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- CAT12.8.1 r2040: 1/1: ./sub-0025345/ses-1/sub-0025345_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 33s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 6s
- Initial correction 8s
- Refine background 4s
- Final correction 7s
- Final scaling 5s
- 46s
- Correct center-of-mass 3s
- Affine registration 17s
- SPM preprocessing 1 (estimate 1 - TPM registration): 8s
- Use initial fine affine registration. 9s
- Use previous fine affine registration. 70s
- SPM preprocessing 1 (estimate 2): 67s
- SPM preprocessing 2 (write):
- Write Segmentation 20s
- Update Segmentation 21s
- Update Skull-Stripping 50s
- Update probability maps 11s
- 102s
- Global intensity correction: 20s
- SANLM denoising after intensity normalization (medium): 27s
- Fast Optimized Shooting registration 35s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 5s
- Prepare segments (LASmod = 1.00) 15s
- Estimate local tissue thresholds (WM) 22s
- Estimate local tissue thresholds (GM) 30s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 48s
- 128s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 13s
- Blood vessel detection 10s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 28s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 73s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 37s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.990.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 3s
- 12s
- 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 | 0.0798 0.0000 0.0798 | 32.0000
- 2 | 2.50 | 0.0779 0.0009 0.0789 | 29.4886
- 3 | 2.50 | 0.0774 0.0014 0.0788 | 26.9772
- 4 | 2.50 | 0.0771 0.0016 0.0787 | 24.6107
- 5 | 2.50 | 0.0768 0.0017 0.0786 | 22.6548
- 6 | 2.50 | 0.0766 0.0018 0.0784 | 20.6989
- 7 | 2.50 | 0.0764 0.0019 0.0783 | 18.9688
- 8 | 2.50 | 0.0762 0.0020 0.0782 | 17.4455
- 9 | 2.50 | 0.0760 0.0021 0.0780 | 15.9223
- 10 | 2.50 | 0.0757 0.0021 0.0779 | 14.6627
- 11 | 2.50 | 0.0755 0.0022 0.0777 | 13.4764
- 12 | 2.50 | 0.0752 0.0023 0.0775 | 12.3015
- 13 | 2.50 | 0.0750 0.0024 0.0773 | 11.3776
- 14 | 2.50 | 0.0747 0.0024 0.0771 | 10.4537
- 15 | 2.25 | 0.0732 0.0025 0.0757 | 9.5920
- 16 | 2.25 | 0.0708 0.0037 0.0745 | 8.8725
- 29 | 2.00 | 0.0720 0.0017 0.0737 | 3.3283
- 30 | 2.00 | 0.0664 0.0039 0.0703 | 3.1221
- 31 | 2.00 | 0.0644 0.0049 0.0692 | 2.9160
- 43 | 1.75 | 0.0632 0.0028 0.0660 | 1.5785
- 44 | 1.75 | 0.0591 0.0049 0.0641 | 1.5194
- 45 | 1.75 | 0.0577 0.0057 0.0635 | 1.4626
- 57 | 1.50 | 0.0562 0.0041 0.0603 | 1.0900
- 58 | 1.50 | 0.0532 0.0060 0.0593 | 1.0730
- 59 | 1.50 | 0.0522 0.0067 0.0589 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 179s
- Prepare output 12s
- 190s
- Jacobian determinant (RMS): 0.011 0.038 0.056 0.080 0.103 | 0.110338
- Template Matching: 0.080 0.212 0.193 0.173 0.157 | 0.156631
- Write result maps: 47s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 29s
- CSF distance: 15s
- PBT2x thickness: 42s
- 92s
- Create initial surface 82s
- Topology correction: 87s
- Surface refinement: 99s
- Reduction of surface collisions with optimization: 64s
- Spherical mapping with areal smoothing 74s
- Spherical registration 288s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 29s
- CSF distance: 15s
- PBT2x thickness: 41s
- 92s
- Create initial surface 83s
- Topology correction: 86s
- Surface refinement: 75s
- Reduction of surface collisions with optimization: 62s
- Spherical mapping with areal smoothing 75s
- Spherical registration 289s
- Final surface processing results:
- Average thickness (FS): 2.6288 0.6224 mm
- Surface intensity / position RMSE: 0.0653 / 0.0608
- Euler number / defect number / defect size: 8.0 / 9.5 / 0.08%
- Display thickness: /var/lib/condor/execute/dir_2613028/ds/LMU_1/sub-0025345/ses-1/surf/lh.thickness.sub-0025345_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2613028/ds/LMU_1/sub-0025345/ses-1/surf/rh.thickness.sub-0025345_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2613028/ds/LMU_1/sub-0025345/ses-1/sub-0025345_ses-1_run-1_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1648s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 11s
- ROI estimation of 'neuromorphometrics' atlas 41s
- ROI estimation of 'lpba40' atlas 12s
- ROI estimation of 'hammers' atlas 30s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 11s
- ROI estimation of 'aal3' atlas 18s
- ROI estimation of 'mori' atlas 26s
- ROI estimation of 'anatomy3' atlas 50s
- ROI estimation of 'julichbrain' atlas 81s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 32s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 57s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 114s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 179s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 16s
- Write results 18s
- 682s
- Quality check: 16s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2613028/ds/LMU_1/sub-0025345/ses-1/report/catreport_sub-0025345_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 56 minute(s) and 7 second(s).
- Image Quality Rating (IQR): 75.99% (C)
- GM volume (GMV): 49.99% (690.34 / 1380.97 ml)
- GM thickness (GMT): 2.63 0.62 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2613028/ds/LMU_1/sub-0025345/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_2613028/ds/LMU_1/sub-0025345/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_2613028/ds/LMU_1/sub-0025345/ses-1/label
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