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- CAT12.8.1 r2040: 1/1: ./sub-0025625/ses-1/sub-0025625_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 58s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 7s
- Initial correction 7s
- Refine background 3s
- Final correction 6s
- Final scaling 5s
- 43s
- Correct center-of-mass 5s
- Affine registration 13s
- SPM preprocessing 1 (estimate 1 - TPM registration): 83s
- SPM preprocessing 1 (estimate 2): 81s
- SPM preprocessing 2 (write):
- Write Segmentation 22s
- Update Segmentation 22s
- Update Skull-Stripping 47s
- Update probability maps 10s
- 101s
- Global intensity correction: 18s
- SANLM denoising after intensity normalization (medium): 31s
- Fast Optimized Shooting registration 39s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 4s
- Prepare segments (LASmod = 1.12) 17s
- Estimate local tissue thresholds (WM) 23s
- Estimate local tissue thresholds (GM) 37s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 49s
- 138s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 19s
- Blood vessel detection 12s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 28s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 83s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 40s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 5s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 3s
- 13s
- 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 | 0.0823 0.0000 0.0823 | 32.0000
- 2 | 2.50 | 0.0802 0.0010 0.0812 | 29.4886
- 3 | 2.50 | 0.0796 0.0015 0.0812 | 26.9772
- 4 | 2.50 | 0.0793 0.0017 0.0810 | 24.6107
- 5 | 2.50 | 0.0791 0.0018 0.0809 | 22.6548
- 6 | 2.50 | 0.0789 0.0019 0.0808 | 20.6989
- 7 | 2.50 | 0.0786 0.0020 0.0806 | 18.9688
- 8 | 2.50 | 0.0784 0.0021 0.0805 | 17.4455
- 9 | 2.50 | 0.0782 0.0021 0.0803 | 15.9223
- 10 | 2.50 | 0.0779 0.0022 0.0802 | 14.6627
- 11 | 2.50 | 0.0777 0.0023 0.0800 | 13.4764
- 12 | 2.50 | 0.0774 0.0024 0.0798 | 12.3015
- 13 | 2.50 | 0.0771 0.0025 0.0796 | 11.3776
- 14 | 2.50 | 0.0769 0.0025 0.0794 | 10.4537
- 15 | 2.25 | 0.0763 0.0026 0.0788 | 9.5920
- 16 | 2.25 | 0.0735 0.0039 0.0774 | 8.8725
- 29 | 2.00 | 0.0750 0.0018 0.0767 | 3.3283
- 30 | 2.00 | 0.0692 0.0041 0.0733 | 3.1221
- 31 | 2.00 | 0.0673 0.0050 0.0723 | 2.9160
- 43 | 1.75 | 0.0664 0.0029 0.0693 | 1.5785
- 44 | 1.75 | 0.0621 0.0051 0.0673 | 1.5194
- 45 | 1.75 | 0.0607 0.0059 0.0666 | 1.4626
- 57 | 1.50 | 0.0594 0.0043 0.0636 | 1.0900
- 58 | 1.50 | 0.0562 0.0064 0.0625 | 1.0730
- 59 | 1.50 | 0.0551 0.0070 0.0621 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 205s
- Prepare output 14s
- 219s
- Jacobian determinant (RMS): 0.010 0.036 0.054 0.078 0.102 | 0.108453
- Template Matching: 0.082 0.221 0.202 0.182 0.165 | 0.165227
- Write result maps: 45s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 38s
- CSF distance: 21s
- PBT2x thickness: 60s
- 127s
- Create initial surface 105s
- Topology correction: 124s
- Surface refinement: 132s
- Reduction of surface collisions with optimization: 88s
- Spherical mapping with areal smoothing 111s
- Spherical registration 317s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 40s
- CSF distance: 20s
- PBT2x thickness: 60s
- 127s
- Create initial surface 102s
- Topology correction: 128s
- Surface refinement: 137s
- Reduction of surface collisions with optimization: 87s
- Spherical mapping with areal smoothing 109s
- Spherical registration 351s
- Final surface processing results:
- Average thickness (FS): 2.4779 0.6458 mm
- Surface intensity / position RMSE: 0.0749 / 0.1057
- Euler number / defect number / defect size: 22.0 / 13.0 / 1.65%
- Display thickness: /var/lib/condor/execute/dir_1682613/ds/JHNU/sub-0025625/ses-1/surf/lh.thickness.sub-0025625_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1682613/ds/JHNU/sub-0025625/ses-1/surf/rh.thickness.sub-0025625_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1682613/ds/JHNU/sub-0025625/ses-1/sub-0025625_ses-1_run-1_T1w.nii
- Surface ROI estimation: 11s
- Surface and thickness estimation takes: 2170s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 13s
- ROI estimation of 'neuromorphometrics' atlas 45s
- ROI estimation of 'lpba40' atlas 13s
- ROI estimation of 'hammers' atlas 31s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 12s
- ROI estimation of 'aal3' atlas 20s
- ROI estimation of 'mori' atlas 27s
- ROI estimation of 'anatomy3' atlas 40s
- ROI estimation of 'julichbrain' atlas 52s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 21s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 37s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 82s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 106s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s
- Write results 10s
- 510s
- Quality check: 14s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1682613/ds/JHNU/sub-0025625/ses-1/report/catreport_sub-0025625_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 63 minute(s) and 16 second(s).
- Image Quality Rating (IQR): 83.02% (B-)
- GM volume (GMV): 49.74% (741.37 / 1490.36 ml)
- GM thickness (GMT): 2.48 0.65 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1682613/ds/JHNU/sub-0025625/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_1682613/ds/JHNU/sub-0025625/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_1682613/ds/JHNU/sub-0025625/ses-1/label
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