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- CAT12.8.1 r2040: 1/1: ./sub-0025748/ses-1/sub-0025748_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 56s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 7s
- Initial correction 8s
- Refine background 4s
- Final correction 6s
- Final scaling 6s
- 47s
- Correct center-of-mass 5s
- Affine registration 11s
- SPM preprocessing 1 (estimate 1 - TPM registration): 84s
- SPM preprocessing 1 (estimate 2): 75s
- SPM preprocessing 2 (write):
- Write Segmentation 21s
- Update Segmentation 23s
- Update Skull-Stripping 54s
- Update probability maps 11s
- 110s
- Global intensity correction: 21s
- SANLM denoising after intensity normalization (medium): 31s
- Fast Optimized Shooting registration 41s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.11) 17s
- Estimate local tissue thresholds (WM) 25s
- Estimate local tissue thresholds (GM) 37s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 56s
- 148s
- ROI segmentation (partitioning):
- Atlas -> subject space 10s
- Major structures 4s
- Ventricle detection 22s
- Blood vessel detection 12s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.01) 28s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 6s
- 87s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 37s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- 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) 4s
- 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 | 0.0829 0.0000 0.0829 | 32.0000
- 2 | 2.50 | 0.0805 0.0011 0.0816 | 29.4886
- 3 | 2.50 | 0.0798 0.0017 0.0815 | 26.9772
- 4 | 2.50 | 0.0794 0.0019 0.0813 | 24.6107
- 5 | 2.50 | 0.0792 0.0020 0.0812 | 22.6548
- 6 | 2.50 | 0.0789 0.0021 0.0810 | 20.6989
- 7 | 2.50 | 0.0786 0.0022 0.0809 | 18.9688
- 8 | 2.50 | 0.0784 0.0023 0.0807 | 17.4455
- 9 | 2.50 | 0.0781 0.0024 0.0805 | 15.9223
- 10 | 2.50 | 0.0778 0.0025 0.0803 | 14.6627
- 11 | 2.50 | 0.0775 0.0026 0.0801 | 13.4764
- 12 | 2.50 | 0.0772 0.0026 0.0798 | 12.3015
- 13 | 2.50 | 0.0769 0.0027 0.0796 | 11.3776
- 14 | 2.50 | 0.0766 0.0028 0.0794 | 10.4537
- 15 | 2.25 | 0.0754 0.0029 0.0783 | 9.5920
- 16 | 2.25 | 0.0726 0.0042 0.0769 | 8.8725
- 29 | 2.00 | 0.0736 0.0019 0.0755 | 3.3283
- 30 | 2.00 | 0.0678 0.0042 0.0720 | 3.1221
- 31 | 2.00 | 0.0658 0.0051 0.0710 | 2.9160
- 43 | 1.75 | 0.0648 0.0030 0.0677 | 1.5785
- 44 | 1.75 | 0.0608 0.0050 0.0658 | 1.5194
- 45 | 1.75 | 0.0594 0.0058 0.0652 | 1.4626
- 57 | 1.50 | 0.0579 0.0042 0.0621 | 1.0900
- 58 | 1.50 | 0.0550 0.0061 0.0611 | 1.0730
- Shooting registration with 2.50:-0.25:1.50 mm takes: 180s
- Prepare output 14s
- 194s
- Jacobian determinant (RMS): 0.011 0.039 0.057 0.080 0.102 | 0.107172
- Template Matching: 0.083 0.218 0.198 0.178 0.165 | 0.165014
- Write result maps: 62s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 44s
- CSF distance: 20s
- PBT2x thickness: 58s
- 129s
- Create initial surface 100s
- Topology correction: 111s
- Surface refinement: 106s
- Reduction of surface collisions with optimization: 82s
- Spherical mapping with areal smoothing 105s
- Spherical registration 308s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 48s
- CSF distance: 19s
- PBT2x thickness: 56s
- 131s
- Create initial surface 99s
- Topology correction: 110s
- Surface refinement: 90s
- Reduction of surface collisions with optimization: 82s
- Spherical mapping with areal smoothing 103s
- Spherical registration 339s
- Final surface processing results:
- Average thickness (FS): 2.5175 0.6337 mm
- Surface intensity / position RMSE: 0.0704 / 0.0772
- Euler number / defect number / defect size: 26.0 / 14.5 / 0.98%
- Display thickness: /var/lib/condor/execute/dir_3501471/ds/SWU_4/sub-0025748/ses-1/surf/lh.thickness.sub-0025748_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3501471/ds/SWU_4/sub-0025748/ses-1/surf/rh.thickness.sub-0025748_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3501471/ds/SWU_4/sub-0025748/ses-1/sub-0025748_ses-1_run-1_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 2017s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 13s
- ROI estimation of 'neuromorphometrics' atlas 49s
- ROI estimation of 'lpba40' atlas 14s
- ROI estimation of 'hammers' atlas 34s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 13s
- ROI estimation of 'aal3' atlas 21s
- ROI estimation of 'mori' atlas 33s
- ROI estimation of 'anatomy3' atlas 46s
- ROI estimation of 'julichbrain' atlas 63s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 26s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 49s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 106s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 174s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 16s
- Write results 18s
- 663s
- Quality check: 16s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3501471/ds/SWU_4/sub-0025748/ses-1/report/catreport_sub-0025748_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 64 minute(s) and 10 second(s).
- Image Quality Rating (IQR): 83.06% (B-)
- GM volume (GMV): 48.50% (700.17 / 1443.60 ml)
- GM thickness (GMT): 2.52 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3501471/ds/SWU_4/sub-0025748/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_3501471/ds/SWU_4/sub-0025748/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_3501471/ds/SWU_4/sub-0025748/ses-1/label
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