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- CAT12.8.1 r1980: 1/1: ./sub-season111_ses-1_acq-MPrageHiRes_T1w.n
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- SANLM denoising (medium): 50s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 10s
- Initial correction 13s
- Refine background 4s
- Final correction 11s
- Final scaling 10s
- 63s
- Correct center-of-mass 6s
- Affine registration 19s
- SPM preprocessing 1 (estimate 1 - TPM registration): 104s
- SPM preprocessing 1 (estimate 2): 103s
- SPM preprocessing 2 (write):
- Write Segmentation 20s
- Update Segmentation 26s
- Update Skull-Stripping 56s
- Update probability maps 11s
- 113s
- Global intensity correction: 21s
- SANLM denoising after intensity normalization (medium): 36s
- Fast Optimized Shooting registration 36s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 7s
- Prepare partitions 6s
- Prepare segments (LASmod = 1.00) 24s
- Estimate local tissue thresholds (WM) 25s
- Estimate local tissue thresholds (GM) 35s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 40s
- 141s
- ROI segmentation (partitioning):
- Atlas -> subject space 11s
- Major structures 6s
- Ventricle detection 27s
- Blood vessel detection 16s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.10) 46s
- Manual stroke lesion detection 0s
- Closing of deep structures 3s
- Side alignment 6s
- Final corrections 5s
- 119s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 52s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 7s
- Level 1 cleanup (brain masking) 4s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 4s
- 18s
- 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 | 0.0831 0.0000 0.0831 | 32.0000
- 2 | 2.50 | 0.0803 0.0012 0.0815 | 29.4886
- 3 | 2.50 | 0.0795 0.0019 0.0813 | 26.9772
- 4 | 2.50 | 0.0790 0.0021 0.0812 | 24.6107
- 5 | 2.50 | 0.0787 0.0023 0.0810 | 22.6548
- 6 | 2.50 | 0.0784 0.0024 0.0808 | 20.6989
- 7 | 2.50 | 0.0781 0.0025 0.0806 | 18.9688
- 8 | 2.50 | 0.0777 0.0026 0.0804 | 17.4455
- 9 | 2.50 | 0.0774 0.0027 0.0802 | 15.9223
- 10 | 2.50 | 0.0771 0.0029 0.0799 | 14.6627
- 11 | 2.50 | 0.0767 0.0030 0.0797 | 13.4764
- 12 | 2.50 | 0.0764 0.0030 0.0794 | 12.3015
- 13 | 2.50 | 0.0760 0.0032 0.0791 | 11.3776
- 14 | 2.50 | 0.0756 0.0032 0.0789 | 10.4537
- 15 | 2.25 | 0.0741 0.0033 0.0775 | 9.5920
- 16 | 2.25 | 0.0713 0.0048 0.0761 | 8.8725
- 29 | 2.00 | 0.0719 0.0022 0.0740 | 3.3283
- 30 | 2.00 | 0.0656 0.0047 0.0703 | 3.1221
- 31 | 2.00 | 0.0635 0.0057 0.0692 | 2.9160
- 43 | 1.75 | 0.0621 0.0033 0.0654 | 1.5785
- 44 | 1.75 | 0.0580 0.0054 0.0634 | 1.5194
- 45 | 1.75 | 0.0566 0.0062 0.0628 | 1.4626
- 57 | 1.50 | 0.0548 0.0045 0.0593 | 1.0900
- 58 | 1.50 | 0.0519 0.0064 0.0583 | 1.0730
- 59 | 1.50 | 0.0509 0.0070 0.0579 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 158s
- Prepare output 13s
- 170s
- Jacobian determinant (RMS): 0.012 0.045 0.066 0.088 0.106 | 0.112344
- Template Matching: 0.083 0.214 0.190 0.170 0.153 | 0.152776
- Write result maps: 30s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 43s
- CSF distance: 18s
- PBT2x thickness: 49s
- 116s
- Create initial surface 96s
- Topology correction: 97s
- Surface refinement: 112s
- Reduction of surface collisions with optimization: 74s
- Spherical mapping with areal smoothing 83s
- Spherical registration 273s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 52s
- CSF distance: 16s
- PBT2x thickness: 46s
- 121s
- Create initial surface 90s
- Topology correction: 97s
- Surface refinement: 81s
- Reduction of surface collisions with optimization: 72s
- Spherical mapping with areal smoothing 75s
- Spherical registration 267s
- Final surface processing results:
- Average thickness (FS): 2.5522 0.6063 mm
- Surface intensity / position RMSE: 0.0616 / 0.0604
- Euler number / defect number / defect size: 14.0 / 14.0 / 0.22%
- Display thickness: /var/lib/condor/execute/dir_21555/ds/sub-season111/surf/lh.thickness.sub-season111_ses-1_acq-MPrageHiRes_T1w
- Display thickness: /var/lib/condor/execute/dir_21555/ds/sub-season111/surf/rh.thickness.sub-season111_ses-1_acq-MPrageHiRes_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_21555/ds/sub-season111/sub-season111_ses-1_acq-MPrageHiRes_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1754s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 10s
- ROI estimation of 'neuromorphometrics' atlas 36s
- 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 20s
- ROI estimation of 'anatomy3' atlas 29s
- ROI estimation of 'julichbrain' atlas 38s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 27s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 66s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 92s
- Write results 92s
- 392s
- Quality check: 7s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_21555/ds/sub-season111/report/catreport_sub-season111_ses-1_acq-MPrageHiRes_T1w.pdf
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- CAT preprocessing takes 55 minute(s) and 59 second(s).
- Image Quality Rating (IQR): 86.86% (B+)
- GM volume (GMV): 44.61% (745.76 / 1671.83 ml)
- GM thickness (GMT): 2.55 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_21555/ds/sub-season111/mri
- Reports are saved in /var/lib/condor/execute/dir_21555/ds/sub-season111/report
- Labels are saved in /var/lib/condor/execute/dir_21555/ds/sub-season111/label
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