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- CAT12.8.1 r2040: 1/1: ./sub-0025348/ses-1/sub-0025348_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 35s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 5s
- Initial correction 6s
- Refine background 3s
- Final correction 4s
- Final scaling 4s
- 33s
- Correct center-of-mass 2s
- Affine registration 13s
- SPM preprocessing 1 (estimate 1 - TPM registration): 77s
- SPM preprocessing 1 (estimate 2): 67s
- SPM preprocessing 2 (write):
- Write Segmentation 16s
- Update Segmentation 19s
- Update Skull-Stripping 41s
- Update probability maps 9s
- 85s
- Global intensity correction: 14s
- SANLM denoising after intensity normalization (medium): 23s
- Fast Optimized Shooting registration 27s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 13s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 24s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 38s
- 101s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 12s
- Blood vessel detection 9s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 21s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 60s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 33s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 3s
- 10s
- 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 | 0.0806 0.0000 0.0806 | 32.0000
- 2 | 2.50 | 0.0776 0.0013 0.0789 | 29.4886
- 3 | 2.50 | 0.0768 0.0019 0.0787 | 26.9772
- 4 | 2.50 | 0.0764 0.0021 0.0785 | 24.6107
- 5 | 2.50 | 0.0761 0.0022 0.0784 | 22.6548
- 6 | 2.50 | 0.0758 0.0023 0.0782 | 20.6989
- 7 | 2.50 | 0.0756 0.0024 0.0780 | 18.9688
- 8 | 2.50 | 0.0753 0.0025 0.0778 | 17.4455
- 9 | 2.50 | 0.0750 0.0026 0.0775 | 15.9223
- 10 | 2.50 | 0.0747 0.0027 0.0773 | 14.6627
- 11 | 2.50 | 0.0744 0.0027 0.0771 | 13.4764
- 12 | 2.50 | 0.0741 0.0028 0.0768 | 12.3015
- 13 | 2.50 | 0.0737 0.0029 0.0766 | 11.3776
- 14 | 2.50 | 0.0734 0.0029 0.0763 | 10.4537
- 15 | 2.25 | 0.0714 0.0030 0.0744 | 9.5920
- 16 | 2.25 | 0.0686 0.0043 0.0730 | 8.8725
- 29 | 2.00 | 0.0692 0.0019 0.0712 | 3.3283
- 30 | 2.00 | 0.0638 0.0041 0.0680 | 3.1221
- 31 | 2.00 | 0.0621 0.0050 0.0671 | 2.9160
- 43 | 1.75 | 0.0611 0.0029 0.0639 | 1.5785
- 44 | 1.75 | 0.0573 0.0049 0.0621 | 1.5194
- 45 | 1.75 | 0.0560 0.0056 0.0616 | 1.4626
- 57 | 1.50 | 0.0545 0.0041 0.0585 | 1.0900
- 58 | 1.50 | 0.0517 0.0058 0.0576 | 1.0730
- Shooting registration with 2.50:-0.25:1.50 mm takes: 113s
- Prepare output 9s
- 122s
- Jacobian determinant (RMS): 0.010 0.038 0.056 0.078 0.100 | 0.104290
- Template Matching: 0.081 0.206 0.186 0.168 0.155 | 0.155138
- Write result maps: 34s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 27s
- CSF distance: 12s
- PBT2x thickness: 35s
- 79s
- Create initial surface 64s
- Topology correction: 76s
- Surface refinement: 78s
- Reduction of surface collisions with optimization: 57s
- Spherical mapping with areal smoothing 66s
- Spherical registration 203s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 24s
- CSF distance: 12s
- PBT2x thickness: 35s
- 76s
- Create initial surface 63s
- Topology correction: 76s
- Surface refinement: 82s
- Reduction of surface collisions with optimization: 53s
- Spherical mapping with areal smoothing 85s
- Spherical registration 236s
- Final surface processing results:
- Average thickness (FS): 2.6209 0.6184 mm
- Surface intensity / position RMSE: 0.0731 / 0.0741
- Euler number / defect number / defect size: 20.0 / 15.5 / 0.39%
- Display thickness: /var/lib/condor/execute/dir_541888/ds/LMU_1/sub-0025348/ses-1/surf/lh.thickness.sub-0025348_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_541888/ds/LMU_1/sub-0025348/ses-1/surf/rh.thickness.sub-0025348_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_541888/ds/LMU_1/sub-0025348/ses-1/sub-0025348_ses-1_run-1_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1381s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 16s
- ROI estimation of 'neuromorphometrics' atlas 57s
- ROI estimation of 'lpba40' atlas 16s
- ROI estimation of 'hammers' atlas 35s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 12s
- ROI estimation of 'aal3' atlas 20s
- ROI estimation of 'mori' atlas 25s
- ROI estimation of 'anatomy3' atlas 37s
- ROI estimation of 'julichbrain' atlas 44s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 19s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 36s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 90s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 127s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 11s
- Write results 11s
- 548s
- Quality check: 11s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_541888/ds/LMU_1/sub-0025348/ses-1/report/catreport_sub-0025348_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 46 minute(s) and 10 second(s).
- Image Quality Rating (IQR): 77.62% (C+)
- GM volume (GMV): 50.61% (810.20 / 1601.02 ml)
- GM thickness (GMT): 2.62 0.62 mm
- Segmentations are saved in /var/lib/condor/execute/dir_541888/ds/LMU_1/sub-0025348/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_541888/ds/LMU_1/sub-0025348/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_541888/ds/LMU_1/sub-0025348/ses-1/label
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