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- CAT12.8.1 r2040: 1/1: ./sub-0025375/ses-1/sub-0025375_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 36s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 5s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 36s
- Correct center-of-mass 4s
- Affine registration 9s
- SPM preprocessing 1 (estimate 1 - TPM registration): 12s
- Use initial fine affine registration. 68s
- SPM preprocessing 1 (estimate 2): 98s
- SPM preprocessing 2 (write):
- Write Segmentation 16s
- Update Segmentation 18s
- Update Skull-Stripping 38s
- Update probability maps 8s
- 80s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 21s
- Fast Optimized Shooting registration 41s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.16) 12s
- Estimate local tissue thresholds (WM) 16s
- Estimate local tissue thresholds (GM) 22s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 37s
- 97s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 3s
- Ventricle detection 11s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.10) 21s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 59s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 25s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- 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) 2s
- 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 | 0.0862 0.0000 0.0862 | 32.0000
- 2 | 2.50 | 0.0834 0.0013 0.0847 | 29.4886
- 3 | 2.50 | 0.0826 0.0019 0.0845 | 26.9772
- 4 | 2.50 | 0.0822 0.0021 0.0843 | 24.6107
- 5 | 2.50 | 0.0819 0.0023 0.0842 | 22.6548
- 6 | 2.50 | 0.0816 0.0024 0.0840 | 20.6989
- 7 | 2.50 | 0.0813 0.0025 0.0838 | 18.9688
- 8 | 2.50 | 0.0810 0.0026 0.0836 | 17.4455
- 9 | 2.50 | 0.0806 0.0027 0.0834 | 15.9223
- 10 | 2.50 | 0.0803 0.0028 0.0831 | 14.6627
- 11 | 2.50 | 0.0800 0.0029 0.0829 | 13.4764
- 12 | 2.50 | 0.0796 0.0030 0.0826 | 12.3015
- 13 | 2.50 | 0.0792 0.0031 0.0824 | 11.3776
- 14 | 2.50 | 0.0789 0.0032 0.0821 | 10.4537
- 15 | 2.25 | 0.0783 0.0033 0.0816 | 9.5920
- 16 | 2.25 | 0.0749 0.0049 0.0798 | 8.8725
- 29 | 2.00 | 0.0755 0.0022 0.0778 | 3.3283
- 30 | 2.00 | 0.0689 0.0049 0.0738 | 3.1221
- 31 | 2.00 | 0.0667 0.0060 0.0727 | 2.9160
- 43 | 1.75 | 0.0652 0.0035 0.0687 | 1.5785
- 44 | 1.75 | 0.0610 0.0057 0.0667 | 1.5194
- 45 | 1.75 | 0.0596 0.0065 0.0661 | 1.4626
- 57 | 1.50 | 0.0579 0.0048 0.0627 | 1.0900
- 58 | 1.50 | 0.0550 0.0067 0.0616 | 1.0730
- 59 | 1.50 | 0.0540 0.0073 0.0613 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 224s
- Prepare output 10s
- 235s
- Jacobian determinant (RMS): 0.012 0.044 0.068 0.096 0.119 | 0.126546
- Template Matching: 0.086 0.225 0.200 0.179 0.162 | 0.162054
- Write result maps: 43s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 30s
- CSF distance: 14s
- PBT2x thickness: 41s
- 91s
- Create initial surface 73s
- Topology correction: 66s
- Surface refinement: 50s
- Reduction of surface collisions with optimization: 45s
- Spherical mapping with areal smoothing 73s
- Spherical registration 271s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 24s
- CSF distance: 14s
- PBT2x thickness: 40s
- 84s
- Create initial surface 70s
- Topology correction: 66s
- Surface refinement: 78s
- Reduction of surface collisions with optimization: 43s
- Spherical mapping with areal smoothing 73s
- Spherical registration 272s
- Final surface processing results:
- Average thickness (FS): 2.4364 0.6848 mm
- Surface intensity / position RMSE: 0.0670 / 0.0709
- Euler number / defect number / defect size: 16.0 / 15.5 / 0.91%
- Display thickness: /var/lib/condor/execute/dir_2292915/ds/LMU_2/sub-0025375/ses-1/surf/lh.thickness.sub-0025375_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2292915/ds/LMU_2/sub-0025375/ses-1/surf/rh.thickness.sub-0025375_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2292915/ds/LMU_2/sub-0025375/ses-1/sub-0025375_ses-1_run-1_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1440s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 12s
- ROI estimation of 'neuromorphometrics' atlas 46s
- ROI estimation of 'lpba40' atlas 13s
- ROI estimation of 'hammers' atlas 32s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 11s
- ROI estimation of 'aal3' atlas 19s
- ROI estimation of 'mori' atlas 29s
- ROI estimation of 'anatomy3' atlas 41s
- ROI estimation of 'julichbrain' atlas 54s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 20s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 28s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 88s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 136s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 10s
- Write results 11s
- 545s
- Quality check: 12s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2292915/ds/LMU_2/sub-0025375/ses-1/report/catreport_sub-0025375_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 49 minute(s) and 48 second(s).
- Image Quality Rating (IQR): 75.02% (C)
- GM volume (GMV): 46.04% (539.61 / 1172.09 ml)
- GM thickness (GMT): 2.44 0.68 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2292915/ds/LMU_2/sub-0025375/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_2292915/ds/LMU_2/sub-0025375/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_2292915/ds/LMU_2/sub-0025375/ses-1/label
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