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- CAT12.8.1 r2040: 1/1: ./sub-0026139/ses-1/sub-0026139_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 36s
- APP: Rough bias correction:
- Initialize 4s
- Estimate background 4s
- Initial correction 4s
- Refine background 2s
- Final correction 3s
- Final scaling 3s
- 25s
- Correct center-of-mass 3s
- Affine registration 6s
- SPM preprocessing 1 (estimate 1 - TPM registration): 57s
- SPM preprocessing 1 (estimate 2): 48s
- SPM preprocessing 2 (write):
- Write Segmentation 12s
- Update Segmentation 14s
- Update Skull-Stripping 29s
- Update probability maps 6s
- 61s
- Global intensity correction: 11s
- SANLM denoising after intensity normalization (medium): 17s
- Fast Optimized Shooting registration 24s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 2s
- Prepare partitions 1s
- Prepare segments (LASmod = 1.12) 9s
- Estimate local tissue thresholds (WM) 12s
- Estimate local tissue thresholds (GM) 17s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 28s
- 72s
- ROI segmentation (partitioning):
- Atlas -> subject space 5s
- Major structures 2s
- Ventricle detection 8s
- Blood vessel detection 6s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.17) 12s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 3s
- 39s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 23s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- 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
- 8s
- 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 | 0.0863 0.0000 0.0863 | 32.0000
- 2 | 2.50 | 0.0837 0.0012 0.0849 | 29.4886
- 3 | 2.50 | 0.0828 0.0018 0.0847 | 26.9772
- 4 | 2.50 | 0.0824 0.0021 0.0845 | 24.6107
- 5 | 2.50 | 0.0821 0.0023 0.0843 | 22.6548
- 6 | 2.50 | 0.0818 0.0024 0.0842 | 20.6989
- 7 | 2.50 | 0.0815 0.0025 0.0840 | 18.9688
- 8 | 2.50 | 0.0811 0.0026 0.0838 | 17.4455
- 9 | 2.50 | 0.0808 0.0027 0.0835 | 15.9223
- 10 | 2.50 | 0.0805 0.0029 0.0833 | 14.6627
- 11 | 2.50 | 0.0801 0.0030 0.0831 | 13.4764
- 12 | 2.50 | 0.0798 0.0031 0.0828 | 12.3015
- 13 | 2.50 | 0.0794 0.0032 0.0826 | 11.3776
- 14 | 2.50 | 0.0790 0.0033 0.0823 | 10.4537
- 15 | 2.25 | 0.0788 0.0034 0.0822 | 9.5920
- 16 | 2.25 | 0.0756 0.0050 0.0806 | 8.8725
- 17 | 2.25 | 0.0742 0.0056 0.0798 | 8.1530
- 29 | 2.00 | 0.0755 0.0026 0.0781 | 3.3283
- 30 | 2.00 | 0.0692 0.0052 0.0744 | 3.1221
- 31 | 2.00 | 0.0670 0.0063 0.0733 | 2.9160
- 43 | 1.75 | 0.0657 0.0036 0.0694 | 1.5785
- 44 | 1.75 | 0.0613 0.0060 0.0673 | 1.5194
- 45 | 1.75 | 0.0599 0.0068 0.0666 | 1.4626
- 57 | 1.50 | 0.0583 0.0050 0.0633 | 1.0900
- 58 | 1.50 | 0.0552 0.0070 0.0622 | 1.0730
- 59 | 1.50 | 0.0542 0.0077 0.0618 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 122s
- Prepare output 7s
- 129s
- Jacobian determinant (RMS): 0.013 0.047 0.073 0.102 0.129 | 0.136951
- Template Matching: 0.086 0.223 0.201 0.180 0.162 | 0.162493
- Write result maps: 26s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 25s
- CSF distance: 9s
- PBT2x thickness: 26s
- 65s
- Create initial surface 48s
- Topology correction: 49s
- Surface refinement: 45s
- Reduction of surface collisions with optimization: 36s
- Spherical mapping with areal smoothing 51s
- Spherical registration 198s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 16s
- CSF distance: 9s
- PBT2x thickness: 26s
- 54s
- Create initial surface 47s
- Topology correction: 50s
- Surface refinement: 43s
- Reduction of surface collisions with optimization: 34s
- Spherical mapping with areal smoothing 49s
- Spherical registration 214s
- Final surface processing results:
- Average thickness (FS): 2.5047 0.6381 mm
- Surface intensity / position RMSE: 0.0620 / 0.0596
- Euler number / defect number / defect size: 10.0 / 7.0 / 0.22%
- Display thickness: /var/lib/condor/execute/dir_888672/ds/UM/sub-0026139/ses-1/surf/lh.thickness.sub-0026139_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_888672/ds/UM/sub-0026139/ses-1/surf/rh.thickness.sub-0026139_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_888672/ds/UM/sub-0026139/ses-1/sub-0026139_ses-1_run-1_T1w.nii
- Surface ROI estimation: 6s
- Surface and thickness estimation takes: 1045s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 28s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 18s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 10s
- ROI estimation of 'mori' atlas 16s
- ROI estimation of 'anatomy3' atlas 21s
- ROI estimation of 'julichbrain' atlas 31s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 13s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 27s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 65s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 88s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s
- Write results 9s
- 350s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_888672/ds/UM/sub-0026139/ses-1/report/catreport_sub-0026139_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 34 minute(s) and 12 second(s).
- Image Quality Rating (IQR): 81.77% (B-)
- GM volume (GMV): 46.69% (583.58 / 1249.87 ml)
- GM thickness (GMT): 2.50 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_888672/ds/UM/sub-0026139/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_888672/ds/UM/sub-0026139/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_888672/ds/UM/sub-0026139/ses-1/label
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