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- CAT12.8.1 r2040: 1/1: ./sub-0025604/ses-1/sub-0025604_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 30s
- APP: Rough bias correction:
- Initialize 4s
- Estimate background 4s
- Initial correction 4s
- Refine background 2s
- Final correction 3s
- Final scaling 3s
- 24s
- Correct center-of-mass 2s
- Affine registration 5s
- SPM preprocessing 1 (estimate 1 - TPM registration): 44s
- SPM preprocessing 1 (estimate 2): 36s
- SPM preprocessing 2 (write):
- Write Segmentation 12s
- Update Segmentation 14s
- Update Skull-Stripping 28s
- Update probability maps 6s
- 60s
- Global intensity correction: 11s
- SANLM denoising after intensity normalization (medium): 19s
- Fast Optimized Shooting registration 23s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 10s
- Estimate local tissue thresholds (WM) 13s
- Estimate local tissue thresholds (GM) 20s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 27s
- 77s
- ROI segmentation (partitioning):
- Atlas -> subject space 5s
- Major structures 2s
- Ventricle detection 8s
- Blood vessel detection 7s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.12) 13s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 3s
- 42s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 26s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.04]
- 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 | 0.0859 0.0000 0.0859 | 32.0000
- 2 | 2.50 | 0.0832 0.0012 0.0844 | 29.4886
- 3 | 2.50 | 0.0824 0.0018 0.0842 | 26.9772
- 4 | 2.50 | 0.0820 0.0020 0.0841 | 24.6107
- 5 | 2.50 | 0.0817 0.0022 0.0839 | 22.6548
- 6 | 2.50 | 0.0815 0.0023 0.0837 | 20.6989
- 7 | 2.50 | 0.0812 0.0024 0.0836 | 18.9688
- 8 | 2.50 | 0.0809 0.0025 0.0834 | 17.4455
- 9 | 2.50 | 0.0806 0.0026 0.0832 | 15.9223
- 10 | 2.50 | 0.0803 0.0027 0.0830 | 14.6627
- 11 | 2.50 | 0.0800 0.0028 0.0827 | 13.4764
- 12 | 2.50 | 0.0797 0.0028 0.0825 | 12.3015
- 13 | 2.50 | 0.0793 0.0029 0.0823 | 11.3776
- 14 | 2.50 | 0.0790 0.0030 0.0820 | 10.4537
- 15 | 2.25 | 0.0786 0.0031 0.0817 | 9.5920
- 16 | 2.25 | 0.0756 0.0045 0.0802 | 8.8725
- 17 | 2.25 | 0.0744 0.0051 0.0795 | 8.1530
- 29 | 2.00 | 0.0763 0.0023 0.0786 | 3.3283
- 30 | 2.00 | 0.0702 0.0049 0.0750 | 3.1221
- 31 | 2.00 | 0.0680 0.0059 0.0739 | 2.9160
- 43 | 1.75 | 0.0669 0.0034 0.0703 | 1.5785
- 44 | 1.75 | 0.0622 0.0059 0.0681 | 1.5194
- 45 | 1.75 | 0.0607 0.0067 0.0674 | 1.4626
- 57 | 1.50 | 0.0591 0.0049 0.0640 | 1.0900
- 58 | 1.50 | 0.0558 0.0071 0.0629 | 1.0730
- 59 | 1.50 | 0.0547 0.0078 0.0625 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 115s
- Prepare output 8s
- 122s
- Jacobian determinant (RMS): 0.011 0.039 0.060 0.085 0.111 | 0.118557
- Template Matching: 0.086 0.223 0.204 0.182 0.164 | 0.164085
- Write result maps: 25s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 32s
- CSF distance: 11s
- PBT2x thickness: 34s
- 81s
- Create initial surface 54s
- Topology correction: 64s
- Surface refinement: 60s
- Reduction of surface collisions with optimization: 44s
- Spherical mapping with areal smoothing 57s
- Spherical registration 186s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 22s
- CSF distance: 10s
- PBT2x thickness: 31s
- 68s
- Create initial surface 50s
- Topology correction: 60s
- Surface refinement: 61s
- Reduction of surface collisions with optimization: 41s
- Spherical mapping with areal smoothing 53s
- Spherical registration 190s
- Final surface processing results:
- Average thickness (FS): 2.5807 0.6337 mm
- Surface intensity / position RMSE: 0.0598 / 0.0592
- Euler number / defect number / defect size: 18.0 / 8.0 / 0.68%
- Display thickness: /var/lib/condor/execute/dir_2623797/ds/JHNU/sub-0025604/ses-1/surf/lh.thickness.sub-0025604_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2623797/ds/JHNU/sub-0025604/ses-1/surf/rh.thickness.sub-0025604_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2623797/ds/JHNU/sub-0025604/ses-1/sub-0025604_ses-1_run-1_T1w.nii
- Surface ROI estimation: 6s
- Surface and thickness estimation takes: 1134s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 6s
- ROI estimation of 'neuromorphometrics' atlas 22s
- ROI estimation of 'lpba40' atlas 6s
- ROI estimation of 'hammers' atlas 15s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 6s
- ROI estimation of 'aal3' atlas 9s
- ROI estimation of 'mori' atlas 14s
- ROI estimation of 'anatomy3' atlas 20s
- ROI estimation of 'julichbrain' atlas 26s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 47s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 72s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s
- Write results 7s
- 283s
- Quality check: 9s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2623797/ds/JHNU/sub-0025604/ses-1/report/catreport_sub-0025604_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 34 minute(s) and 0 second(s).
- Image Quality Rating (IQR): 84.13% (B)
- GM volume (GMV): 45.88% (694.14 / 1513.10 ml)
- GM thickness (GMT): 2.58 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2623797/ds/JHNU/sub-0025604/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_2623797/ds/JHNU/sub-0025604/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_2623797/ds/JHNU/sub-0025604/ses-1/label
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