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- CAT12.8.1 r2040: 1/1: ./sub-0025708/ses-2/sub-0025708_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 67s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 7s
- Initial correction 7s
- Refine background 3s
- Final correction 6s
- Final scaling 7s
- 42s
- Correct center-of-mass 3s
- Affine registration 13s
- SPM preprocessing 1 (estimate 1 - TPM registration): 71s
- SPM preprocessing 1 (estimate 2): 80s
- SPM preprocessing 2 (write):
- Write Segmentation 17s
- Update Segmentation 20s
- Update Skull-Stripping 43s
- Update probability maps 9s
- 89s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 26s
- Fast Optimized Shooting registration 32s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.10) 15s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 26s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 47s
- 116s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 15s
- Blood vessel detection 10s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.11) 26s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 4s
- 71s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 35s
- 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) 3s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 3s
- 12s
- 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 | 0.0864 0.0000 0.0864 | 32.0000
- 2 | 2.50 | 0.0841 0.0011 0.0852 | 29.4886
- 3 | 2.50 | 0.0834 0.0017 0.0851 | 26.9772
- 4 | 2.50 | 0.0831 0.0019 0.0849 | 24.6107
- 5 | 2.50 | 0.0828 0.0020 0.0848 | 22.6548
- 6 | 2.50 | 0.0825 0.0021 0.0846 | 20.6989
- 7 | 2.50 | 0.0823 0.0022 0.0845 | 18.9688
- 8 | 2.50 | 0.0820 0.0023 0.0843 | 17.4455
- 9 | 2.50 | 0.0818 0.0023 0.0841 | 15.9223
- 10 | 2.50 | 0.0815 0.0024 0.0839 | 14.6627
- 11 | 2.50 | 0.0812 0.0025 0.0837 | 13.4764
- 12 | 2.50 | 0.0809 0.0026 0.0835 | 12.3015
- 13 | 2.50 | 0.0806 0.0027 0.0832 | 11.3776
- 14 | 2.50 | 0.0803 0.0027 0.0830 | 10.4537
- 15 | 2.25 | 0.0809 0.0028 0.0837 | 9.5920
- 16 | 2.25 | 0.0776 0.0044 0.0820 | 8.8725
- 17 | 2.25 | 0.0764 0.0050 0.0813 | 8.1530
- 18 | 2.25 | 0.0756 0.0052 0.0808 | 7.5234
- 19 | 2.25 | 0.0749 0.0053 0.0803 | 6.9630
- 29 | 2.00 | 0.0772 0.0027 0.0800 | 3.3283
- 30 | 2.00 | 0.0717 0.0052 0.0769 | 3.1221
- 31 | 2.00 | 0.0698 0.0061 0.0759 | 2.9160
- 43 | 1.75 | 0.0690 0.0034 0.0724 | 1.5785
- 44 | 1.75 | 0.0642 0.0060 0.0702 | 1.5194
- 45 | 1.75 | 0.0626 0.0068 0.0695 | 1.4626
- 57 | 1.50 | 0.0612 0.0049 0.0662 | 1.0900
- 58 | 1.50 | 0.0578 0.0072 0.0650 | 1.0730
- 59 | 1.50 | 0.0567 0.0079 0.0646 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 187s
- Prepare output 11s
- 198s
- Jacobian determinant (RMS): 0.009 0.033 0.055 0.079 0.104 | 0.111022
- Template Matching: 0.086 0.225 0.209 0.188 0.170 | 0.170054
- Write result maps: 34s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 31s
- CSF distance: 17s
- PBT2x thickness: 47s
- 101s
- Create initial surface 91s
- Topology correction: 101s
- Surface refinement: 122s
- Reduction of surface collisions with optimization: 80s
- Spherical mapping with areal smoothing 84s
- Spherical registration 301s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 29s
- CSF distance: 16s
- PBT2x thickness: 45s
- 96s
- Create initial surface 88s
- Topology correction: 99s
- Surface refinement: 82s
- Reduction of surface collisions with optimization: 78s
- Spherical mapping with areal smoothing 85s
- Spherical registration 292s
- Final surface processing results:
- Average thickness (FS): 2.4507 0.6572 mm
- Surface intensity / position RMSE: 0.0700 / 0.0808
- Euler number / defect number / defect size: 16.0 / 11.5 / 1.12%
- Display thickness: /var/lib/condor/execute/dir_787955/ds/SWU_4/sub-0025708/ses-2/surf/lh.thickness.sub-0025708_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_787955/ds/SWU_4/sub-0025708/ses-2/surf/rh.thickness.sub-0025708_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_787955/ds/SWU_4/sub-0025708/ses-2/sub-0025708_ses-2_run-1_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 1802s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 33s
- ROI estimation of 'lpba40' atlas 10s
- ROI estimation of 'hammers' atlas 24s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 8s
- ROI estimation of 'aal3' atlas 14s
- ROI estimation of 'mori' atlas 22s
- ROI estimation of 'anatomy3' atlas 33s
- ROI estimation of 'julichbrain' atlas 46s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 20s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 36s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 77s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 114s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 10s
- Write results 11s
- 459s
- Quality check: 13s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_787955/ds/SWU_4/sub-0025708/ses-2/report/catreport_sub-0025708_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 55 minute(s) and 2 second(s).
- Image Quality Rating (IQR): 81.36% (B-)
- GM volume (GMV): 46.46% (703.59 / 1514.47 ml)
- GM thickness (GMT): 2.45 0.66 mm
- Segmentations are saved in /var/lib/condor/execute/dir_787955/ds/SWU_4/sub-0025708/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_787955/ds/SWU_4/sub-0025708/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_787955/ds/SWU_4/sub-0025708/ses-2/label
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