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- CAT12.8.1 r2040: 1/1: ./sub-0027417/ses-1/sub-0027417_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 111s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 9s
- Initial correction 10s
- Refine background 4s
- Final correction 8s
- Final scaling 7s
- 53s
- Correct center-of-mass 5s
- Affine registration 13s
- SPM preprocessing 1 (estimate 1 - TPM registration): 88s
- SPM preprocessing 1 (estimate 2): 70s
- SPM preprocessing 2 (write):
- Write Segmentation 22s
- Update Segmentation 24s
- Update Skull-Stripping 56s
- Update probability maps 11s
- 113s
- Global intensity correction: 21s
- SANLM denoising after intensity normalization (medium): 37s
- Fast Optimized Shooting registration 44s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.00) 18s
- Estimate local tissue thresholds (WM) 26s
- Estimate local tissue thresholds (GM) 37s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 64s
- 157s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 4s
- Ventricle detection 15s
- Blood vessel detection 12s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 30s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 6s
- 83s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 38s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 5s
- Level 1 cleanup (brain masking) 4s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 3s
- 14s
- 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 | 0.0806 0.0000 0.0806 | 32.0000
- 2 | 2.50 | 0.0785 0.0010 0.0795 | 29.4886
- 3 | 2.50 | 0.0779 0.0016 0.0795 | 26.9772
- 4 | 2.50 | 0.0776 0.0018 0.0793 | 24.6107
- 5 | 2.50 | 0.0773 0.0019 0.0792 | 22.6548
- 6 | 2.50 | 0.0771 0.0020 0.0791 | 20.6989
- 7 | 2.50 | 0.0769 0.0021 0.0790 | 18.9688
- 8 | 2.50 | 0.0767 0.0021 0.0788 | 17.4455
- 9 | 2.50 | 0.0764 0.0022 0.0786 | 15.9223
- 10 | 2.50 | 0.0762 0.0023 0.0785 | 14.6627
- 11 | 2.50 | 0.0759 0.0024 0.0783 | 13.4764
- 12 | 2.50 | 0.0757 0.0024 0.0781 | 12.3015
- 13 | 2.50 | 0.0754 0.0025 0.0779 | 11.3776
- 14 | 2.50 | 0.0751 0.0026 0.0777 | 10.4537
- 15 | 2.25 | 0.0732 0.0026 0.0758 | 9.5920
- 16 | 2.25 | 0.0707 0.0039 0.0746 | 8.8725
- 29 | 2.00 | 0.0714 0.0017 0.0731 | 3.3283
- 30 | 2.00 | 0.0657 0.0040 0.0697 | 3.1221
- 31 | 2.00 | 0.0638 0.0049 0.0688 | 2.9160
- 43 | 1.75 | 0.0628 0.0028 0.0656 | 1.5785
- 44 | 1.75 | 0.0587 0.0049 0.0637 | 1.5194
- 45 | 1.75 | 0.0574 0.0057 0.0631 | 1.4626
- 57 | 1.50 | 0.0557 0.0041 0.0598 | 1.0900
- 58 | 1.50 | 0.0529 0.0059 0.0588 | 1.0730
- 59 | 1.50 | 0.0519 0.0066 0.0585 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 199s
- Prepare output 14s
- 214s
- Jacobian determinant (RMS): 0.011 0.038 0.056 0.077 0.098 | 0.104824
- Template Matching: 0.081 0.212 0.192 0.172 0.156 | 0.155789
- Write result maps: 44s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 58s
- CSF distance: 19s
- PBT2x thickness: 55s
- 139s
- Create initial surface 100s
- Topology correction: 110s
- Surface refinement: 100s
- Reduction of surface collisions with optimization: 74s
- Spherical mapping with areal smoothing 98s
- Spherical registration 327s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 39s
- CSF distance: 19s
- PBT2x thickness: 55s
- 120s
- Create initial surface 94s
- Topology correction: 109s
- Surface refinement: 87s
- Reduction of surface collisions with optimization: 77s
- Spherical mapping with areal smoothing 106s
- Spherical registration 326s
- Final surface processing results:
- Average thickness (FS): 2.5507 0.5892 mm
- Surface intensity / position RMSE: 0.0643 / 0.0628
- Euler number / defect number / defect size: 8.0 / 8.0 / 0.16%
- Display thickness: /var/lib/condor/execute/dir_1701027/ds/MRN/sub-0027417/ses-1/surf/lh.thickness.sub-0027417_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1701027/ds/MRN/sub-0027417/ses-1/surf/rh.thickness.sub-0027417_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1701027/ds/MRN/sub-0027417/ses-1/sub-0027417_ses-1_run-1_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 1981s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 11s
- ROI estimation of 'neuromorphometrics' atlas 40s
- ROI estimation of 'lpba40' atlas 11s
- ROI estimation of 'hammers' atlas 27s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 10s
- ROI estimation of 'aal3' atlas 17s
- ROI estimation of 'mori' atlas 24s
- ROI estimation of 'anatomy3' atlas 34s
- ROI estimation of 'julichbrain' atlas 46s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 19s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 32s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 75s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 112s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 9s
- Write results 11s
- 471s
- Quality check: 15s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1701027/ds/MRN/sub-0027417/ses-1/report/catreport_sub-0027417_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 62 minute(s) and 24 second(s).
- Image Quality Rating (IQR): 84.32% (B)
- GM volume (GMV): 47.31% (682.21 / 1442.13 ml)
- GM thickness (GMT): 2.55 0.59 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1701027/ds/MRN/sub-0027417/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_1701027/ds/MRN/sub-0027417/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_1701027/ds/MRN/sub-0027417/ses-1/label
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