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- CAT12.8.1 r2040: 1/1: ./sub-0025631/ses-2/sub-0025631_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 38s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 5s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 6s
- 38s
- Correct center-of-mass 5s
- Affine registration 8s
- SPM preprocessing 1 (estimate 1 - TPM registration): 67s
- SPM preprocessing 1 (estimate 2): 52s
- SPM preprocessing 2 (write):
- Write Segmentation 14s
- Update Segmentation 16s
- Update Skull-Stripping 36s
- Update probability maps 8s
- 74s
- Global intensity correction: 13s
- SANLM denoising after intensity normalization (medium): 21s
- Fast Optimized Shooting registration 26s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.13) 11s
- Estimate local tissue thresholds (WM) 14s
- Estimate local tissue thresholds (GM) 21s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 36s
- 89s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 3s
- Ventricle detection 10s
- Blood vessel detection 7s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.07) 15s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 4s
- 48s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 27s
- 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
- 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 | 0.0859 0.0000 0.0859 | 32.0000
- 2 | 2.50 | 0.0829 0.0013 0.0842 | 29.4886
- 3 | 2.50 | 0.0820 0.0019 0.0840 | 26.9772
- 4 | 2.50 | 0.0816 0.0022 0.0838 | 24.6107
- 5 | 2.50 | 0.0813 0.0023 0.0836 | 22.6548
- 6 | 2.50 | 0.0810 0.0024 0.0834 | 20.6989
- 7 | 2.50 | 0.0807 0.0025 0.0832 | 18.9688
- 8 | 2.50 | 0.0803 0.0026 0.0830 | 17.4455
- 9 | 2.50 | 0.0800 0.0027 0.0827 | 15.9223
- 10 | 2.50 | 0.0797 0.0028 0.0825 | 14.6627
- 11 | 2.50 | 0.0794 0.0029 0.0822 | 13.4764
- 12 | 2.50 | 0.0790 0.0029 0.0820 | 12.3015
- 13 | 2.50 | 0.0787 0.0030 0.0817 | 11.3776
- 14 | 2.50 | 0.0784 0.0031 0.0814 | 10.4537
- 15 | 2.25 | 0.0786 0.0031 0.0817 | 9.5920
- 16 | 2.25 | 0.0755 0.0046 0.0801 | 8.8725
- 17 | 2.25 | 0.0743 0.0051 0.0794 | 8.1530
- 29 | 2.00 | 0.0769 0.0023 0.0792 | 3.3283
- 30 | 2.00 | 0.0709 0.0048 0.0757 | 3.1221
- 31 | 2.00 | 0.0688 0.0058 0.0747 | 2.9160
- 43 | 1.75 | 0.0681 0.0033 0.0715 | 1.5785
- 44 | 1.75 | 0.0635 0.0058 0.0693 | 1.5194
- 45 | 1.75 | 0.0619 0.0067 0.0686 | 1.4626
- 57 | 1.50 | 0.0608 0.0048 0.0656 | 1.0900
- 58 | 1.50 | 0.0573 0.0071 0.0645 | 1.0730
- 59 | 1.50 | 0.0562 0.0078 0.0640 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 126s
- Prepare output 8s
- 134s
- Jacobian determinant (RMS): 0.011 0.038 0.058 0.082 0.107 | 0.113010
- Template Matching: 0.086 0.223 0.207 0.186 0.169 | 0.168565
- Write result maps: 27s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 33s
- CSF distance: 12s
- PBT2x thickness: 34s
- 83s
- Create initial surface 60s
- Topology correction: 78s
- Surface refinement: 83s
- Reduction of surface collisions with optimization: 55s
- Spherical mapping with areal smoothing 85s
- Spherical registration 210s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 25s
- CSF distance: 12s
- PBT2x thickness: 35s
- 77s
- Create initial surface 63s
- Topology correction: 76s
- Surface refinement: 64s
- Reduction of surface collisions with optimization: 56s
- Spherical mapping with areal smoothing 69s
- Spherical registration 212s
- Final surface processing results:
- Average thickness (FS): 2.5285 0.6595 mm
- Surface intensity / position RMSE: 0.0713 / 0.0897
- Euler number / defect number / defect size: 32.0 / 16.0 / 1.39%
- Display thickness: /var/lib/condor/execute/dir_3472619/ds/SWU_4/sub-0025631/ses-2/surf/lh.thickness.sub-0025631_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3472619/ds/SWU_4/sub-0025631/ses-2/surf/rh.thickness.sub-0025631_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3472619/ds/SWU_4/sub-0025631/ses-2/sub-0025631_ses-2_run-1_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1349s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 26s
- ROI estimation of 'lpba40' atlas 7s
- ROI estimation of 'hammers' atlas 18s
- 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 31s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 23s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 51s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 77s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s
- Write results 8s
- 320s
- Quality check: 9s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3472619/ds/SWU_4/sub-0025631/ses-2/report/catreport_sub-0025631_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 40 minute(s) and 43 second(s).
- Image Quality Rating (IQR): 82.57% (B-)
- GM volume (GMV): 48.20% (730.77 / 1516.26 ml)
- GM thickness (GMT): 2.53 0.66 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3472619/ds/SWU_4/sub-0025631/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_3472619/ds/SWU_4/sub-0025631/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_3472619/ds/SWU_4/sub-0025631/ses-2/label
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