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- CAT12.8.1 r2040: 1/1: ./sub-0025922/ses-2/sub-0025922_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 36s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 4s
- Initial correction 5s
- Refine background 2s
- Final correction 4s
- Final scaling 4s
- 29s
- Correct center-of-mass 3s
- Affine registration 6s
- SPM preprocessing 1 (estimate 1 - TPM registration): 58s
- SPM preprocessing 1 (estimate 2): 48s
- SPM preprocessing 2 (write):
- Write Segmentation 14s
- Update Segmentation 15s
- Update Skull-Stripping 34s
- Update probability maps 8s
- 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 2s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.08) 10s
- Estimate local tissue thresholds (WM) 14s
- Estimate local tissue thresholds (GM) 20s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 30s
- 81s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 2s
- Ventricle detection 9s
- Blood vessel detection 6s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 14s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 4s
- 45s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 25s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.990.04]
- 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 | 0.0823 0.0000 0.0823 | 32.0000
- 2 | 2.50 | 0.0796 0.0012 0.0808 | 29.4886
- 3 | 2.50 | 0.0788 0.0018 0.0806 | 26.9772
- 4 | 2.50 | 0.0784 0.0021 0.0804 | 24.6107
- 5 | 2.50 | 0.0781 0.0022 0.0803 | 22.6548
- 6 | 2.50 | 0.0778 0.0023 0.0801 | 20.6989
- 7 | 2.50 | 0.0775 0.0024 0.0799 | 18.9688
- 8 | 2.50 | 0.0772 0.0025 0.0797 | 17.4455
- 9 | 2.50 | 0.0769 0.0026 0.0795 | 15.9223
- 10 | 2.50 | 0.0766 0.0027 0.0793 | 14.6627
- 11 | 2.50 | 0.0762 0.0028 0.0790 | 13.4764
- 12 | 2.50 | 0.0759 0.0029 0.0788 | 12.3015
- 13 | 2.50 | 0.0756 0.0030 0.0785 | 11.3776
- 14 | 2.50 | 0.0752 0.0030 0.0783 | 10.4537
- 15 | 2.25 | 0.0743 0.0031 0.0774 | 9.5920
- 16 | 2.25 | 0.0712 0.0046 0.0758 | 8.8725
- 29 | 2.00 | 0.0720 0.0021 0.0741 | 3.3283
- 30 | 2.00 | 0.0660 0.0045 0.0705 | 3.1221
- 31 | 2.00 | 0.0639 0.0055 0.0694 | 2.9160
- 43 | 1.75 | 0.0629 0.0032 0.0660 | 1.5785
- 44 | 1.75 | 0.0588 0.0053 0.0641 | 1.5194
- 45 | 1.75 | 0.0574 0.0060 0.0635 | 1.4626
- 57 | 1.50 | 0.0559 0.0044 0.0603 | 1.0900
- 58 | 1.50 | 0.0530 0.0063 0.0593 | 1.0730
- 59 | 1.50 | 0.0521 0.0069 0.0590 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 157s
- Prepare output 8s
- 165s
- Jacobian determinant (RMS): 0.012 0.042 0.061 0.083 0.105 | 0.111125
- Template Matching: 0.082 0.214 0.192 0.172 0.156 | 0.156271
- Write result maps: 35s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 20s
- CSF distance: 10s
- PBT2x thickness: 31s
- 66s
- Create initial surface 57s
- Topology correction: 72s
- Surface refinement: 57s
- Reduction of surface collisions with optimization: 52s
- Spherical mapping with areal smoothing 65s
- Spherical registration 232s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 18s
- CSF distance: 10s
- PBT2x thickness: 31s
- 63s
- Create initial surface 57s
- Topology correction: 72s
- Surface refinement: 72s
- Reduction of surface collisions with optimization: 52s
- Spherical mapping with areal smoothing 64s
- Spherical registration 213s
- Final surface processing results:
- Average thickness (FS): 2.5241 0.6109 mm
- Surface intensity / position RMSE: 0.0683 / 0.0705
- Euler number / defect number / defect size: 20.0 / 13.0 / 0.76%
- Display thickness: /var/lib/condor/execute/dir_2391280/ds/BNU_2/sub-0025922/ses-2/surf/lh.thickness.sub-0025922_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2391280/ds/BNU_2/sub-0025922/ses-2/surf/rh.thickness.sub-0025922_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2391280/ds/BNU_2/sub-0025922/ses-2/sub-0025922_ses-2_run-1_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1266s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 11s
- ROI estimation of 'neuromorphometrics' atlas 50s
- ROI estimation of 'lpba40' atlas 18s
- ROI estimation of 'hammers' atlas 46s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 17s
- ROI estimation of 'aal3' atlas 31s
- ROI estimation of 'mori' atlas 53s
- ROI estimation of 'anatomy3' atlas 77s
- ROI estimation of 'julichbrain' atlas 102s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 43s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 81s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 158s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 224s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 18s
- Write results 19s
- 933s
- Quality check: 12s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2391280/ds/BNU_2/sub-0025922/ses-2/report/catreport_sub-0025922_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 49 minute(s) and 21 second(s).
- Image Quality Rating (IQR): 83.87% (B)
- GM volume (GMV): 50.13% (679.85 / 1356.09 ml)
- GM thickness (GMT): 2.52 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2391280/ds/BNU_2/sub-0025922/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_2391280/ds/BNU_2/sub-0025922/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_2391280/ds/BNU_2/sub-0025922/ses-2/label
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