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- CAT12.8.1 r2040: 1/1: ./sub-0025252/ses-1/sub-0025252_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 63s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 7s
- Initial correction 7s
- Refine background 3s
- Final correction 6s
- Final scaling 7s
- 43s
- Correct center-of-mass 7s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 101s
- SPM preprocessing 1 (estimate 2): 73s
- SPM preprocessing 2 (write):
- Write Segmentation 19s
- Update Segmentation 23s
- Update Skull-Stripping 46s
- Update probability maps 9s
- 96s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 34s
- Fast Optimized Shooting registration 40s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.00) 19s
- Estimate local tissue thresholds (WM) 23s
- Estimate local tissue thresholds (GM) 36s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 47s
- 134s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 5s
- Ventricle detection 22s
- Blood vessel detection 13s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.02) 32s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 4s
- 90s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 40s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.07,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 6s
- Level 1 cleanup (brain masking) 4s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 4s
- 15s
- 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 | 0.0839 0.0000 0.0839 | 32.0000
- 2 | 2.50 | 0.0810 0.0012 0.0822 | 29.4886
- 3 | 2.50 | 0.0801 0.0019 0.0820 | 26.9772
- 4 | 2.50 | 0.0797 0.0021 0.0819 | 24.6107
- 5 | 2.50 | 0.0794 0.0023 0.0817 | 22.6548
- 6 | 2.50 | 0.0791 0.0024 0.0815 | 20.6989
- 7 | 2.50 | 0.0788 0.0025 0.0813 | 18.9688
- 8 | 2.50 | 0.0785 0.0026 0.0811 | 17.4455
- 9 | 2.50 | 0.0782 0.0027 0.0809 | 15.9223
- 10 | 2.50 | 0.0779 0.0028 0.0807 | 14.6627
- 11 | 2.50 | 0.0776 0.0029 0.0805 | 13.4764
- 12 | 2.50 | 0.0772 0.0030 0.0802 | 12.3015
- 13 | 2.50 | 0.0769 0.0031 0.0800 | 11.3776
- 14 | 2.50 | 0.0766 0.0031 0.0797 | 10.4537
- 15 | 2.25 | 0.0760 0.0032 0.0793 | 9.5920
- 16 | 2.25 | 0.0731 0.0047 0.0778 | 8.8725
- 29 | 2.00 | 0.0745 0.0021 0.0766 | 3.3283
- 30 | 2.00 | 0.0681 0.0047 0.0728 | 3.1221
- 31 | 2.00 | 0.0659 0.0057 0.0716 | 2.9160
- 43 | 1.75 | 0.0649 0.0033 0.0682 | 1.5785
- 44 | 1.75 | 0.0605 0.0056 0.0661 | 1.5194
- 45 | 1.75 | 0.0589 0.0064 0.0653 | 1.4626
- 57 | 1.50 | 0.0574 0.0047 0.0621 | 1.0900
- 58 | 1.50 | 0.0543 0.0067 0.0610 | 1.0730
- 59 | 1.50 | 0.0532 0.0074 0.0606 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 213s
- Prepare output 14s
- 227s
- Jacobian determinant (RMS): 0.013 0.045 0.066 0.091 0.113 | 0.119861
- Template Matching: 0.084 0.219 0.198 0.177 0.160 | 0.159675
- Write result maps: 51s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 46s
- CSF distance: 21s
- PBT2x thickness: 65s
- 141s
- Create initial surface 119s
- Topology correction: 124s
- Surface refinement: 129s
- Reduction of surface collisions with optimization: 100s
- Spherical mapping with areal smoothing 116s
- Spherical registration 341s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 37s
- CSF distance: 21s
- PBT2x thickness: 64s
- 130s
- Create initial surface 114s
- Topology correction: 124s
- Surface refinement: 94s
- Reduction of surface collisions with optimization: 92s
- Spherical mapping with areal smoothing 115s
- Spherical registration 363s
- Final surface processing results:
- Average thickness (FS): 2.6012 0.5844 mm
- Surface intensity / position RMSE: 0.0686 / 0.0686
- Euler number / defect number / defect size: 16.0 / 8.5 / 0.68%
- Display thickness: /var/lib/condor/execute/dir_3468861/ds/UPSM_1/sub-0025252/ses-1/surf/lh.thickness.sub-0025252_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3468861/ds/UPSM_1/sub-0025252/ses-1/surf/rh.thickness.sub-0025252_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3468861/ds/UPSM_1/sub-0025252/ses-1/sub-0025252_ses-1_run-1_T1w.nii
- Surface ROI estimation: 13s
- Surface and thickness estimation takes: 2230s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 11s
- ROI estimation of 'neuromorphometrics' atlas 38s
- ROI estimation of 'lpba40' atlas 11s
- ROI estimation of 'hammers' atlas 28s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 10s
- ROI estimation of 'aal3' atlas 18s
- ROI estimation of 'mori' atlas 26s
- ROI estimation of 'anatomy3' atlas 32s
- ROI estimation of 'julichbrain' atlas 41s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 26s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 58s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 82s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s
- Write results 8s
- 409s
- Quality check: 13s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3468861/ds/UPSM_1/sub-0025252/ses-1/report/catreport_sub-0025252_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 63 minute(s) and 8 second(s).
- Image Quality Rating (IQR): 83.04% (B-)
- GM volume (GMV): 49.05% (761.60 / 1552.72 ml)
- GM thickness (GMT): 2.60 0.59 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3468861/ds/UPSM_1/sub-0025252/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_3468861/ds/UPSM_1/sub-0025252/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_3468861/ds/UPSM_1/sub-0025252/ses-1/label
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