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- CAT12.8.1 r1980: 1/1: ./dir_24497/ds/sub-0581/sub-0581_ses-01_T1w.n
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- SANLM denoising (medium): 144s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 8s
- Initial correction 14s
- Refine background 4s
- Final correction 8s
- Final scaling 6s
- 58s
- Correct center-of-mass 6s
- Affine registration 12s
- SPM preprocessing 1 (estimate 1 - TPM registration): 9s
- Use initial fine affine registration. 73s
- SPM preprocessing 1 (estimate 2): 61s
- SPM preprocessing 2 (write):
- Write Segmentation 21s
- Update Segmentation 21s
- Update Skull-Stripping 52s
- Update probability maps 12s
- 106s
- Global intensity correction: 22s
- SANLM denoising after intensity normalization (medium): 18s
- Fast Optimized Shooting registration 35s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 4s
- Prepare segments (LASmod = 1.21) 15s
- Estimate local tissue thresholds (WM) 22s
- Estimate local tissue thresholds (GM) 31s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 38s
- 119s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 13s
- Blood vessel detection 10s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.04) 25s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 6s
- 71s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 34s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 3s
- 11s
- 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 | 0.0883 0.0000 0.0883 | 32.0000
- 2 | 2.50 | 0.0845 0.0014 0.0860 | 29.4886
- 3 | 2.50 | 0.0835 0.0022 0.0857 | 26.9772
- 4 | 2.50 | 0.0830 0.0024 0.0854 | 24.6107
- 5 | 2.50 | 0.0826 0.0026 0.0852 | 22.6548
- 6 | 2.50 | 0.0823 0.0027 0.0850 | 20.6989
- 7 | 2.50 | 0.0820 0.0028 0.0847 | 18.9688
- 8 | 2.50 | 0.0816 0.0029 0.0845 | 17.4455
- 9 | 2.50 | 0.0813 0.0029 0.0842 | 15.9223
- 10 | 2.50 | 0.0809 0.0030 0.0839 | 14.6627
- 11 | 2.50 | 0.0806 0.0031 0.0836 | 13.4764
- 12 | 2.50 | 0.0802 0.0031 0.0833 | 12.3015
- 13 | 2.50 | 0.0798 0.0032 0.0830 | 11.3776
- 14 | 2.50 | 0.0795 0.0032 0.0827 | 10.4537
- 15 | 2.25 | 0.0797 0.0033 0.0830 | 9.5920
- 16 | 2.25 | 0.0764 0.0048 0.0813 | 8.8725
- 17 | 2.25 | 0.0751 0.0054 0.0805 | 8.1530
- 18 | 2.25 | 0.0743 0.0056 0.0799 | 7.5234
- 29 | 2.00 | 0.0769 0.0027 0.0796 | 3.3283
- 30 | 2.00 | 0.0713 0.0051 0.0765 | 3.1221
- 31 | 2.00 | 0.0694 0.0061 0.0755 | 2.9160
- 43 | 1.75 | 0.0688 0.0035 0.0722 | 1.5785
- 44 | 1.75 | 0.0640 0.0060 0.0700 | 1.5194
- 45 | 1.75 | 0.0624 0.0068 0.0692 | 1.4626
- 57 | 1.50 | 0.0611 0.0050 0.0661 | 1.0900
- 58 | 1.50 | 0.0577 0.0072 0.0649 | 1.0730
- 59 | 1.50 | 0.0566 0.0079 0.0644 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 156s
- Prepare output 11s
- 167s
- Jacobian determinant (RMS): 0.011 0.038 0.060 0.085 0.110 | 0.115959
- Template Matching: 0.088 0.223 0.208 0.187 0.170 | 0.169666
- Write result maps: 31s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 28s
- CSF distance: 14s
- PBT2x thickness: 38s
- 86s
- Create initial surface 71s
- Topology correction: 75s
- Surface refinement: 69s
- Reduction of surface collisions with optimization: 55s
- Spherical mapping with areal smoothing 68s
- Spherical registration 295s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 31s
- CSF distance: 13s
- PBT2x thickness: 39s
- 89s
- Create initial surface 71s
- Topology correction: 72s
- Surface refinement: 86s
- Reduction of surface collisions with optimization: 57s
- Spherical mapping with areal smoothing 68s
- Spherical registration 296s
- Final surface processing results:
- Average thickness (FS): 2.5140 0.6581 mm
- Surface intensity / position RMSE: 0.0814 / 0.0947
- Euler number / defect number / defect size: 82.0 / 38.5 / 2.80%
- Display thickness: /var/lib/condor/execute/dir_24497/ds/sub-0581/surf/lh.thickness.sub-0581_ses-01_T1w
- Display thickness: /var/lib/condor/execute/dir_24497/ds/sub-0581/surf/rh.thickness.sub-0581_ses-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_24497/ds/sub-0581/sub-0581_ses-01_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1549s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 11s
- ROI estimation of 'neuromorphometrics' atlas 39s
- ROI estimation of 'lpba40' atlas 11s
- ROI estimation of 'hammers' atlas 28s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 10s
- ROI estimation of 'aal3' atlas 17s
- ROI estimation of 'mori' atlas 25s
- ROI estimation of 'anatomy3' atlas 35s
- ROI estimation of 'julichbrain' atlas 47s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 18s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 33s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 76s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 110s
- Write results 111s
- 463s
- Quality check: 5s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_24497/ds/sub-0581/report/catreport_sub-0581_ses-01_T1w.pdf
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- CAT preprocessing takes 51 minute(s) and 29 second(s).
- Image Quality Rating (IQR): 81.34% (B-)
- GM volume (GMV): 50.22% (631.47 / 1257.54 ml)
- GM thickness (GMT): 2.51 0.66 mm
- Segmentations are saved in /var/lib/condor/execute/dir_24497/ds/sub-0581/mri
- Reports are saved in /var/lib/condor/execute/dir_24497/ds/sub-0581/report
- Labels are saved in /var/lib/condor/execute/dir_24497/ds/sub-0581/label
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