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- CAT12.8.1 r2040: 1/1: ./sub-0025469/ses-1/sub-0025469_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 23s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 4s
- Initial correction 4s
- Refine background 2s
- Final correction 4s
- Final scaling 4s
- 27s
- Correct center-of-mass 4s
- Affine registration 6s
- SPM preprocessing 1 (estimate 1 - TPM registration): 29s
- Use previous fine affine registration. 46s
- SPM preprocessing 1 (estimate 2): 45s
- SPM preprocessing 2 (write):
- Write Segmentation 13s
- Update Segmentation 14s
- Update Skull-Stripping 30s
- Update probability maps 6s
- 63s
- Global intensity correction: 11s
- SANLM denoising after intensity normalization (medium): 19s
- Fast Optimized Shooting registration 24s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 10s
- Estimate local tissue thresholds (WM) 13s
- Estimate local tissue thresholds (GM) 19s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 33s
- 82s
- ROI segmentation (partitioning):
- Atlas -> subject space 5s
- Major structures 2s
- Ventricle detection 9s
- Blood vessel detection 7s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.04) 15s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 3s
- 45s
- 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) 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 | 0.0882 0.0000 0.0882 | 32.0000
- 2 | 2.50 | 0.0845 0.0014 0.0860 | 29.4886
- 3 | 2.50 | 0.0835 0.0022 0.0857 | 26.9772
- 4 | 2.50 | 0.0829 0.0025 0.0854 | 24.6107
- 5 | 2.50 | 0.0825 0.0026 0.0852 | 22.6548
- 6 | 2.50 | 0.0822 0.0027 0.0849 | 20.6989
- 7 | 2.50 | 0.0818 0.0028 0.0847 | 18.9688
- 8 | 2.50 | 0.0814 0.0030 0.0844 | 17.4455
- 9 | 2.50 | 0.0810 0.0030 0.0841 | 15.9223
- 10 | 2.50 | 0.0806 0.0031 0.0838 | 14.6627
- 11 | 2.50 | 0.0803 0.0032 0.0835 | 13.4764
- 12 | 2.50 | 0.0799 0.0033 0.0832 | 12.3015
- 13 | 2.50 | 0.0794 0.0034 0.0829 | 11.3776
- 14 | 2.50 | 0.0791 0.0035 0.0825 | 10.4537
- 15 | 2.25 | 0.0789 0.0036 0.0825 | 9.5920
- 16 | 2.25 | 0.0755 0.0052 0.0807 | 8.8725
- 17 | 2.25 | 0.0741 0.0058 0.0799 | 8.1530
- 29 | 2.00 | 0.0754 0.0027 0.0780 | 3.3283
- 30 | 2.00 | 0.0695 0.0051 0.0746 | 3.1221
- 31 | 2.00 | 0.0675 0.0061 0.0736 | 2.9160
- 43 | 1.75 | 0.0664 0.0035 0.0699 | 1.5785
- 44 | 1.75 | 0.0620 0.0058 0.0678 | 1.5194
- 45 | 1.75 | 0.0606 0.0066 0.0672 | 1.4626
- 57 | 1.50 | 0.0593 0.0048 0.0641 | 1.0900
- 58 | 1.50 | 0.0561 0.0069 0.0630 | 1.0730
- 59 | 1.50 | 0.0551 0.0076 0.0627 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 109s
- Prepare output 7s
- 117s
- Jacobian determinant (RMS): 0.011 0.042 0.064 0.089 0.112 | 0.119208
- Template Matching: 0.088 0.222 0.202 0.182 0.165 | 0.165278
- Write result maps: 23s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 38s
- CSF distance: 11s
- PBT2x thickness: 31s
- 85s
- Create initial surface 57s
- Topology correction: 72s
- Surface refinement: 66s
- Reduction of surface collisions with optimization: 54s
- Spherical mapping with areal smoothing 62s
- Spherical registration 184s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 24s
- CSF distance: 11s
- PBT2x thickness: 32s
- 71s
- Create initial surface 59s
- Topology correction: 74s
- Surface refinement: 76s
- Reduction of surface collisions with optimization: 56s
- Spherical mapping with areal smoothing 74s
- Spherical registration 196s
- Final surface processing results:
- Average thickness (FS): 2.4056 0.6345 mm
- Surface intensity / position RMSE: 0.0689 / 0.0746
- Euler number / defect number / defect size: 54.0 / 29.5 / 1.47%
- Display thickness: /var/lib/condor/execute/dir_2670505/ds/IACAS/sub-0025469/ses-1/surf/lh.thickness.sub-0025469_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2670505/ds/IACAS/sub-0025469/ses-1/surf/rh.thickness.sub-0025469_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2670505/ds/IACAS/sub-0025469/ses-1/sub-0025469_ses-1_run-1_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1256s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 26s
- ROI estimation of 'lpba40' atlas 7s
- ROI estimation of 'hammers' atlas 18s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 6s
- ROI estimation of 'aal3' atlas 9s
- ROI estimation of 'mori' atlas 13s
- ROI estimation of 'anatomy3' atlas 19s
- ROI estimation of 'julichbrain' atlas 25s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 10s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 17s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 39s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 59s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 5s
- Write results 6s
- 265s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2670505/ds/IACAS/sub-0025469/ses-1/report/catreport_sub-0025469_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 36 minute(s) and 34 second(s).
- Image Quality Rating (IQR): 76.71% (C+)
- GM volume (GMV): 44.47% (727.86 / 1636.72 ml)
- GM thickness (GMT): 2.41 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2670505/ds/IACAS/sub-0025469/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_2670505/ds/IACAS/sub-0025469/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_2670505/ds/IACAS/sub-0025469/ses-1/label
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