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- CAT12.8.1 r2040: 1/1: ./sub-0027035/ses-2/sub-0027035_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 37s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 4s
- Initial correction 4s
- Refine background 3s
- Final correction 4s
- Final scaling 4s
- 30s
- Correct center-of-mass 3s
- Affine registration 6s
- SPM preprocessing 1 (estimate 1 - TPM registration): 58s
- SPM preprocessing 1 (estimate 2): 56s
- SPM preprocessing 2 (write):
- Write Segmentation 14s
- Update Segmentation 15s
- Update Skull-Stripping 34s
- Update probability maps 8s
- 72s
- Global intensity correction: 13s
- SANLM denoising after intensity normalization (medium): 19s
- Fast Optimized Shooting registration 27s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 2s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.06) 10s
- Estimate local tissue thresholds (WM) 14s
- Estimate local tissue thresholds (GM) 21s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 37s
- 90s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 2s
- Ventricle detection 8s
- Blood vessel detection 6s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.19) 14s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 4s
- 44s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 25s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 3s
- Level 1 cleanup (brain masking) 2s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 8s
- 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 | 0.0873 0.0000 0.0873 | 32.0000
- 2 | 2.50 | 0.0844 0.0013 0.0856 | 29.4886
- 3 | 2.50 | 0.0835 0.0020 0.0854 | 26.9772
- 4 | 2.50 | 0.0831 0.0022 0.0853 | 24.6107
- 5 | 2.50 | 0.0827 0.0024 0.0851 | 22.6548
- 6 | 2.50 | 0.0824 0.0025 0.0849 | 20.6989
- 7 | 2.50 | 0.0821 0.0026 0.0847 | 18.9688
- 8 | 2.50 | 0.0817 0.0027 0.0845 | 17.4455
- 9 | 2.50 | 0.0814 0.0028 0.0842 | 15.9223
- 10 | 2.50 | 0.0810 0.0030 0.0840 | 14.6627
- 11 | 2.50 | 0.0807 0.0031 0.0838 | 13.4764
- 12 | 2.50 | 0.0803 0.0032 0.0835 | 12.3015
- 13 | 2.50 | 0.0799 0.0033 0.0832 | 11.3776
- 14 | 2.50 | 0.0795 0.0034 0.0829 | 10.4537
- 15 | 2.25 | 0.0790 0.0035 0.0825 | 9.5920
- 16 | 2.25 | 0.0757 0.0052 0.0808 | 8.8725
- 17 | 2.25 | 0.0743 0.0058 0.0801 | 8.1530
- 29 | 2.00 | 0.0758 0.0026 0.0784 | 3.3283
- 30 | 2.00 | 0.0695 0.0053 0.0748 | 3.1221
- 31 | 2.00 | 0.0674 0.0063 0.0737 | 2.9160
- 43 | 1.75 | 0.0661 0.0036 0.0697 | 1.5785
- 44 | 1.75 | 0.0616 0.0060 0.0676 | 1.5194
- 45 | 1.75 | 0.0601 0.0068 0.0669 | 1.4626
- 57 | 1.50 | 0.0583 0.0050 0.0633 | 1.0900
- 58 | 1.50 | 0.0551 0.0070 0.0622 | 1.0730
- 59 | 1.50 | 0.0541 0.0077 0.0618 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 140s
- Prepare output 8s
- 148s
- Jacobian determinant (RMS): 0.013 0.048 0.074 0.103 0.128 | 0.135783
- Template Matching: 0.087 0.223 0.202 0.180 0.162 | 0.162299
- Write result maps: 31s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 31s
- CSF distance: 11s
- PBT2x thickness: 30s
- 76s
- Create initial surface 53s
- Topology correction: 65s
- Surface refinement: 48s
- Reduction of surface collisions with optimization: 42s
- Spherical mapping with areal smoothing 57s
- Spherical registration 207s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 21s
- CSF distance: 10s
- PBT2x thickness: 29s
- 64s
- Create initial surface 52s
- Topology correction: 66s
- Surface refinement: 52s
- Reduction of surface collisions with optimization: 41s
- Spherical mapping with areal smoothing 54s
- Spherical registration 202s
- Final surface processing results:
- Average thickness (FS): 2.4985 0.5934 mm
- Surface intensity / position RMSE: 0.0573 / 0.0540
- Euler number / defect number / defect size: 6.0 / 9.0 / 0.04%
- Display thickness: /var/lib/condor/execute/dir_3516173/ds/MRN/sub-0027035/ses-2/surf/lh.thickness.sub-0027035_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3516173/ds/MRN/sub-0027035/ses-2/surf/rh.thickness.sub-0027035_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3516173/ds/MRN/sub-0027035/ses-2/sub-0027035_ses-2_run-1_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1154s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 16s
- ROI estimation of 'neuromorphometrics' atlas 61s
- ROI estimation of 'lpba40' atlas 17s
- ROI estimation of 'hammers' atlas 43s
- ROI estimation of 'thalamus' atlas 4s
- ROI estimation of 'ibsr' atlas 19s
- ROI estimation of 'aal3' atlas 34s
- ROI estimation of 'mori' atlas 56s
- ROI estimation of 'anatomy3' atlas 84s
- ROI estimation of 'julichbrain' atlas 111s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 44s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 84s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 151s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 153s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 13s
- Write results 14s
- 890s
- Quality check: 10s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3516173/ds/MRN/sub-0027035/ses-2/report/catreport_sub-0027035_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 46 minute(s) and 47 second(s).
- Image Quality Rating (IQR): 85.65% (B)
- GM volume (GMV): 44.83% (624.88 / 1393.78 ml)
- GM thickness (GMT): 2.50 0.59 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3516173/ds/MRN/sub-0027035/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_3516173/ds/MRN/sub-0027035/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_3516173/ds/MRN/sub-0027035/ses-2/label
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