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- CAT12.8.1 r2040: 1/1: ./sub-0025663/ses-1/sub-0025663_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 33s
- 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 6s
- SPM preprocessing 1 (estimate 1 - TPM registration): 46s
- SPM preprocessing 1 (estimate 2): 40s
- SPM preprocessing 2 (write):
- Write Segmentation 11s
- Update Segmentation 12s
- Update Skull-Stripping 27s
- Update probability maps 6s
- 56s
- Global intensity correction: 11s
- SANLM denoising after intensity normalization (medium): 16s
- Fast Optimized Shooting registration 21s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 2s
- Prepare partitions 1s
- Prepare segments (LASmod = 1.09) 9s
- Estimate local tissue thresholds (WM) 12s
- Estimate local tissue thresholds (GM) 17s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 30s
- 74s
- ROI segmentation (partitioning):
- Atlas -> subject space 5s
- Major structures 2s
- Ventricle detection 6s
- Blood vessel detection 6s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.10) 13s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 3s
- 39s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 23s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- 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
- 7s
- 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 | 0.0854 0.0000 0.0854 | 32.0000
- 2 | 2.50 | 0.0827 0.0012 0.0839 | 29.4886
- 3 | 2.50 | 0.0819 0.0018 0.0837 | 26.9772
- 4 | 2.50 | 0.0815 0.0020 0.0836 | 24.6107
- 5 | 2.50 | 0.0812 0.0022 0.0834 | 22.6548
- 6 | 2.50 | 0.0809 0.0023 0.0832 | 20.6989
- 7 | 2.50 | 0.0806 0.0024 0.0830 | 18.9688
- 8 | 2.50 | 0.0803 0.0025 0.0828 | 17.4455
- 9 | 2.50 | 0.0800 0.0025 0.0826 | 15.9223
- 10 | 2.50 | 0.0797 0.0027 0.0823 | 14.6627
- 11 | 2.50 | 0.0794 0.0027 0.0821 | 13.4764
- 12 | 2.50 | 0.0791 0.0028 0.0818 | 12.3015
- 13 | 2.50 | 0.0787 0.0029 0.0816 | 11.3776
- 14 | 2.50 | 0.0784 0.0030 0.0813 | 10.4537
- 15 | 2.25 | 0.0786 0.0030 0.0817 | 9.5920
- 16 | 2.25 | 0.0757 0.0044 0.0802 | 8.8725
- 17 | 2.25 | 0.0745 0.0050 0.0795 | 8.1530
- 29 | 2.00 | 0.0767 0.0023 0.0790 | 3.3283
- 30 | 2.00 | 0.0709 0.0047 0.0757 | 3.1221
- 31 | 2.00 | 0.0690 0.0057 0.0747 | 2.9160
- 43 | 1.75 | 0.0682 0.0033 0.0715 | 1.5785
- 44 | 1.75 | 0.0637 0.0057 0.0694 | 1.5194
- 45 | 1.75 | 0.0621 0.0066 0.0687 | 1.4626
- 57 | 1.50 | 0.0609 0.0048 0.0657 | 1.0900
- 58 | 1.50 | 0.0575 0.0071 0.0645 | 1.0730
- 59 | 1.50 | 0.0563 0.0078 0.0641 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 112s
- Prepare output 7s
- 118s
- Jacobian determinant (RMS): 0.011 0.039 0.059 0.084 0.110 | 0.116355
- Template Matching: 0.085 0.224 0.207 0.186 0.169 | 0.168854
- Write result maps: 23s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 24s
- CSF distance: 10s
- PBT2x thickness: 29s
- 68s
- Create initial surface 55s
- Topology correction: 65s
- Surface refinement: 54s
- Reduction of surface collisions with optimization: 41s
- Spherical mapping with areal smoothing 57s
- Spherical registration 189s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 22s
- CSF distance: 10s
- PBT2x thickness: 28s
- 64s
- Create initial surface 50s
- Topology correction: 66s
- Surface refinement: 51s
- Reduction of surface collisions with optimization: 45s
- Spherical mapping with areal smoothing 56s
- Spherical registration 198s
- Final surface processing results:
- Average thickness (FS): 2.4818 0.6442 mm
- Surface intensity / position RMSE: 0.0685 / 0.0718
- Euler number / defect number / defect size: 16.0 / 16.0 / 0.62%
- Display thickness: /var/lib/condor/execute/dir_2926811/ds/SWU_4/sub-0025663/ses-1/surf/lh.thickness.sub-0025663_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2926811/ds/SWU_4/sub-0025663/ses-1/surf/rh.thickness.sub-0025663_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2926811/ds/SWU_4/sub-0025663/ses-1/sub-0025663_ses-1_run-1_T1w.nii
- Surface ROI estimation: 6s
- Surface and thickness estimation takes: 1122s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 6s
- ROI estimation of 'neuromorphometrics' atlas 23s
- ROI estimation of 'lpba40' atlas 7s
- ROI estimation of 'hammers' atlas 16s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 6s
- ROI estimation of 'aal3' atlas 8s
- ROI estimation of 'mori' atlas 12s
- ROI estimation of 'anatomy3' atlas 18s
- ROI estimation of 'julichbrain' atlas 25s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 10s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 17s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 41s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 60s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 5s
- Write results 6s
- 256s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2926811/ds/SWU_4/sub-0025663/ses-1/report/catreport_sub-0025663_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 33 minute(s) and 29 second(s).
- Image Quality Rating (IQR): 80.10% (B-)
- GM volume (GMV): 47.18% (702.62 / 1489.09 ml)
- GM thickness (GMT): 2.48 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2926811/ds/SWU_4/sub-0025663/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_2926811/ds/SWU_4/sub-0025663/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_2926811/ds/SWU_4/sub-0025663/ses-1/label
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