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- CAT12.8.1 r2040: 1/1: ./sub-0027205/ses-3/sub-0027205_ses-3_run-2_T1w.n
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- SANLM denoising (medium): 36s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 4s
- Initial correction 5s
- Refine background 2s
- Final correction 5s
- Final scaling 3s
- 30s
- Correct center-of-mass 2s
- Affine registration 6s
- SPM preprocessing 1 (estimate 1 - TPM registration): 6s
- Use initial fine affine registration. 45s
- SPM preprocessing 1 (estimate 2): 48s
- SPM preprocessing 2 (write):
- Write Segmentation 13s
- Update Segmentation 14s
- Update Skull-Stripping 32s
- Update probability maps 7s
- 67s
- Global intensity correction: 13s
- SANLM denoising after intensity normalization (medium): 18s
- Fast Optimized Shooting registration 26s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 2s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.18) 10s
- Estimate local tissue thresholds (WM) 14s
- Estimate local tissue thresholds (GM) 20s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 34s
- 85s
- ROI segmentation (partitioning):
- Atlas -> subject space 5s
- Major structures 2s
- Ventricle detection 7s
- Blood vessel detection 6s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 14s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 4s
- 42s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 24s
- 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
- 8s
- 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 | 0.0810 0.0000 0.0810 | 32.0000
- 2 | 2.50 | 0.0787 0.0011 0.0798 | 29.4886
- 3 | 2.50 | 0.0780 0.0016 0.0797 | 26.9772
- 4 | 2.50 | 0.0777 0.0018 0.0795 | 24.6107
- 5 | 2.50 | 0.0774 0.0020 0.0794 | 22.6548
- 6 | 2.50 | 0.0772 0.0021 0.0792 | 20.6989
- 7 | 2.50 | 0.0769 0.0021 0.0791 | 18.9688
- 8 | 2.50 | 0.0767 0.0022 0.0789 | 17.4455
- 9 | 2.50 | 0.0764 0.0023 0.0787 | 15.9223
- 10 | 2.50 | 0.0761 0.0024 0.0785 | 14.6627
- 11 | 2.50 | 0.0758 0.0024 0.0783 | 13.4764
- 12 | 2.50 | 0.0756 0.0025 0.0781 | 12.3015
- 13 | 2.50 | 0.0753 0.0026 0.0779 | 11.3776
- 14 | 2.50 | 0.0750 0.0026 0.0776 | 10.4537
- 15 | 2.25 | 0.0730 0.0027 0.0757 | 9.5920
- 16 | 2.25 | 0.0703 0.0040 0.0743 | 8.8725
- 29 | 2.00 | 0.0711 0.0018 0.0729 | 3.3283
- 30 | 2.00 | 0.0653 0.0041 0.0694 | 3.1221
- 31 | 2.00 | 0.0634 0.0050 0.0683 | 2.9160
- 43 | 1.75 | 0.0621 0.0028 0.0649 | 1.5785
- 44 | 1.75 | 0.0581 0.0049 0.0630 | 1.5194
- 45 | 1.75 | 0.0568 0.0056 0.0624 | 1.4626
- 57 | 1.50 | 0.0550 0.0041 0.0591 | 1.0900
- 58 | 1.50 | 0.0522 0.0059 0.0581 | 1.0730
- Shooting registration with 2.50:-0.25:1.50 mm takes: 118s
- Prepare output 8s
- 125s
- Jacobian determinant (RMS): 0.010 0.035 0.052 0.074 0.095 | 0.099078
- Template Matching: 0.081 0.211 0.190 0.170 0.157 | 0.156732
- Write result maps: 32s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 29s
- CSF distance: 10s
- PBT2x thickness: 30s
- 73s
- Create initial surface 60s
- Topology correction: 58s
- Surface refinement: 47s
- Reduction of surface collisions with optimization: 45s
- Spherical mapping with areal smoothing 66s
- Spherical registration 216s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 20s
- CSF distance: 10s
- PBT2x thickness: 29s
- 63s
- Create initial surface 53s
- Topology correction: 56s
- Surface refinement: 50s
- Reduction of surface collisions with optimization: 42s
- Spherical mapping with areal smoothing 59s
- Spherical registration 209s
- Final surface processing results:
- Average thickness (FS): 2.5444 0.6107 mm
- Surface intensity / position RMSE: 0.0642 / 0.0626
- Euler number / defect number / defect size: 12.0 / 5.5 / 0.49%
- Display thickness: /var/lib/condor/execute/dir_2875144/ds/SWU_1/sub-0027205/ses-3/surf/lh.thickness.sub-0027205_ses-3_run-2_T1w
- Display thickness: /var/lib/condor/execute/dir_2875144/ds/SWU_1/sub-0027205/ses-3/surf/rh.thickness.sub-0027205_ses-3_run-2_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2875144/ds/SWU_1/sub-0027205/ses-3/sub-0027205_ses-3_run-2_T1w.nii
- Surface ROI estimation: 6s
- Surface and thickness estimation takes: 1166s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 25s
- ROI estimation of 'lpba40' atlas 7s
- ROI estimation of 'hammers' atlas 18s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 6s
- ROI estimation of 'aal3' atlas 10s
- ROI estimation of 'mori' atlas 15s
- ROI estimation of 'anatomy3' atlas 21s
- ROI estimation of 'julichbrain' atlas 29s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 22s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 48s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 75s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s
- Write results 8s
- 304s
- Quality check: 9s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2875144/ds/SWU_1/sub-0027205/ses-3/report/catreport_sub-0027205_ses-3_run-2_T1w.pdf
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- CAT preprocessing takes 36 minute(s) and 21 second(s).
- Image Quality Rating (IQR): 82.83% (B-)
- GM volume (GMV): 47.37% (617.37 / 1303.28 ml)
- GM thickness (GMT): 2.54 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2875144/ds/SWU_1/sub-0027205/ses-3/mri
- Reports are saved in /var/lib/condor/execute/dir_2875144/ds/SWU_1/sub-0027205/ses-3/report
- Labels are saved in /var/lib/condor/execute/dir_2875144/ds/SWU_1/sub-0027205/ses-3/label
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