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- CAT12.8.1 r2040: 1/1: ./sub-0025985/ses-2/sub-0025985_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 37s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 5s
- Initial correction 4s
- Refine background 2s
- Final correction 4s
- Final scaling 3s
- 29s
- Correct center-of-mass 3s
- Affine registration 7s
- SPM preprocessing 1 (estimate 1 - TPM registration): 58s
- SPM preprocessing 1 (estimate 2): 66s
- SPM preprocessing 2 (write):
- Write Segmentation 13s
- Update Segmentation 15s
- Update Skull-Stripping 33s
- Update probability maps 7s
- 67s
- Global intensity correction: 14s
- SANLM denoising after intensity normalization (medium): 17s
- Fast Optimized Shooting registration 26s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 10s
- Estimate local tissue thresholds (WM) 14s
- Estimate local tissue thresholds (GM) 20s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 36s
- 87s
- ROI segmentation (partitioning):
- Atlas -> subject space 5s
- Major structures 2s
- Ventricle detection 9s
- Blood vessel detection 6s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.15) 16s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 4s
- 46s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 24s
- 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
- 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 | 0.0883 0.0000 0.0883 | 32.0000
- 2 | 2.50 | 0.0849 0.0014 0.0863 | 29.4886
- 3 | 2.50 | 0.0839 0.0022 0.0860 | 26.9772
- 4 | 2.50 | 0.0833 0.0025 0.0858 | 24.6107
- 5 | 2.50 | 0.0829 0.0027 0.0856 | 22.6548
- 6 | 2.50 | 0.0826 0.0028 0.0854 | 20.6989
- 7 | 2.50 | 0.0822 0.0029 0.0851 | 18.9688
- 8 | 2.50 | 0.0818 0.0031 0.0849 | 17.4455
- 9 | 2.50 | 0.0814 0.0032 0.0846 | 15.9223
- 10 | 2.50 | 0.0810 0.0033 0.0843 | 14.6627
- 11 | 2.50 | 0.0806 0.0034 0.0840 | 13.4764
- 12 | 2.50 | 0.0802 0.0035 0.0837 | 12.3015
- 13 | 2.50 | 0.0798 0.0036 0.0834 | 11.3776
- 14 | 2.50 | 0.0794 0.0037 0.0831 | 10.4537
- 15 | 2.25 | 0.0797 0.0038 0.0835 | 9.5920
- 16 | 2.25 | 0.0762 0.0055 0.0818 | 8.8725
- 17 | 2.25 | 0.0748 0.0062 0.0810 | 8.1530
- 29 | 2.00 | 0.0767 0.0028 0.0795 | 3.3283
- 30 | 2.00 | 0.0700 0.0056 0.0756 | 3.1221
- 31 | 2.00 | 0.0676 0.0067 0.0743 | 2.9160
- 43 | 1.75 | 0.0662 0.0039 0.0701 | 1.5785
- 44 | 1.75 | 0.0616 0.0063 0.0679 | 1.5194
- 45 | 1.75 | 0.0600 0.0071 0.0671 | 1.4626
- 57 | 1.50 | 0.0584 0.0052 0.0637 | 1.0900
- 58 | 1.50 | 0.0553 0.0073 0.0626 | 1.0730
- 59 | 1.50 | 0.0543 0.0079 0.0621 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 136s
- Prepare output 8s
- 144s
- Jacobian determinant (RMS): 0.012 0.045 0.068 0.094 0.125 | 0.124004
- Template Matching: 0.088 0.224 0.203 0.180 0.163 | 0.162802
- Write result maps: 26s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 21s
- CSF distance: 10s
- PBT2x thickness: 30s
- 65s
- Create initial surface 58s
- Topology correction: 58s
- Surface refinement: 69s
- Reduction of surface collisions with optimization: 42s
- Spherical mapping with areal smoothing 56s
- Spherical registration 255s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 20s
- CSF distance: 10s
- PBT2x thickness: 30s
- 64s
- Create initial surface 58s
- Topology correction: 58s
- Surface refinement: 53s
- Reduction of surface collisions with optimization: 44s
- Spherical mapping with areal smoothing 56s
- Spherical registration 233s
- Final surface processing results:
- Average thickness (FS): 2.3929 0.6276 mm
- Surface intensity / position RMSE: 0.0625 / 0.0656
- Euler number / defect number / defect size: 22.0 / 12.0 / 0.69%
- Display thickness: /var/lib/condor/execute/dir_4034311/ds/XHCUMS/sub-0025985/ses-2/surf/lh.thickness.sub-0025985_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_4034311/ds/XHCUMS/sub-0025985/ses-2/surf/rh.thickness.sub-0025985_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_4034311/ds/XHCUMS/sub-0025985/ses-2/sub-0025985_ses-2_run-1_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1238s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 25s
- ROI estimation of 'lpba40' atlas 7s
- ROI estimation of 'hammers' atlas 18s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 6s
- ROI estimation of 'aal3' atlas 11s
- ROI estimation of 'mori' atlas 16s
- ROI estimation of 'anatomy3' atlas 22s
- ROI estimation of 'julichbrain' atlas 30s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s
- 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 71s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s
- Write results 7s
- 301s
- Quality check: 9s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_4034311/ds/XHCUMS/sub-0025985/ses-2/report/catreport_sub-0025985_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 38 minute(s) and 2 second(s).
- Image Quality Rating (IQR): 82.30% (B-)
- GM volume (GMV): 45.85% (559.53 / 1220.48 ml)
- GM thickness (GMT): 2.39 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_4034311/ds/XHCUMS/sub-0025985/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_4034311/ds/XHCUMS/sub-0025985/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_4034311/ds/XHCUMS/sub-0025985/ses-2/label
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