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- CAT12.8.1 r1980: 1/1: ./ds/sub-f3300jh/sub-f3300jh_ses-wave1bas_T1w.n
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- SANLM denoising (medium): 183s
- APP: Rough bias correction:
- Initialize 16s
- Estimate background 16s
- Initial correction 15s
- Refine background 8s
- Final correction 13s
- Final scaling 15s
- 98s
- Correct center-of-mass 5s
- Affine registration 19s
- SPM preprocessing 1 (estimate 1 - TPM registration): 175s
- SPM preprocessing 1 (estimate 2): 88s
- SPM preprocessing 2 (write):
- Write Segmentation 40s
- Update Segmentation 47s
- Update Skull-Stripping 101s
- Update probability maps 20s
- 208s
- Global intensity correction: 40s
- SANLM denoising after intensity normalization (medium): 37s
- Fast Optimized Shooting registration 62s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 12s
- Prepare partitions 6s
- Prepare segments (LASmod = 1.00) 38s
- Estimate local tissue thresholds (WM) 40s
- Estimate local tissue thresholds (GM) 57s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 62s
- 222s
- ROI segmentation (partitioning):
- Atlas -> subject space 21s
- Major structures 9s
- Ventricle detection 37s
- Blood vessel detection 25s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.08) 65s
- Manual stroke lesion detection 0s
- Closing of deep structures 5s
- Side alignment 11s
- Final corrections 11s
- 183s
- Blood vessel correction (BVCstr=0.50): 4s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 88s
- AMAP peaks: [CSF,GM,WM] = [0.360.07,0.680.07,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 11s
- Level 1 cleanup (brain masking) 6s
- Level 2 cleanup (CSF correction) 4s
- Level 3 cleanup (CSF/WM PVE) 7s
- 29s
- 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 | 0.0911 0.0000 0.0911 | 32.0000
- 2 | 2.50 | 0.0860 0.0018 0.0878 | 29.4886
- 3 | 2.50 | 0.0844 0.0029 0.0873 | 26.9772
- 4 | 2.50 | 0.0837 0.0033 0.0869 | 24.6107
- 5 | 2.50 | 0.0831 0.0035 0.0866 | 22.6548
- 6 | 2.50 | 0.0826 0.0037 0.0863 | 20.6989
- 7 | 2.50 | 0.0821 0.0038 0.0859 | 18.9688
- 8 | 2.50 | 0.0815 0.0040 0.0855 | 17.4455
- 9 | 2.50 | 0.0810 0.0041 0.0851 | 15.9223
- 10 | 2.50 | 0.0805 0.0043 0.0848 | 14.6627
- 11 | 2.50 | 0.0800 0.0044 0.0844 | 13.4764
- 12 | 2.50 | 0.0794 0.0045 0.0839 | 12.3015
- 13 | 2.50 | 0.0789 0.0046 0.0835 | 11.3776
- 14 | 2.50 | 0.0784 0.0047 0.0831 | 10.4537
- 15 | 2.25 | 0.0787 0.0049 0.0835 | 9.5920
- 16 | 2.25 | 0.0746 0.0069 0.0815 | 8.8725
- 17 | 2.25 | 0.0730 0.0076 0.0805 | 8.1530
- 29 | 2.00 | 0.0742 0.0035 0.0776 | 3.3283
- 30 | 2.00 | 0.0679 0.0061 0.0740 | 3.1221
- 31 | 2.00 | 0.0657 0.0071 0.0728 | 2.9160
- 43 | 1.75 | 0.0648 0.0041 0.0689 | 1.5785
- 44 | 1.75 | 0.0603 0.0064 0.0667 | 1.5194
- 45 | 1.75 | 0.0587 0.0072 0.0660 | 1.4626
- 57 | 1.50 | 0.0571 0.0054 0.0625 | 1.0900
- 58 | 1.50 | 0.0539 0.0074 0.0613 | 1.0730
- 59 | 1.50 | 0.0528 0.0081 0.0609 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 267s
- Prepare output 19s
- 286s
- Jacobian determinant (RMS): 0.015 0.056 0.082 0.108 0.131 | 0.137608
- Template Matching: 0.091 0.219 0.197 0.176 0.158 | 0.158321
- Write result maps: 59s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 56s
- CSF distance: 24s
- PBT2x thickness: 66s
- 155s
- Create initial surface 116s
- Topology correction: 133s
- Surface refinement: 112s
- Reduction of surface collisions with optimization: 110s
- Spherical mapping with areal smoothing 120s
- Spherical registration 302s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 103s
- CSF distance: 23s
- PBT2x thickness: 64s
- 199s
- Create initial surface 111s
- Topology correction: 131s
- Surface refinement: 138s
- Reduction of surface collisions with optimization: 101s
- Spherical mapping with areal smoothing 116s
- Spherical registration 289s
- Final surface processing results:
- Average thickness (FS): 2.5040 0.5645 mm
- Surface intensity / position RMSE: 0.0644 / 0.0583
- Euler number / defect number / defect size: 8.0 / 6.0 / 0.22%
- Display thickness: /var/lib/condor/execute/dir_17538/ds/sub-f3300jh/surf/lh.thickness.sub-f3300jh_ses-wave1bas_T1w
- Display thickness: /var/lib/condor/execute/dir_17538/ds/sub-f3300jh/surf/rh.thickness.sub-f3300jh_ses-wave1bas_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_17538/ds/sub-f3300jh/sub-f3300jh_ses-wave1bas_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 2286s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 27s
- ROI estimation of 'neuromorphometrics' atlas 101s
- ROI estimation of 'lpba40' atlas 29s
- ROI estimation of 'hammers' atlas 72s
- ROI estimation of 'thalamus' atlas 5s
- ROI estimation of 'ibsr' atlas 26s
- ROI estimation of 'aal3' atlas 43s
- ROI estimation of 'mori' atlas 62s
- ROI estimation of 'anatomy3' atlas 91s
- ROI estimation of 'julichbrain' atlas 120s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 45s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 59s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 201s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 284s
- Write results 286s
- 1168s
- Quality check: 11s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_17538/ds/sub-f3300jh/report/catreport_sub-f3300jh_ses-wave1bas_T1w.pdf
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- CAT preprocessing takes 90 minute(s) and 51 second(s).
- Image Quality Rating (IQR): 86.74% (B+)
- GM volume (GMV): 48.04% (699.10 / 1455.32 ml)
- GM thickness (GMT): 2.50 0.56 mm
- Segmentations are saved in /var/lib/condor/execute/dir_17538/ds/sub-f3300jh/mri
- Reports are saved in /var/lib/condor/execute/dir_17538/ds/sub-f3300jh/report
- Labels are saved in /var/lib/condor/execute/dir_17538/ds/sub-f3300jh/label
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