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- CAT12.8.1 r1980: 1/1: ./dir_399/ds/sub-35/sub-35_acq-highres_T1w.n
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- SANLM denoising (medium): 57s
- APP: Rough bias correction:
- Initialize 10s
- Estimate background 9s
- Initial correction 8s
- Refine background 5s
- Final correction 7s
- Final scaling 7s
- 56s
- Correct center-of-mass 9s
- Affine registration 15s
- SPM preprocessing 1 (estimate 1 - TPM registration): 7s
- Use initial fine affine registration. 6s
- Use previous fine affine registration. 86s
- SPM preprocessing 1 (estimate 2): 93s
- SPM preprocessing 2 (write):
- Write Segmentation 26s
- Update Segmentation 27s
- Update Skull-Stripping 60s
- Update probability maps 13s
- 125s
- Global intensity correction: 25s
- SANLM denoising after intensity normalization (medium): 13s
- Fast Optimized Shooting registration 51s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 6s
- Prepare partitions 4s
- Prepare segments (LASmod = 1.04) 20s
- Estimate local tissue thresholds (WM) 23s
- Estimate local tissue thresholds (GM) 31s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 40s
- 128s
- ROI segmentation (partitioning):
- Atlas -> subject space 12s
- Major structures 5s
- Ventricle detection 17s
- Blood vessel detection 12s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.16) 31s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 5s
- Final corrections 7s
- 91s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 53s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- 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
- 15s
- 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 | 0.0879 0.0000 0.0879 | 32.0000
- 2 | 2.50 | 0.0851 0.0012 0.0863 | 29.4886
- 3 | 2.50 | 0.0842 0.0019 0.0861 | 26.9772
- 4 | 2.50 | 0.0838 0.0021 0.0860 | 24.6107
- 5 | 2.50 | 0.0835 0.0023 0.0858 | 22.6548
- 6 | 2.50 | 0.0832 0.0024 0.0856 | 20.6989
- 7 | 2.50 | 0.0830 0.0025 0.0854 | 18.9688
- 8 | 2.50 | 0.0826 0.0026 0.0852 | 17.4455
- 9 | 2.50 | 0.0823 0.0027 0.0850 | 15.9223
- 10 | 2.50 | 0.0820 0.0028 0.0848 | 14.6627
- 11 | 2.50 | 0.0817 0.0029 0.0845 | 13.4764
- 12 | 2.50 | 0.0814 0.0029 0.0843 | 12.3015
- 13 | 2.50 | 0.0810 0.0030 0.0840 | 11.3776
- 14 | 2.50 | 0.0807 0.0031 0.0838 | 10.4537
- 15 | 2.25 | 0.0800 0.0032 0.0832 | 9.5920
- 16 | 2.25 | 0.0768 0.0047 0.0815 | 8.8725
- 17 | 2.25 | 0.0756 0.0053 0.0808 | 8.1530
- 18 | 2.25 | 0.0748 0.0055 0.0803 | 7.5234
- 29 | 2.00 | 0.0769 0.0026 0.0795 | 3.3283
- 30 | 2.00 | 0.0711 0.0052 0.0762 | 3.1221
- 31 | 2.00 | 0.0691 0.0061 0.0752 | 2.9160
- 43 | 1.75 | 0.0681 0.0035 0.0716 | 1.5785
- 44 | 1.75 | 0.0633 0.0060 0.0694 | 1.5194
- 45 | 1.75 | 0.0617 0.0069 0.0687 | 1.4626
- 57 | 1.50 | 0.0600 0.0050 0.0650 | 1.0900
- 58 | 1.50 | 0.0566 0.0072 0.0639 | 1.0730
- 59 | 1.50 | 0.0555 0.0079 0.0634 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 274s
- Prepare output 14s
- 287s
- Jacobian determinant (RMS): 0.012 0.043 0.065 0.090 0.115 | 0.121315
- Template Matching: 0.088 0.224 0.207 0.185 0.167 | 0.166602
- Write result maps: 38s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 59s
- CSF distance: 21s
- PBT2x thickness: 62s
- 150s
- Create initial surface 109s
- Topology correction: 121s
- Surface refinement: 112s
- Reduction of surface collisions with optimization: 100s
- Spherical mapping with areal smoothing 109s
- Spherical registration 321s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 60s
- CSF distance: 24s
- PBT2x thickness: 62s
- 154s
- Create initial surface 108s
- Topology correction: 121s
- Surface refinement: 109s
- Reduction of surface collisions with optimization: 92s
- Spherical mapping with areal smoothing 107s
- Spherical registration 302s
- Final surface processing results:
- Average thickness (FS): 2.5961 0.6375 mm
- Surface intensity / position RMSE: 0.0585 / 0.0559
- Euler number / defect number / defect size: 6.0 / 10.5 / 0.13%
- Display thickness: /var/lib/condor/execute/dir_399/ds/sub-35/surf/lh.thickness.sub-35_acq-highres_T1w
- Display thickness: /var/lib/condor/execute/dir_399/ds/sub-35/surf/rh.thickness.sub-35_acq-highres_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_399/ds/sub-35/sub-35_acq-highres_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 2136s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 18s
- ROI estimation of 'neuromorphometrics' atlas 64s
- ROI estimation of 'lpba40' atlas 18s
- ROI estimation of 'hammers' atlas 45s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 16s
- ROI estimation of 'aal3' atlas 26s
- ROI estimation of 'mori' atlas 39s
- ROI estimation of 'anatomy3' atlas 58s
- ROI estimation of 'julichbrain' atlas 76s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 27s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 35s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 120s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 183s
- Write results 184s
- 732s
- Quality check: 7s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_399/ds/sub-35/report/catreport_sub-35_acq-highres_T1w.pdf
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- CAT preprocessing takes 69 minute(s) and 29 second(s).
- Image Quality Rating (IQR): 85.25% (B)
- GM volume (GMV): 45.15% (653.72 / 1447.83 ml)
- GM thickness (GMT): 2.60 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_399/ds/sub-35/mri
- Reports are saved in /var/lib/condor/execute/dir_399/ds/sub-35/report
- Labels are saved in /var/lib/condor/execute/dir_399/ds/sub-35/label
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