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- CAT12.8.1 r1980: 1/1: ./sub-season104_ses-3_acq-MPrageHiRes_T1w.n
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- SANLM denoising (medium): 37s
- APP: Rough bias correction:
- Initialize 11s
- Estimate background 12s
- Initial correction 11s
- Refine background 6s
- Final correction 10s
- Final scaling 12s
- 73s
- Correct center-of-mass 5s
- Affine registration 17s
- SPM preprocessing 1 (estimate 1 - TPM registration): 8s
- Use initial fine affine registration. 141s
- SPM preprocessing 1 (estimate 2): 129s
- SPM preprocessing 2 (write):
- Write Segmentation 30s
- Update Segmentation 35s
- Update Skull-Stripping 75s
- Update probability maps 15s
- 155s
- Global intensity correction: 29s
- SANLM denoising after intensity normalization (medium): 13s
- Fast Optimized Shooting registration 53s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 9s
- Prepare partitions 4s
- Prepare segments (LASmod = 1.03) 30s
- Estimate local tissue thresholds (WM) 31s
- Estimate local tissue thresholds (GM) 42s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 35s
- 157s
- ROI segmentation (partitioning):
- Atlas -> subject space 16s
- Major structures 8s
- Ventricle detection 29s
- Blood vessel detection 18s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.02) 50s
- Manual stroke lesion detection 0s
- Closing of deep structures 3s
- Side alignment 7s
- Final corrections 8s
- 137s
- Blood vessel correction (BVCstr=0.50): 3s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 69s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 9s
- Level 1 cleanup (brain masking) 5s
- Level 2 cleanup (CSF correction) 3s
- Level 3 cleanup (CSF/WM PVE) 5s
- 21s
- 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 | 0.0800 0.0000 0.0800 | 32.0000
- 2 | 2.50 | 0.0778 0.0011 0.0789 | 29.4886
- 3 | 2.50 | 0.0771 0.0016 0.0787 | 26.9772
- 4 | 2.50 | 0.0768 0.0018 0.0786 | 24.6107
- 5 | 2.50 | 0.0765 0.0019 0.0785 | 22.6548
- 6 | 2.50 | 0.0763 0.0020 0.0783 | 20.6989
- 7 | 2.50 | 0.0760 0.0021 0.0782 | 18.9688
- 8 | 2.50 | 0.0758 0.0022 0.0780 | 17.4455
- 9 | 2.50 | 0.0755 0.0023 0.0778 | 15.9223
- 10 | 2.50 | 0.0752 0.0024 0.0776 | 14.6627
- 11 | 2.50 | 0.0750 0.0024 0.0774 | 13.4764
- 12 | 2.50 | 0.0747 0.0025 0.0772 | 12.3015
- 13 | 2.50 | 0.0744 0.0026 0.0770 | 11.3776
- 14 | 2.50 | 0.0741 0.0026 0.0768 | 10.4537
- 15 | 2.25 | 0.0731 0.0027 0.0758 | 9.5920
- 16 | 2.25 | 0.0703 0.0041 0.0744 | 8.8725
- 29 | 2.00 | 0.0718 0.0019 0.0736 | 3.3283
- 30 | 2.00 | 0.0659 0.0042 0.0702 | 3.1221
- 31 | 2.00 | 0.0639 0.0052 0.0691 | 2.9160
- 43 | 1.75 | 0.0630 0.0030 0.0660 | 1.5785
- 44 | 1.75 | 0.0588 0.0052 0.0640 | 1.5194
- 45 | 1.75 | 0.0574 0.0060 0.0633 | 1.4626
- 57 | 1.50 | 0.0559 0.0043 0.0603 | 1.0900
- 58 | 1.50 | 0.0528 0.0063 0.0592 | 1.0730
- 59 | 1.50 | 0.0518 0.0070 0.0588 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 247s
- Prepare output 15s
- 262s
- Jacobian determinant (RMS): 0.010 0.038 0.056 0.078 0.100 | 0.107037
- Template Matching: 0.080 0.211 0.192 0.172 0.155 | 0.155427
- Write result maps: 42s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 65s
- CSF distance: 20s
- PBT2x thickness: 62s
- 157s
- Create initial surface 111s
- Topology correction: 130s
- Surface refinement: 147s
- Reduction of surface collisions with optimization: 98s
- Spherical mapping with areal smoothing 109s
- Spherical registration 281s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 47s
- CSF distance: 18s
- PBT2x thickness: 57s
- 132s
- Create initial surface 102s
- Topology correction: 111s
- Surface refinement: 100s
- Reduction of surface collisions with optimization: 94s
- Spherical mapping with areal smoothing 97s
- Spherical registration 256s
- Final surface processing results:
- Average thickness (FS): 2.5893 0.6774 mm
- Surface intensity / position RMSE: 0.0763 / 0.0875
- Euler number / defect number / defect size: 46.0 / 20.0 / 1.16%
- Display thickness: /var/lib/condor/execute/dir_32760/ds/sub-season104/surf/lh.thickness.sub-season104_ses-3_acq-MPrageHiRes_T1w
- Display thickness: /var/lib/condor/execute/dir_32760/ds/sub-season104/surf/rh.thickness.sub-season104_ses-3_acq-MPrageHiRes_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_32760/ds/sub-season104/sub-season104_ses-3_acq-MPrageHiRes_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 2046s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 18s
- ROI estimation of 'neuromorphometrics' atlas 66s
- ROI estimation of 'lpba40' atlas 19s
- ROI estimation of 'hammers' atlas 47s
- ROI estimation of 'thalamus' atlas 4s
- ROI estimation of 'ibsr' atlas 17s
- ROI estimation of 'aal3' atlas 27s
- ROI estimation of 'mori' atlas 40s
- ROI estimation of 'anatomy3' atlas 59s
- ROI estimation of 'julichbrain' atlas 77s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 29s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 37s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 124s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 186s
- Write results 187s
- 751s
- Quality check: 7s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_32760/ds/sub-season104/report/catreport_sub-season104_ses-3_acq-MPrageHiRes_T1w.pdf
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- CAT preprocessing takes 71 minute(s) and 47 second(s).
- Image Quality Rating (IQR): 87.04% (B+)
- GM volume (GMV): 49.79% (715.80 / 1437.54 ml)
- GM thickness (GMT): 2.59 0.68 mm
- Segmentations are saved in /var/lib/condor/execute/dir_32760/ds/sub-season104/mri
- Reports are saved in /var/lib/condor/execute/dir_32760/ds/sub-season104/report
- Labels are saved in /var/lib/condor/execute/dir_32760/ds/sub-season104/label
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