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- CAT12.8.1 r2040: 1/1: ./sub-0025764/ses-2/sub-0025764_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 56s
- APP: Rough bias correction:
- Initialize 4s
- 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): 47s
- SPM preprocessing 1 (estimate 2): 41s
- SPM preprocessing 2 (write):
- Write Segmentation 12s
- Update Segmentation 13s
- Update Skull-Stripping 32s
- Update probability maps 6s
- 63s
- Global intensity correction: 10s
- SANLM denoising after intensity normalization (medium): 20s
- Fast Optimized Shooting registration 22s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 2s
- Prepare partitions 1s
- Prepare segments (LASmod = 1.10) 10s
- Estimate local tissue thresholds (WM) 12s
- Estimate local tissue thresholds (GM) 17s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 31s
- 77s
- ROI segmentation (partitioning):
- Atlas -> subject space 5s
- Major structures 2s
- Ventricle detection 7s
- Blood vessel detection 6s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.08) 14s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 3s
- 41s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 23s
- 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
- 7s
- 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 | 0.0884 0.0000 0.0884 | 32.0000
- 2 | 2.50 | 0.0855 0.0013 0.0868 | 29.4886
- 3 | 2.50 | 0.0847 0.0019 0.0866 | 26.9772
- 4 | 2.50 | 0.0843 0.0021 0.0864 | 24.6107
- 5 | 2.50 | 0.0839 0.0023 0.0862 | 22.6548
- 6 | 2.50 | 0.0836 0.0024 0.0860 | 20.6989
- 7 | 2.50 | 0.0833 0.0024 0.0858 | 18.9688
- 8 | 2.50 | 0.0830 0.0025 0.0856 | 17.4455
- 9 | 2.50 | 0.0827 0.0026 0.0853 | 15.9223
- 10 | 2.50 | 0.0824 0.0027 0.0851 | 14.6627
- 11 | 2.50 | 0.0821 0.0028 0.0848 | 13.4764
- 12 | 2.50 | 0.0817 0.0028 0.0846 | 12.3015
- 13 | 2.50 | 0.0814 0.0029 0.0843 | 11.3776
- 14 | 2.50 | 0.0810 0.0030 0.0840 | 10.4537
- 15 | 2.25 | 0.0817 0.0031 0.0848 | 9.5920
- 16 | 2.25 | 0.0785 0.0046 0.0832 | 8.8725
- 17 | 2.25 | 0.0772 0.0052 0.0824 | 8.1530
- 18 | 2.25 | 0.0764 0.0054 0.0819 | 7.5234
- 19 | 2.25 | 0.0758 0.0055 0.0814 | 6.9630
- 20 | 2.25 | 0.0753 0.0056 0.0808 | 6.4027
- 21 | 2.25 | 0.0748 0.0056 0.0804 | 5.9447
- 29 | 2.00 | 0.0775 0.0033 0.0808 | 3.3283
- 30 | 2.00 | 0.0729 0.0054 0.0784 | 3.1221
- 31 | 2.00 | 0.0713 0.0062 0.0776 | 2.9160
- 43 | 1.75 | 0.0710 0.0035 0.0745 | 1.5785
- 44 | 1.75 | 0.0662 0.0061 0.0723 | 1.5194
- 45 | 1.75 | 0.0646 0.0070 0.0716 | 1.4626
- 57 | 1.50 | 0.0635 0.0051 0.0686 | 1.0900
- 58 | 1.50 | 0.0598 0.0075 0.0674 | 1.0730
- 59 | 1.50 | 0.0586 0.0082 0.0669 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 114s
- Prepare output 7s
- 120s
- Jacobian determinant (RMS): 0.010 0.037 0.061 0.085 0.114 | 0.117767
- Template Matching: 0.088 0.224 0.214 0.194 0.176 | 0.175913
- Write result maps: 23s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 24s
- CSF distance: 10s
- PBT2x thickness: 30s
- 68s
- Create initial surface 53s
- Topology correction: 66s
- Surface refinement: 58s
- Reduction of surface collisions with optimization: 49s
- Spherical mapping with areal smoothing 60s
- Spherical registration 176s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 20s
- CSF distance: 11s
- PBT2x thickness: 30s
- 64s
- Create initial surface 52s
- Topology correction: 66s
- Surface refinement: 60s
- Reduction of surface collisions with optimization: 49s
- Spherical mapping with areal smoothing 58s
- Spherical registration 188s
- Final surface processing results:
- Average thickness (FS): 2.5263 0.6743 mm
- Surface intensity / position RMSE: 0.0695 / 0.0742
- Euler number / defect number / defect size: 18.0 / 12.0 / 1.09%
- Display thickness: /var/lib/condor/execute/dir_2199173/ds/SWU_4/sub-0025764/ses-2/surf/lh.thickness.sub-0025764_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2199173/ds/SWU_4/sub-0025764/ses-2/surf/rh.thickness.sub-0025764_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2199173/ds/SWU_4/sub-0025764/ses-2/sub-0025764_ses-2_run-1_T1w.nii
- Surface ROI estimation: 6s
- Surface and thickness estimation takes: 1133s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 6s
- ROI estimation of 'neuromorphometrics' atlas 22s
- ROI estimation of 'lpba40' atlas 6s
- ROI estimation of 'hammers' atlas 15s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 5s
- ROI estimation of 'aal3' atlas 9s
- ROI estimation of 'mori' atlas 13s
- ROI estimation of 'anatomy3' atlas 18s
- ROI estimation of 'julichbrain' atlas 24s
- 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
- 251s
- Quality check: 7s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2199173/ds/SWU_4/sub-0025764/ses-2/report/catreport_sub-0025764_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 35 minute(s) and 20 second(s).
- Image Quality Rating (IQR): 81.65% (B-)
- GM volume (GMV): 48.17% (730.73 / 1516.87 ml)
- GM thickness (GMT): 2.53 0.67 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2199173/ds/SWU_4/sub-0025764/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_2199173/ds/SWU_4/sub-0025764/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_2199173/ds/SWU_4/sub-0025764/ses-2/label
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