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- CAT12.8.1 r1980: 1/1: ./sub-season216_ses-2_acq-MPrageHiRes_T1w.n
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- SANLM denoising (medium): 56s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 10s
- Initial correction 12s
- Refine background 4s
- Final correction 10s
- Final scaling 9s
- 62s
- Correct center-of-mass 8s
- Affine registration 19s
- SPM preprocessing 1 (estimate 1 - TPM registration): 100s
- SPM preprocessing 1 (estimate 2): 71s
- SPM preprocessing 2 (write):
- Write Segmentation 20s
- Update Segmentation 27s
- Update Skull-Stripping 55s
- Update probability maps 11s
- 112s
- Global intensity correction: 20s
- SANLM denoising after intensity normalization (medium): 31s
- Fast Optimized Shooting registration 37s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 6s
- Prepare partitions 7s
- Prepare segments (LASmod = 1.00) 21s
- Estimate local tissue thresholds (WM) 23s
- Estimate local tissue thresholds (GM) 32s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 51s
- 144s
- ROI segmentation (partitioning):
- Atlas -> subject space 10s
- Major structures 5s
- Ventricle detection 20s
- Blood vessel detection 14s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.05) 41s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 5s
- Final corrections 6s
- 103s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 46s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 6s
- Level 1 cleanup (brain masking) 4s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 4s
- 16s
- 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 | 0.0833 0.0000 0.0833 | 32.0000
- 2 | 2.50 | 0.0807 0.0012 0.0819 | 29.4886
- 3 | 2.50 | 0.0799 0.0018 0.0817 | 26.9772
- 4 | 2.50 | 0.0795 0.0020 0.0816 | 24.6107
- 5 | 2.50 | 0.0792 0.0022 0.0814 | 22.6548
- 6 | 2.50 | 0.0789 0.0023 0.0812 | 20.6989
- 7 | 2.50 | 0.0786 0.0024 0.0810 | 18.9688
- 8 | 2.50 | 0.0783 0.0025 0.0808 | 17.4455
- 9 | 2.50 | 0.0780 0.0026 0.0806 | 15.9223
- 10 | 2.50 | 0.0777 0.0027 0.0804 | 14.6627
- 11 | 2.50 | 0.0773 0.0028 0.0802 | 13.4764
- 12 | 2.50 | 0.0770 0.0029 0.0799 | 12.3015
- 13 | 2.50 | 0.0766 0.0030 0.0796 | 11.3776
- 14 | 2.50 | 0.0763 0.0031 0.0794 | 10.4537
- 15 | 2.25 | 0.0751 0.0032 0.0783 | 9.5920
- 16 | 2.25 | 0.0719 0.0047 0.0766 | 8.8725
- 29 | 2.00 | 0.0723 0.0021 0.0745 | 3.3283
- 30 | 2.00 | 0.0657 0.0048 0.0705 | 3.1221
- 31 | 2.00 | 0.0635 0.0059 0.0693 | 2.9160
- 43 | 1.75 | 0.0619 0.0034 0.0653 | 1.5785
- 44 | 1.75 | 0.0577 0.0056 0.0633 | 1.5194
- 45 | 1.75 | 0.0563 0.0064 0.0627 | 1.4626
- 57 | 1.50 | 0.0543 0.0047 0.0590 | 1.0900
- 58 | 1.50 | 0.0515 0.0065 0.0580 | 1.0730
- 59 | 1.50 | 0.0506 0.0071 0.0577 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 171s
- Prepare output 12s
- 183s
- Jacobian determinant (RMS): 0.012 0.044 0.067 0.094 0.119 | 0.127053
- Template Matching: 0.083 0.216 0.190 0.169 0.152 | 0.151657
- Write result maps: 31s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 31s
- CSF distance: 14s
- PBT2x thickness: 39s
- 90s
- Create initial surface 74s
- Topology correction: 70s
- Surface refinement: 67s
- Reduction of surface collisions with optimization: 55s
- Spherical mapping with areal smoothing 74s
- Spherical registration 293s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 37s
- CSF distance: 13s
- PBT2x thickness: 39s
- 95s
- Create initial surface 74s
- Topology correction: 68s
- Surface refinement: 69s
- Reduction of surface collisions with optimization: 54s
- Spherical mapping with areal smoothing 68s
- Spherical registration 265s
- Final surface processing results:
- Average thickness (FS): 2.6493 0.6298 mm
- Surface intensity / position RMSE: 0.0599 / 0.0597
- Euler number / defect number / defect size: 6.0 / 7.0 / 0.04%
- Display thickness: /var/lib/condor/execute/dir_9449/ds/sub-season216/surf/lh.thickness.sub-season216_ses-2_acq-MPrageHiRes_T1w
- Display thickness: /var/lib/condor/execute/dir_9449/ds/sub-season216/surf/rh.thickness.sub-season216_ses-2_acq-MPrageHiRes_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_9449/ds/sub-season216/sub-season216_ses-2_acq-MPrageHiRes_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1510s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 35s
- ROI estimation of 'lpba40' atlas 10s
- ROI estimation of 'hammers' atlas 25s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 9s
- ROI estimation of 'aal3' atlas 14s
- ROI estimation of 'mori' atlas 21s
- ROI estimation of 'anatomy3' atlas 29s
- ROI estimation of 'julichbrain' atlas 39s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 16s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 28s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 63s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 93s
- Write results 93s
- 393s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_9449/ds/sub-season216/report/catreport_sub-season216_ses-2_acq-MPrageHiRes_T1w.pdf
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- CAT preprocessing takes 51 minute(s) and 22 second(s).
- Image Quality Rating (IQR): 87.33% (B+)
- GM volume (GMV): 45.55% (649.12 / 1424.94 ml)
- GM thickness (GMT): 2.65 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_9449/ds/sub-season216/mri
- Reports are saved in /var/lib/condor/execute/dir_9449/ds/sub-season216/report
- Labels are saved in /var/lib/condor/execute/dir_9449/ds/sub-season216/label
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