 | 2.50 | 0.0780 0.0018 0.0799 | 26.9772
- 4 | 2.50 | 0.0776 0.0021 0.0797 | 24.6107
- 5 | 2.50 | 0.0773 0.0022 0.0795 | 22.6548
- 6 | 2.50 | 0.0770 0.0023 0.0793 | 20.6989
- 7 | 2.50 | 0.0767 0.0024 0.0791 | 18.9688
- 8 | 2.50 | 0.0764 0.0025 0.0789 | 17.4455
- 9 | 2.50 | 0.0761 0.0026 0.0787 | 15.9223
- 10 | 2.50 | 0.0757 0.0027 0.0785 | 14.6627
- 11 | 2.50 | 0.0754 0.0028 0.0782 | 13.4764
- 12 | 2.50 | 0.0751 0.0029 0.0780 | 12.3015
- 13 | 2.50 | 0.0747 0.0030 0.0777 | 11.3776
- 14 | 2.50 | 0.0744 0.0031 0.0775 | 10.4537
- 15 | 2.25 | 0.0729 0.0032 0.0761 | 9.5920
- 16 | 2.25 | 0.0701 0.0045 0.0747 | 8.8725
- 29 | 2.00 | 0.0711 0.0020 0.0731 | 3.3283
- 30 | 2.00 | 0.0652 0.0044 0.0696 | 3.1221
- 31 | 2.00 | 0.0632 0.0054 0.0685 | 2.9160
- 43 | 1.75 | 0.0621 0.0031 0.0651 | 1.5785
- 44 | 1.75 | 0.0581 0.0052 0.0633 | 1.5194
- 45 | 1.75 | 0.0568 0.0059 0.0627 | 1.4626
- 57 | 1.50 | 0.0553 0.0043 0.0596 | 1.0900
- 58 | 1.50 | 0.0524 0.0062 0.0586 | 1.0730
- 59 | 1.50 | 0.0515 0.0068 0.0583 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 176s
- Prepare output 11s
- 188s
- Jacobian determinant (RMS): 0.011 0.040 0.058 0.080 0.101 | 0.107062
- Template Matching: 0.082 0.210 0.190 0.170 0.154 | 0.154406
- Write result maps: 83s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 35s
- CSF distance: 15s
- PBT2x thickness: 46s
- 102s
- Create initial surface 89s
- Topology correction: 101s
- Surface refinement: 108s
- Reduction of surface collisions with optimization: 82s
- Spherical mapping with areal smoothing 86s
- Spherical registration 280s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 39s
- CSF distance: 15s
- PBT2x thickness: 45s
- 105s
- Create initial surface 84s
- Topology correction: 98s
- Surface refinement: 84s
- Reduction of surface collisions with optimization: 79s
- Spherical mapping with areal smoothing 83s
- Spherical registration 306s
- Final surface processing results:
- Average thickness (FS): 2.4720 0.5653 mm
- Surface intensity / position RMSE: 0.0683 / 0.0684
- Euler number / defect number / defect size: 26.0 / 15.5 / 0.84%
- Display thickness: /var/lib/condor/execute/dir_4187641/ds/BNU_1/sub-0025905/ses-2/surf/lh.thickness.sub-0025905_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_4187641/ds/BNU_1/sub-0025905/ses-2/surf/rh.thickness.sub-0025905_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_4187641/ds/BNU_1/sub-0025905/ses-2/sub-0025905_ses-2_run-1_T1w.nii
- Surface ROI estimation: 11s
- Surface and thickness estimation takes: 1796s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 13s
- ROI estimation of 'neuromorphometrics' atlas 49s
- ROI estimation of 'lpba40' atlas 14s
- ROI estimation of 'hammers' atlas 37s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 13s
- ROI estimation of 'aal3' atlas 22s
- ROI estimation of 'mori' atlas 33s
- ROI estimation of 'anatomy3' atlas 47s
- ROI estimation of 'julichbrain' atlas 73s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 32s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 63s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 120s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 129s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 9s
- Write results 10s
- 660s
- Quality check: 12s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_4187641/ds/BNU_1/sub-0025905/ses-2/report/catreport_sub-0025905_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 57 minute(s) and 51 second(s).
- Image Quality Rating (IQR): 82.80% (B-)
- GM volume (GMV): 49.25% (735.86 / 1494.21 ml)
- GM thickness (GMT): 2.47 0.57 mm
- Segmentations are saved in /var/lib/condor/execute/dir_4187641/ds/BNU_1/sub-0025905/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_4187641/ds/BNU_1/sub-0025905/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_4187641/ds/BNU_1/sub-0025905/ses-2/label
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