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- CAT12.8.1 r2040: 1/1: ./sub-0025460/ses-2/sub-0025460_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 25s
- 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 2s
- Affine registration 9s
- SPM preprocessing 1 (estimate 1 - TPM registration): 67s
- SPM preprocessing 1 (estimate 2): 63s
- SPM preprocessing 2 (write):
- Write Segmentation 14s
- Update Segmentation 16s
- Update Skull-Stripping 36s
- Update probability maps 8s
- 74s
- Global intensity correction: 13s
- SANLM denoising after intensity normalization (medium): 20s
- Fast Optimized Shooting registration 26s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 11s
- Estimate local tissue thresholds (WM) 15s
- Estimate local tissue thresholds (GM) 20s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 36s
- 90s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 3s
- Ventricle detection 8s
- Blood vessel detection 7s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.09) 17s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 49s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 29s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- 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
- 9s
- 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 | 0.0914 0.0000 0.0914 | 32.0000
- 2 | 2.50 | 0.0875 0.0016 0.0891 | 29.4886
- 3 | 2.50 | 0.0863 0.0025 0.0887 | 26.9772
- 4 | 2.50 | 0.0857 0.0028 0.0885 | 24.6107
- 5 | 2.50 | 0.0852 0.0030 0.0882 | 22.6548
- 6 | 2.50 | 0.0848 0.0031 0.0880 | 20.6989
- 7 | 2.50 | 0.0844 0.0033 0.0877 | 18.9688
- 8 | 2.50 | 0.0840 0.0034 0.0874 | 17.4455
- 9 | 2.50 | 0.0835 0.0036 0.0871 | 15.9223
- 10 | 2.50 | 0.0830 0.0037 0.0867 | 14.6627
- 11 | 2.50 | 0.0826 0.0038 0.0864 | 13.4764
- 12 | 2.50 | 0.0821 0.0039 0.0860 | 12.3015
- 13 | 2.50 | 0.0816 0.0041 0.0857 | 11.3776
- 14 | 2.50 | 0.0811 0.0042 0.0853 | 10.4537
- 15 | 2.25 | 0.0832 0.0043 0.0875 | 9.5920
- 16 | 2.25 | 0.0789 0.0065 0.0854 | 8.8725
- 17 | 2.25 | 0.0771 0.0073 0.0844 | 8.1530
- 18 | 2.25 | 0.0760 0.0076 0.0836 | 7.5234
- 19 | 2.25 | 0.0751 0.0078 0.0829 | 6.9630
- 20 | 2.25 | 0.0744 0.0078 0.0822 | 6.4027
- 29 | 2.00 | 0.0766 0.0043 0.0810 | 3.3283
- 30 | 2.00 | 0.0711 0.0069 0.0780 | 3.1221
- 31 | 2.00 | 0.0691 0.0078 0.0769 | 2.9160
- 43 | 1.75 | 0.0682 0.0044 0.0727 | 1.5785
- 44 | 1.75 | 0.0634 0.0070 0.0704 | 1.5194
- 45 | 1.75 | 0.0618 0.0079 0.0696 | 1.4626
- 57 | 1.50 | 0.0607 0.0058 0.0665 | 1.0900
- 58 | 1.50 | 0.0572 0.0081 0.0653 | 1.0730
- 59 | 1.50 | 0.0560 0.0088 0.0648 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 141s
- Prepare output 8s
- 149s
- Jacobian determinant (RMS): 0.011 0.045 0.074 0.099 0.124 | 0.131103
- Template Matching: 0.091 0.223 0.207 0.185 0.168 | 0.167941
- Write result maps: 32s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 51s
- CSF distance: 12s
- PBT2x thickness: 34s
- 102s
- Create initial surface 64s
- Topology correction: 77s
- Surface refinement: 74s
- Reduction of surface collisions with optimization: 56s
- Spherical mapping with areal smoothing 65s
- Spherical registration 225s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 24s
- CSF distance: 12s
- PBT2x thickness: 33s
- 74s
- Create initial surface 63s
- Topology correction: 78s
- Surface refinement: 85s
- Reduction of surface collisions with optimization: 60s
- Spherical mapping with areal smoothing 85s
- Spherical registration 250s
- Final surface processing results:
- Average thickness (FS): 2.3105 0.6865 mm
- Surface intensity / position RMSE: 0.0747 / 0.0893
- Euler number / defect number / defect size: 32.0 / 30.0 / 1.38%
- Display thickness: /var/lib/condor/execute/dir_578326/ds/IACAS/sub-0025460/ses-2/surf/lh.thickness.sub-0025460_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_578326/ds/IACAS/sub-0025460/ses-2/surf/rh.thickness.sub-0025460_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_578326/ds/IACAS/sub-0025460/ses-2/sub-0025460_ses-2_run-1_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 1444s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 25s
- ROI estimation of 'neuromorphometrics' atlas 91s
- ROI estimation of 'lpba40' atlas 24s
- ROI estimation of 'hammers' atlas 62s
- ROI estimation of 'thalamus' atlas 5s
- ROI estimation of 'ibsr' atlas 21s
- ROI estimation of 'aal3' atlas 35s
- ROI estimation of 'mori' atlas 48s
- ROI estimation of 'anatomy3' atlas 69s
- ROI estimation of 'julichbrain' atlas 88s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 33s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 62s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 103s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 127s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s
- Write results 9s
- 803s
- Quality check: 10s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_578326/ds/IACAS/sub-0025460/ses-2/report/catreport_sub-0025460_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 50 minute(s) and 53 second(s).
- Image Quality Rating (IQR): 79.80% (C+)
- GM volume (GMV): 44.43% (706.91 / 1591.13 ml)
- GM thickness (GMT): 2.31 0.69 mm
- Segmentations are saved in /var/lib/condor/execute/dir_578326/ds/IACAS/sub-0025460/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_578326/ds/IACAS/sub-0025460/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_578326/ds/IACAS/sub-0025460/ses-2/label
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