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- CAT12.8.1 r2040: 1/1: ./sub-0026003/ses-3/sub-0026003_ses-3_run-1_T1w.n
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- SANLM denoising (medium): 44s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 5s
- Initial correction 5s
- Refine background 3s
- Final correction 4s
- Final scaling 4s
- 31s
- Correct center-of-mass 3s
- Affine registration 7s
- SPM preprocessing 1 (estimate 1 - TPM registration): 55s
- SPM preprocessing 1 (estimate 2): 49s
- SPM preprocessing 2 (write):
- Write Segmentation 14s
- Update Segmentation 16s
- Update Skull-Stripping 34s
- Update probability maps 7s
- 70s
- Global intensity correction: 14s
- SANLM denoising after intensity normalization (medium): 20s
- Fast Optimized Shooting registration 26s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.04) 12s
- Estimate local tissue thresholds (WM) 15s
- Estimate local tissue thresholds (GM) 22s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 38s
- 94s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 3s
- Ventricle detection 11s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.17) 18s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 53s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 28s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 3s
- Level 1 cleanup (brain masking) 2s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 9s
- 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 | 0.0858 0.0000 0.0858 | 32.0000
- 2 | 2.50 | 0.0829 0.0013 0.0841 | 29.4886
- 3 | 2.50 | 0.0820 0.0020 0.0839 | 26.9772
- 4 | 2.50 | 0.0815 0.0022 0.0837 | 24.6107
- 5 | 2.50 | 0.0811 0.0024 0.0835 | 22.6548
- 6 | 2.50 | 0.0808 0.0025 0.0833 | 20.6989
- 7 | 2.50 | 0.0805 0.0026 0.0831 | 18.9688
- 8 | 2.50 | 0.0801 0.0028 0.0829 | 17.4455
- 9 | 2.50 | 0.0798 0.0029 0.0826 | 15.9223
- 10 | 2.50 | 0.0794 0.0030 0.0824 | 14.6627
- 11 | 2.50 | 0.0790 0.0031 0.0821 | 13.4764
- 12 | 2.50 | 0.0787 0.0032 0.0818 | 12.3015
- 13 | 2.50 | 0.0783 0.0033 0.0816 | 11.3776
- 14 | 2.50 | 0.0779 0.0034 0.0813 | 10.4537
- 15 | 2.25 | 0.0776 0.0035 0.0811 | 9.5920
- 16 | 2.25 | 0.0745 0.0050 0.0796 | 8.8725
- 29 | 2.00 | 0.0757 0.0023 0.0780 | 3.3283
- 30 | 2.00 | 0.0689 0.0050 0.0739 | 3.1221
- 31 | 2.00 | 0.0665 0.0061 0.0727 | 2.9160
- 43 | 1.75 | 0.0654 0.0036 0.0689 | 1.5785
- 44 | 1.75 | 0.0609 0.0059 0.0668 | 1.5194
- 45 | 1.75 | 0.0594 0.0068 0.0662 | 1.4626
- 57 | 1.50 | 0.0580 0.0049 0.0630 | 1.0900
- 58 | 1.50 | 0.0548 0.0070 0.0618 | 1.0730
- 59 | 1.50 | 0.0538 0.0077 0.0615 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 131s
- Prepare output 8s
- 140s
- Jacobian determinant (RMS): 0.011 0.041 0.063 0.090 0.113 | 0.121344
- Template Matching: 0.086 0.224 0.200 0.178 0.161 | 0.161320
- Write result maps: 27s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 46s
- CSF distance: 12s
- PBT2x thickness: 36s
- 99s
- Create initial surface 67s
- Topology correction: 79s
- Surface refinement: 86s
- Reduction of surface collisions with optimization: 57s
- Spherical mapping with areal smoothing 65s
- Spherical registration 237s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 40s
- CSF distance: 12s
- PBT2x thickness: 37s
- 94s
- Create initial surface 67s
- Topology correction: 77s
- Surface refinement: 58s
- Reduction of surface collisions with optimization: 57s
- Spherical mapping with areal smoothing 64s
- Spherical registration 247s
- Final surface processing results:
- Average thickness (FS): 2.4485 0.6439 mm
- Surface intensity / position RMSE: 0.0707 / 0.0758
- Euler number / defect number / defect size: 36.0 / 20.5 / 1.27%
- Display thickness: /var/lib/condor/execute/dir_3011310/ds/XHCUMS/sub-0026003/ses-3/surf/lh.thickness.sub-0026003_ses-3_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3011310/ds/XHCUMS/sub-0026003/ses-3/surf/rh.thickness.sub-0026003_ses-3_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3011310/ds/XHCUMS/sub-0026003/ses-3/sub-0026003_ses-3_run-1_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1432s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 27s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 19s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 11s
- ROI estimation of 'mori' atlas 16s
- ROI estimation of 'anatomy3' atlas 23s
- ROI estimation of 'julichbrain' atlas 30s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 22s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 49s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 73s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s
- Write results 7s
- 312s
- Quality check: 9s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3011310/ds/XHCUMS/sub-0026003/ses-3/report/catreport_sub-0026003_ses-3_run-1_T1w.pdf
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- CAT preprocessing takes 41 minute(s) and 40 second(s).
- Image Quality Rating (IQR): 83.77% (B)
- GM volume (GMV): 44.90% (676.13 / 1505.96 ml)
- GM thickness (GMT): 2.45 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3011310/ds/XHCUMS/sub-0026003/ses-3/mri
- Reports are saved in /var/lib/condor/execute/dir_3011310/ds/XHCUMS/sub-0026003/ses-3/report
- Labels are saved in /var/lib/condor/execute/dir_3011310/ds/XHCUMS/sub-0026003/ses-3/label
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