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- CAT12.8.1 r2040: 1/1: ./sub-0025273/ses-3/sub-0025273_ses-3_run-1_T1w.n
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- SANLM denoising (medium): 57s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 7s
- Initial correction 7s
- Refine background 3s
- Final correction 5s
- Final scaling 6s
- 41s
- Correct center-of-mass 5s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 96s
- SPM preprocessing 1 (estimate 2): 88s
- SPM preprocessing 2 (write):
- Write Segmentation 19s
- Update Segmentation 22s
- Update Skull-Stripping 45s
- Update probability maps 8s
- 94s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 31s
- Fast Optimized Shooting registration 39s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 17s
- Estimate local tissue thresholds (WM) 20s
- Estimate local tissue thresholds (GM) 32s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 44s
- 123s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 17s
- Blood vessel detection 12s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.04) 29s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 4s
- 79s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 37s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.04]
- 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
- 14s
- 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 | 0.0898 0.0000 0.0898 | 32.0000
- 2 | 2.50 | 0.0851 0.0017 0.0869 | 29.4886
- 3 | 2.50 | 0.0838 0.0027 0.0865 | 26.9772
- 4 | 2.50 | 0.0831 0.0030 0.0862 | 24.6107
- 5 | 2.50 | 0.0826 0.0033 0.0859 | 22.6548
- 6 | 2.50 | 0.0822 0.0034 0.0856 | 20.6989
- 7 | 2.50 | 0.0817 0.0035 0.0852 | 18.9688
- 8 | 2.50 | 0.0812 0.0037 0.0849 | 17.4455
- 9 | 2.50 | 0.0807 0.0038 0.0845 | 15.9223
- 10 | 2.50 | 0.0802 0.0040 0.0842 | 14.6627
- 11 | 2.50 | 0.0797 0.0041 0.0838 | 13.4764
- 12 | 2.50 | 0.0792 0.0042 0.0834 | 12.3015
- 13 | 2.50 | 0.0787 0.0043 0.0830 | 11.3776
- 14 | 2.50 | 0.0782 0.0044 0.0826 | 10.4537
- 15 | 2.25 | 0.0786 0.0046 0.0831 | 9.5920
- 16 | 2.25 | 0.0746 0.0065 0.0812 | 8.8725
- 29 | 2.00 | 0.0756 0.0030 0.0785 | 3.3283
- 30 | 2.00 | 0.0685 0.0058 0.0743 | 3.1221
- 31 | 2.00 | 0.0661 0.0069 0.0730 | 2.9160
- 43 | 1.75 | 0.0649 0.0040 0.0690 | 1.5785
- 44 | 1.75 | 0.0606 0.0063 0.0669 | 1.5194
- 45 | 1.75 | 0.0591 0.0071 0.0662 | 1.4626
- 57 | 1.50 | 0.0577 0.0053 0.0630 | 1.0900
- 58 | 1.50 | 0.0545 0.0073 0.0618 | 1.0730
- 59 | 1.50 | 0.0535 0.0080 0.0614 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 206s
- Prepare output 14s
- 220s
- Jacobian determinant (RMS): 0.014 0.054 0.080 0.109 0.135 | 0.140827
- Template Matching: 0.090 0.224 0.198 0.177 0.160 | 0.160449
- Write result maps: 38s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 49s
- CSF distance: 20s
- PBT2x thickness: 59s
- 135s
- Create initial surface 101s
- Topology correction: 114s
- Surface refinement: 98s
- Reduction of surface collisions with optimization: 84s
- Spherical mapping with areal smoothing 106s
- Spherical registration 326s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 43s
- CSF distance: 20s
- PBT2x thickness: 58s
- 127s
- Create initial surface 100s
- Topology correction: 117s
- Surface refinement: 93s
- Reduction of surface collisions with optimization: 86s
- Spherical mapping with areal smoothing 106s
- Spherical registration 340s
- Final surface processing results:
- Average thickness (FS): 2.4989 0.6032 mm
- Surface intensity / position RMSE: 0.0651 / 0.0624
- Euler number / defect number / defect size: 18.0 / 12.0 / 0.48%
- Display thickness: /var/lib/condor/execute/dir_1701246/ds/UPSM_1/sub-0025273/ses-3/surf/lh.thickness.sub-0025273_ses-3_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1701246/ds/UPSM_1/sub-0025273/ses-3/surf/rh.thickness.sub-0025273_ses-3_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1701246/ds/UPSM_1/sub-0025273/ses-3/sub-0025273_ses-3_run-1_T1w.nii
- Surface ROI estimation: 11s
- Surface and thickness estimation takes: 2048s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 32s
- ROI estimation of 'lpba40' atlas 9s
- ROI estimation of 'hammers' atlas 23s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 8s
- ROI estimation of 'aal3' atlas 14s
- ROI estimation of 'mori' atlas 20s
- ROI estimation of 'anatomy3' atlas 29s
- ROI estimation of 'julichbrain' atlas 38s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 16s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 28s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 63s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 91s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s
- Write results 10s
- 392s
- Quality check: 14s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1701246/ds/UPSM_1/sub-0025273/ses-3/report/catreport_sub-0025273_ses-3_run-1_T1w.pdf
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- CAT preprocessing takes 58 minute(s) and 57 second(s).
- Image Quality Rating (IQR): 80.76% (B-)
- GM volume (GMV): 48.23% (699.88 / 1451.12 ml)
- GM thickness (GMT): 2.50 0.60 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1701246/ds/UPSM_1/sub-0025273/ses-3/mri
- Reports are saved in /var/lib/condor/execute/dir_1701246/ds/UPSM_1/sub-0025273/ses-3/report
- Labels are saved in /var/lib/condor/execute/dir_1701246/ds/UPSM_1/sub-0025273/ses-3/label
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