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- CAT12.8.1 r2040: 1/1: ./sub-0027250/ses-1/sub-0027250_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 53s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 7s
- Initial correction 7s
- Refine background 4s
- Final correction 5s
- Final scaling 5s
- 43s
- Correct center-of-mass 5s
- Affine registration 13s
- SPM preprocessing 1 (estimate 1 - TPM registration): 15s
- Use initial fine affine registration. 71s
- SPM preprocessing 1 (estimate 2): 60s
- SPM preprocessing 2 (write):
- Write Segmentation 20s
- Update Segmentation 20s
- Update Skull-Stripping 47s
- Update probability maps 10s
- 96s
- Global intensity correction: 19s
- SANLM denoising after intensity normalization (medium): 29s
- Fast Optimized Shooting registration 38s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 15s
- Estimate local tissue thresholds (WM) 21s
- Estimate local tissue thresholds (GM) 32s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 49s
- 127s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 3s
- Ventricle detection 13s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.08) 23s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 3s
- Final corrections 5s
- 67s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 36s
- AMAP peaks: [CSF,GM,WM] = [0.370.05,0.680.08,0.990.05]
- 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 | 0.0876 0.0000 0.0876 | 32.0000
- 2 | 2.50 | 0.0844 0.0013 0.0858 | 29.4886
- 3 | 2.50 | 0.0835 0.0020 0.0855 | 26.9772
- 4 | 2.50 | 0.0830 0.0023 0.0853 | 24.6107
- 5 | 2.50 | 0.0827 0.0025 0.0851 | 22.6548
- 6 | 2.50 | 0.0824 0.0026 0.0849 | 20.6989
- 7 | 2.50 | 0.0820 0.0027 0.0847 | 18.9688
- 8 | 2.50 | 0.0817 0.0028 0.0845 | 17.4455
- 9 | 2.50 | 0.0813 0.0029 0.0842 | 15.9223
- 10 | 2.50 | 0.0810 0.0030 0.0840 | 14.6627
- 11 | 2.50 | 0.0806 0.0031 0.0837 | 13.4764
- 12 | 2.50 | 0.0802 0.0032 0.0834 | 12.3015
- 13 | 2.50 | 0.0798 0.0033 0.0832 | 11.3776
- 14 | 2.50 | 0.0795 0.0034 0.0829 | 10.4537
- 15 | 2.25 | 0.0794 0.0035 0.0829 | 9.5920
- 16 | 2.25 | 0.0760 0.0052 0.0812 | 8.8725
- 17 | 2.25 | 0.0746 0.0058 0.0804 | 8.1530
- 29 | 2.00 | 0.0764 0.0027 0.0791 | 3.3283
- 30 | 2.00 | 0.0700 0.0054 0.0754 | 3.1221
- 31 | 2.00 | 0.0677 0.0065 0.0742 | 2.9160
- 43 | 1.75 | 0.0664 0.0037 0.0702 | 1.5785
- 44 | 1.75 | 0.0616 0.0063 0.0679 | 1.5194
- 45 | 1.75 | 0.0600 0.0071 0.0671 | 1.4626
- 57 | 1.50 | 0.0583 0.0052 0.0636 | 1.0900
- 58 | 1.50 | 0.0550 0.0074 0.0624 | 1.0730
- 59 | 1.50 | 0.0540 0.0080 0.0620 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 196s
- Prepare output 13s
- 209s
- Jacobian determinant (RMS): 0.012 0.045 0.069 0.096 0.120 | 0.126214
- Template Matching: 0.088 0.224 0.203 0.180 0.162 | 0.161856
- Write result maps: 39s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 36s
- CSF distance: 17s
- PBT2x thickness: 50s
- 109s
- Create initial surface 91s
- Topology correction: 86s
- Surface refinement: 100s
- Reduction of surface collisions with optimization: 62s
- Spherical mapping with areal smoothing 93s
- Spherical registration 363s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 30s
- CSF distance: 17s
- PBT2x thickness: 50s
- 104s
- Create initial surface 89s
- Topology correction: 84s
- Surface refinement: 99s
- Reduction of surface collisions with optimization: 60s
- Spherical mapping with areal smoothing 85s
- Spherical registration 357s
- Final surface processing results:
- Average thickness (FS): 2.5477 0.6622 mm
- Surface intensity / position RMSE: 0.0603 / 0.0605
- Euler number / defect number / defect size: 8.0 / 6.5 / 0.15%
- Display thickness: /var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-1/surf/lh.thickness.sub-0027250_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-1/surf/rh.thickness.sub-0027250_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-1/sub-0027250_ses-1_run-1_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 1881s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 10s
- ROI estimation of 'neuromorphometrics' atlas 35s
- ROI estimation of 'lpba40' atlas 10s
- ROI estimation of 'hammers' atlas 24s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 9s
- ROI estimation of 'aal3' atlas 14s
- ROI estimation of 'mori' atlas 21s
- ROI estimation of 'anatomy3' atlas 29s
- ROI estimation of 'julichbrain' atlas 40s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 16s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 27s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 63s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 94s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s
- Write results 9s
- 402s
- Quality check: 13s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-1/report/catreport_sub-0027250_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 55 minute(s) and 6 second(s).
- Image Quality Rating (IQR): 85.77% (B)
- GM volume (GMV): 46.23% (593.46 / 1283.73 ml)
- GM thickness (GMT): 2.55 0.66 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-1/label
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