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- CAT12.8.1 r2040: 1/1: ./sub-0025997/ses-3/sub-0025997_ses-3_run-1_T1w.n
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- SANLM denoising (medium): 43s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 5s
- Initial correction 5s
- Refine background 3s
- Final correction 4s
- Final scaling 4s
- 32s
- Correct center-of-mass 3s
- Affine registration 9s
- SPM preprocessing 1 (estimate 1 - TPM registration): 62s
- SPM preprocessing 1 (estimate 2): 50s
- SPM preprocessing 2 (write):
- Write Segmentation 14s
- Update Segmentation 17s
- Update Skull-Stripping 35s
- Update probability maps 7s
- 73s
- Global intensity correction: 14s
- SANLM denoising after intensity normalization (medium): 22s
- Fast Optimized Shooting registration 27s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.03) 12s
- Estimate local tissue thresholds (WM) 15s
- Estimate local tissue thresholds (GM) 21s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 37s
- 94s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 3s
- Ventricle detection 12s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.20) 20s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 57s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 29s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 2s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 10s
- 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 | 0.0874 0.0000 0.0874 | 32.0000
- 2 | 2.50 | 0.0849 0.0012 0.0861 | 29.4886
- 3 | 2.50 | 0.0841 0.0018 0.0859 | 26.9772
- 4 | 2.50 | 0.0837 0.0020 0.0857 | 24.6107
- 5 | 2.50 | 0.0834 0.0022 0.0855 | 22.6548
- 6 | 2.50 | 0.0831 0.0023 0.0853 | 20.6989
- 7 | 2.50 | 0.0828 0.0024 0.0852 | 18.9688
- 8 | 2.50 | 0.0825 0.0025 0.0850 | 17.4455
- 9 | 2.50 | 0.0822 0.0025 0.0847 | 15.9223
- 10 | 2.50 | 0.0819 0.0026 0.0845 | 14.6627
- 11 | 2.50 | 0.0815 0.0027 0.0843 | 13.4764
- 12 | 2.50 | 0.0812 0.0028 0.0840 | 12.3015
- 13 | 2.50 | 0.0809 0.0029 0.0838 | 11.3776
- 14 | 2.50 | 0.0806 0.0030 0.0835 | 10.4537
- 15 | 2.25 | 0.0805 0.0030 0.0835 | 9.5920
- 16 | 2.25 | 0.0774 0.0045 0.0819 | 8.8725
- 17 | 2.25 | 0.0762 0.0051 0.0813 | 8.1530
- 18 | 2.25 | 0.0755 0.0053 0.0807 | 7.5234
- 19 | 2.25 | 0.0748 0.0054 0.0802 | 6.9630
- 29 | 2.00 | 0.0766 0.0028 0.0794 | 3.3283
- 30 | 2.00 | 0.0713 0.0051 0.0764 | 3.1221
- 31 | 2.00 | 0.0695 0.0060 0.0755 | 2.9160
- 43 | 1.75 | 0.0686 0.0034 0.0719 | 1.5785
- 44 | 1.75 | 0.0640 0.0059 0.0699 | 1.5194
- 45 | 1.75 | 0.0625 0.0067 0.0692 | 1.4626
- 57 | 1.50 | 0.0609 0.0048 0.0658 | 1.0900
- 58 | 1.50 | 0.0576 0.0070 0.0647 | 1.0730
- 59 | 1.50 | 0.0566 0.0077 0.0643 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 141s
- Prepare output 9s
- 149s
- Jacobian determinant (RMS): 0.010 0.036 0.057 0.081 0.105 | 0.112387
- Template Matching: 0.087 0.225 0.209 0.188 0.170 | 0.169734
- Write result maps: 28s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 56s
- CSF distance: 13s
- PBT2x thickness: 38s
- 113s
- Create initial surface 73s
- Topology correction: 83s
- Surface refinement: 90s
- Reduction of surface collisions with optimization: 57s
- Spherical mapping with areal smoothing 65s
- Spherical registration 256s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 44s
- CSF distance: 13s
- PBT2x thickness: 39s
- 101s
- Create initial surface 75s
- Topology correction: 81s
- Surface refinement: 70s
- Reduction of surface collisions with optimization: 59s
- Spherical mapping with areal smoothing 67s
- Spherical registration 244s
- Final surface processing results:
- Average thickness (FS): 2.3640 0.5870 mm
- Surface intensity / position RMSE: 0.0576 / 0.0585
- Euler number / defect number / defect size: 12.0 / 15.5 / 0.17%
- Display thickness: /var/lib/condor/execute/dir_912710/ds/XHCUMS/sub-0025997/ses-3/surf/lh.thickness.sub-0025997_ses-3_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_912710/ds/XHCUMS/sub-0025997/ses-3/surf/rh.thickness.sub-0025997_ses-3_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_912710/ds/XHCUMS/sub-0025997/ses-3/sub-0025997_ses-3_run-1_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1516s
- 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 10s
- ROI estimation of 'mori' atlas 15s
- ROI estimation of 'anatomy3' atlas 21s
- ROI estimation of 'julichbrain' atlas 28s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 20s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 45s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 68s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s
- Write results 7s
- 291s
- Quality check: 10s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_912710/ds/XHCUMS/sub-0025997/ses-3/report/catreport_sub-0025997_ses-3_run-1_T1w.pdf
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- CAT preprocessing takes 43 minute(s) and 18 second(s).
- Image Quality Rating (IQR): 82.44% (B-)
- GM volume (GMV): 40.93% (672.39 / 1642.74 ml)
- GM thickness (GMT): 2.36 0.59 mm
- Segmentations are saved in /var/lib/condor/execute/dir_912710/ds/XHCUMS/sub-0025997/ses-3/mri
- Reports are saved in /var/lib/condor/execute/dir_912710/ds/XHCUMS/sub-0025997/ses-3/report
- Labels are saved in /var/lib/condor/execute/dir_912710/ds/XHCUMS/sub-0025997/ses-3/label
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