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- CAT12.8.1 r2040: 1/1: ./sub-0027162/ses-2/sub-0027162_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 56s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 8s
- Initial correction 11s
- Refine background 4s
- Final correction 8s
- Final scaling 5s
- 52s
- Correct center-of-mass 5s
- Affine registration 11s
- SPM preprocessing 1 (estimate 1 - TPM registration): 94s
- SPM preprocessing 1 (estimate 2): 80s
- SPM preprocessing 2 (write):
- Write Segmentation 21s
- Update Segmentation 23s
- Update Skull-Stripping 54s
- Update probability maps 11s
- 110s
- Global intensity correction: 21s
- SANLM denoising after intensity normalization (medium): 31s
- Fast Optimized Shooting registration 41s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.05) 18s
- Estimate local tissue thresholds (WM) 26s
- Estimate local tissue thresholds (GM) 38s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 56s
- 151s
- ROI segmentation (partitioning):
- Atlas -> subject space 11s
- Major structures 4s
- Ventricle detection 19s
- Blood vessel detection 12s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 33s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 6s
- 91s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 39s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 5s
- Level 1 cleanup (brain masking) 4s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 3s
- 14s
- 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 | 0.0817 0.0000 0.0817 | 32.0000
- 2 | 2.50 | 0.0793 0.0011 0.0804 | 29.4886
- 3 | 2.50 | 0.0786 0.0017 0.0802 | 26.9772
- 4 | 2.50 | 0.0782 0.0019 0.0801 | 24.6107
- 5 | 2.50 | 0.0780 0.0020 0.0800 | 22.6548
- 6 | 2.50 | 0.0777 0.0021 0.0798 | 20.6989
- 7 | 2.50 | 0.0775 0.0022 0.0796 | 18.9688
- 8 | 2.50 | 0.0772 0.0022 0.0794 | 17.4455
- 9 | 2.50 | 0.0770 0.0023 0.0792 | 15.9223
- 10 | 2.50 | 0.0767 0.0024 0.0791 | 14.6627
- 11 | 2.50 | 0.0764 0.0024 0.0789 | 13.4764
- 12 | 2.50 | 0.0761 0.0025 0.0786 | 12.3015
- 13 | 2.50 | 0.0758 0.0026 0.0784 | 11.3776
- 14 | 2.50 | 0.0756 0.0026 0.0782 | 10.4537
- 15 | 2.25 | 0.0743 0.0027 0.0769 | 9.5920
- 16 | 2.25 | 0.0716 0.0040 0.0755 | 8.8725
- 29 | 2.00 | 0.0731 0.0018 0.0749 | 3.3283
- 30 | 2.00 | 0.0677 0.0040 0.0716 | 3.1221
- 31 | 2.00 | 0.0659 0.0048 0.0707 | 2.9160
- 43 | 1.75 | 0.0652 0.0027 0.0680 | 1.5785
- 44 | 1.75 | 0.0611 0.0049 0.0660 | 1.5194
- 45 | 1.75 | 0.0597 0.0057 0.0654 | 1.4626
- 57 | 1.50 | 0.0584 0.0041 0.0625 | 1.0900
- 58 | 1.50 | 0.0553 0.0061 0.0614 | 1.0730
- 59 | 1.50 | 0.0542 0.0068 0.0610 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 210s
- Prepare output 14s
- 224s
- Jacobian determinant (RMS): 0.010 0.036 0.053 0.076 0.100 | 0.107425
- Template Matching: 0.082 0.215 0.198 0.179 0.163 | 0.162666
- Write result maps: 69s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 42s
- CSF distance: 21s
- PBT2x thickness: 58s
- 128s
- Create initial surface 103s
- Topology correction: 117s
- Surface refinement: 100s
- Reduction of surface collisions with optimization: 89s
- Spherical mapping with areal smoothing 109s
- Spherical registration 333s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 38s
- CSF distance: 20s
- PBT2x thickness: 58s
- 123s
- Create initial surface 103s
- Topology correction: 115s
- Surface refinement: 128s
- Reduction of surface collisions with optimization: 87s
- Spherical mapping with areal smoothing 105s
- Spherical registration 338s
- Final surface processing results:
- Average thickness (FS): 2.5158 0.6106 mm
- Surface intensity / position RMSE: 0.0722 / 0.0809
- Euler number / defect number / defect size: 20.0 / 19.0 / 0.87%
- Display thickness: /var/lib/condor/execute/dir_3501198/ds/SWU_3/sub-0027162/ses-2/surf/lh.thickness.sub-0027162_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3501198/ds/SWU_3/sub-0027162/ses-2/surf/rh.thickness.sub-0027162_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3501198/ds/SWU_3/sub-0027162/ses-2/sub-0027162_ses-2_run-1_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 2104s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 14s
- ROI estimation of 'neuromorphometrics' atlas 51s
- ROI estimation of 'lpba40' atlas 15s
- ROI estimation of 'hammers' atlas 38s
- 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 50s
- ROI estimation of 'julichbrain' atlas 66s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 28s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 56s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 118s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 166s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 13s
- Write results 15s
- 691s
- Quality check: 17s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3501198/ds/SWU_3/sub-0027162/ses-2/report/catreport_sub-0027162_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 67 minute(s) and 27 second(s).
- Image Quality Rating (IQR): 82.73% (B-)
- GM volume (GMV): 50.47% (715.88 / 1418.32 ml)
- GM thickness (GMT): 2.52 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3501198/ds/SWU_3/sub-0027162/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_3501198/ds/SWU_3/sub-0027162/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_3501198/ds/SWU_3/sub-0027162/ses-2/label
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