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- CAT12.8.1 r1980: 1/1: ./condor/execute/dir_22601/ds/sub-35/sub-35_T1w.n
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- SANLM denoising (medium): 150s
- APP: Rough bias correction:
- Initialize 14s
- Estimate background 12s
- Initial correction 12s
- Refine background 7s
- Final correction 11s
- Final scaling 12s
- 82s
- Correct center-of-mass 6s
- Affine registration 15s
- SPM preprocessing 1 (estimate 1 - TPM registration): 155s
- SPM preprocessing 1 (estimate 2): 90s
- SPM preprocessing 2 (write):
- Write Segmentation 36s
- Update Segmentation 40s
- Update Skull-Stripping 86s
- Update probability maps 18s
- 180s
- Global intensity correction: 35s
- SANLM denoising after intensity normalization (medium): 29s
- Fast Optimized Shooting registration 55s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 10s
- Prepare partitions 5s
- Prepare segments (LASmod = 1.09) 30s
- Estimate local tissue thresholds (WM) 35s
- Estimate local tissue thresholds (GM) 49s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 63s
- 198s
- ROI segmentation (partitioning):
- Atlas -> subject space 18s
- Major structures 8s
- Ventricle detection 25s
- Blood vessel detection 20s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 55s
- Manual stroke lesion detection 0s
- Closing of deep structures 4s
- Side alignment 8s
- Final corrections 9s
- 147s
- Blood vessel correction (BVCstr=0.50): 3s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 74s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 9s
- Level 1 cleanup (brain masking) 5s
- Level 2 cleanup (CSF correction) 3s
- Level 3 cleanup (CSF/WM PVE) 5s
- 22s
- 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 | 0.0844 0.0000 0.0844 | 32.0000
- 2 | 2.50 | 0.0806 0.0015 0.0821 | 29.4886
- 3 | 2.50 | 0.0795 0.0023 0.0818 | 26.9772
- 4 | 2.50 | 0.0790 0.0026 0.0816 | 24.6107
- 5 | 2.50 | 0.0785 0.0028 0.0814 | 22.6548
- 6 | 2.50 | 0.0782 0.0029 0.0811 | 20.6989
- 7 | 2.50 | 0.0778 0.0031 0.0808 | 18.9688
- 8 | 2.50 | 0.0774 0.0032 0.0806 | 17.4455
- 9 | 2.50 | 0.0770 0.0033 0.0802 | 15.9223
- 10 | 2.50 | 0.0765 0.0034 0.0799 | 14.6627
- 11 | 2.50 | 0.0761 0.0035 0.0796 | 13.4764
- 12 | 2.50 | 0.0757 0.0036 0.0793 | 12.3015
- 13 | 2.50 | 0.0752 0.0037 0.0789 | 11.3776
- 14 | 2.50 | 0.0748 0.0038 0.0786 | 10.4537
- 15 | 2.25 | 0.0738 0.0039 0.0778 | 9.5920
- 16 | 2.25 | 0.0702 0.0057 0.0759 | 8.8725
- 29 | 2.00 | 0.0705 0.0026 0.0730 | 3.3283
- 30 | 2.00 | 0.0643 0.0050 0.0693 | 3.1221
- 31 | 2.00 | 0.0621 0.0060 0.0681 | 2.9160
- 43 | 1.75 | 0.0608 0.0035 0.0643 | 1.5785
- 44 | 1.75 | 0.0569 0.0055 0.0624 | 1.5194
- 45 | 1.75 | 0.0556 0.0062 0.0618 | 1.4626
- 57 | 1.50 | 0.0540 0.0045 0.0585 | 1.0900
- 58 | 1.50 | 0.0512 0.0063 0.0575 | 1.0730
- 59 | 1.50 | 0.0503 0.0069 0.0572 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 224s
- Prepare output 17s
- 241s
- Jacobian determinant (RMS): 0.014 0.050 0.073 0.096 0.115 | 0.120866
- Template Matching: 0.084 0.211 0.186 0.167 0.151 | 0.150848
- Write result maps: 51s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 33s
- CSF distance: 18s
- PBT2x thickness: 54s
- 113s
- Create initial surface 84s
- Topology correction: 106s
- Surface refinement: 74s
- Reduction of surface collisions with optimization: 85s
- Spherical mapping with areal smoothing 95s
- Spherical registration 258s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 35s
- CSF distance: 17s
- PBT2x thickness: 53s
- 113s
- Create initial surface 82s
- Topology correction: 107s
- Surface refinement: 86s
- Reduction of surface collisions with optimization: 83s
- Spherical mapping with areal smoothing 94s
- Spherical registration 252s
- Final surface processing results:
- Average thickness (FS): 2.5290 0.5953 mm
- Surface intensity / position RMSE: 0.0679 / 0.0657
- Euler number / defect number / defect size: 8.0 / 10.5 / 0.40%
- Display thickness: /var/lib/condor/execute/dir_22601/ds/sub-35/surf/lh.thickness.sub-35_T1w
- Display thickness: /var/lib/condor/execute/dir_22601/ds/sub-35/surf/rh.thickness.sub-35_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_22601/ds/sub-35/sub-35_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1768s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 24s
- ROI estimation of 'neuromorphometrics' atlas 89s
- ROI estimation of 'lpba40' atlas 26s
- ROI estimation of 'hammers' atlas 63s
- ROI estimation of 'thalamus' atlas 5s
- ROI estimation of 'ibsr' atlas 22s
- ROI estimation of 'aal3' atlas 36s
- ROI estimation of 'mori' atlas 54s
- ROI estimation of 'anatomy3' atlas 78s
- ROI estimation of 'julichbrain' atlas 103s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 38s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 48s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 165s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 247s
- Write results 249s
- 998s
- Quality check: 9s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_22601/ds/sub-35/report/catreport_sub-35_T1w.pdf
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- CAT preprocessing takes 74 minute(s) and 55 second(s).
- Image Quality Rating (IQR): 86.61% (B)
- GM volume (GMV): 49.64% (667.54 / 1344.78 ml)
- GM thickness (GMT): 2.53 0.60 mm
- Segmentations are saved in /var/lib/condor/execute/dir_22601/ds/sub-35/mri
- Reports are saved in /var/lib/condor/execute/dir_22601/ds/sub-35/report
- Labels are saved in /var/lib/condor/execute/dir_22601/ds/sub-35/label
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