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- CAT12.8.1 r1980: 1/1: ./condor/execute/dir_26305/ds/sub-74/sub-74_T1w.n
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- SANLM denoising (medium): 56s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 10s
- Initial correction 7s
- Refine background 4s
- Final correction 6s
- Final scaling 7s
- 47s
- Correct center-of-mass 3s
- Affine registration 9s
- SPM preprocessing 1 (estimate 1 - TPM registration): 7s
- Use initial fine affine registration. 55s
- SPM preprocessing 1 (estimate 2): 56s
- SPM preprocessing 2 (write):
- Write Segmentation 16s
- Update Segmentation 17s
- Update Skull-Stripping 39s
- Update probability maps 9s
- 81s
- Global intensity correction: 15s
- SANLM denoising after intensity normalization (medium): 13s
- Fast Optimized Shooting registration 33s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.34) 12s
- Estimate local tissue thresholds (WM) 16s
- Estimate local tissue thresholds (GM) 20s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 30s
- 88s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 13s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.48 > WMHCstr'=0.00) 23s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 62s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 32s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.24):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 10s
- 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 | 0.0821 0.0000 0.0821 | 32.0000
- 2 | 2.50 | 0.0803 0.0009 0.0812 | 29.4886
- 3 | 2.50 | 0.0798 0.0014 0.0811 | 26.9772
- 4 | 2.50 | 0.0795 0.0015 0.0811 | 24.6107
- 5 | 2.50 | 0.0793 0.0016 0.0810 | 22.6548
- 6 | 2.50 | 0.0791 0.0017 0.0808 | 20.6989
- 7 | 2.50 | 0.0789 0.0018 0.0807 | 18.9688
- 8 | 2.50 | 0.0787 0.0019 0.0806 | 17.4455
- 9 | 2.50 | 0.0785 0.0019 0.0804 | 15.9223
- 10 | 2.50 | 0.0783 0.0020 0.0803 | 14.6627
- 11 | 2.50 | 0.0781 0.0021 0.0801 | 13.4764
- 12 | 2.50 | 0.0779 0.0021 0.0800 | 12.3015
- 13 | 2.50 | 0.0776 0.0022 0.0798 | 11.3776
- 14 | 2.50 | 0.0774 0.0023 0.0796 | 10.4537
- 15 | 2.25 | 0.0764 0.0023 0.0787 | 9.5920
- 16 | 2.25 | 0.0739 0.0036 0.0774 | 8.8725
- 29 | 2.00 | 0.0753 0.0016 0.0770 | 3.3283
- 30 | 2.00 | 0.0697 0.0039 0.0736 | 3.1221
- 31 | 2.00 | 0.0678 0.0048 0.0726 | 2.9160
- 43 | 1.75 | 0.0670 0.0027 0.0697 | 1.5785
- 44 | 1.75 | 0.0628 0.0050 0.0678 | 1.5194
- 45 | 1.75 | 0.0614 0.0058 0.0671 | 1.4626
- 57 | 1.50 | 0.0603 0.0042 0.0644 | 1.0900
- 58 | 1.50 | 0.0572 0.0062 0.0633 | 1.0730
- 59 | 1.50 | 0.0561 0.0069 0.0630 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 172s
- Prepare output 9s
- 181s
- Jacobian determinant (RMS): 0.009 0.033 0.051 0.078 0.107 | 0.115142
- Template Matching: 0.082 0.222 0.203 0.184 0.168 | 0.168402
- Write result maps: 23s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 25s
- CSF distance: 15s
- PBT2x thickness: 43s
- 88s
- Create initial surface 79s
- Topology correction: 103s
- Surface refinement: 68s
- Reduction of surface collisions with optimization: 68s
- Spherical mapping with areal smoothing 89s
- Spherical registration 291s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 25s
- CSF distance: 13s
- PBT2x thickness: 40s
- 84s
- Create initial surface 75s
- Topology correction: 90s
- Surface refinement: 82s
- Reduction of surface collisions with optimization: 63s
- Spherical mapping with areal smoothing 74s
- Spherical registration 262s
- Final surface processing results:
- Average thickness (FS): 2.5493 0.6465 mm
- Surface intensity / position RMSE: 0.0834 / 0.1045
- Euler number / defect number / defect size: 56.0 / 24.0 / 1.82%
- Display thickness: /var/lib/condor/execute/dir_26305/ds/sub-74/surf/lh.thickness.sub-74_T1w
- Display thickness: /var/lib/condor/execute/dir_26305/ds/sub-74/surf/rh.thickness.sub-74_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_26305/ds/sub-74/sub-74_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1603s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 25s
- 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 10s
- ROI estimation of 'mori' atlas 15s
- ROI estimation of 'anatomy3' atlas 22s
- ROI estimation of 'julichbrain' atlas 29s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 20s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 47s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 70s
- Write results 71s
- 291s
- Quality check: 5s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_26305/ds/sub-74/report/catreport_sub-74_T1w.pdf
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- CAT preprocessing takes 45 minute(s) and 51 second(s).
- Image Quality Rating (IQR): 74.63% (C)
- GM volume (GMV): 51.43% (694.42 / 1350.31 ml)
- GM thickness (GMT): 2.55 0.65 mm
- Segmentations are saved in /var/lib/condor/execute/dir_26305/ds/sub-74/mri
- Reports are saved in /var/lib/condor/execute/dir_26305/ds/sub-74/report
- Labels are saved in /var/lib/condor/execute/dir_26305/ds/sub-74/label
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