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- CAT12.8.1 r1980: 1/1: ./execute/dir_59863/ds/sub-011/sub-011_T1w.n
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- SANLM denoising (medium): 41s
- APP: Rough bias correction:
- Initialize 11s
- Estimate background 13s
- Initial correction 14s
- Refine background 6s
- Final correction 14s
- Final scaling 15s
- 85s
- Correct center-of-mass 3s
- Affine registration 17s
- SPM preprocessing 1 (estimate 1 - TPM registration): 161s
- SPM preprocessing 1 (estimate 2): 59s
- SPM preprocessing 2 (write):
- Write Segmentation 30s
- Update Segmentation 41s
- Update Skull-Stripping 84s
- Update probability maps 14s
- 169s
- Global intensity correction: 28s
- SANLM denoising after intensity normalization (medium): 22s
- Fast Optimized Shooting registration 48s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 10s
- Prepare partitions 4s
- Prepare segments (LASmod = 1.00) 38s
- Estimate local tissue thresholds (WM) 42s
- Estimate local tissue thresholds (GM) 66s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 51s
- 218s
- ROI segmentation (partitioning):
- Atlas -> subject space 16s
- Major structures 10s
- Ventricle detection 37s
- Blood vessel detection 31s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.02) 75s
- Manual stroke lesion detection 0s
- Closing of deep structures 5s
- Side alignment 11s
- Final corrections 7s
- 192s
- Blood vessel correction (BVCstr=0.50): 3s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 71s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 12s
- Level 1 cleanup (brain masking) 6s
- Level 2 cleanup (CSF correction) 4s
- Level 3 cleanup (CSF/WM PVE) 7s
- 29s
- 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 | 0.0872 0.0000 0.0872 | 32.0000
- 2 | 2.50 | 0.0839 0.0014 0.0853 | 29.4886
- 3 | 2.50 | 0.0829 0.0021 0.0850 | 26.9772
- 4 | 2.50 | 0.0824 0.0024 0.0848 | 24.6107
- 5 | 2.50 | 0.0820 0.0026 0.0846 | 22.6548
- 6 | 2.50 | 0.0817 0.0027 0.0844 | 20.6989
- 7 | 2.50 | 0.0813 0.0028 0.0842 | 18.9688
- 8 | 2.50 | 0.0810 0.0030 0.0839 | 17.4455
- 9 | 2.50 | 0.0806 0.0030 0.0836 | 15.9223
- 10 | 2.50 | 0.0802 0.0032 0.0834 | 14.6627
- 11 | 2.50 | 0.0798 0.0033 0.0831 | 13.4764
- 12 | 2.50 | 0.0794 0.0034 0.0828 | 12.3015
- 13 | 2.50 | 0.0790 0.0035 0.0825 | 11.3776
- 14 | 2.50 | 0.0786 0.0036 0.0821 | 10.4537
- 15 | 2.25 | 0.0793 0.0037 0.0830 | 9.5920
- 16 | 2.25 | 0.0757 0.0055 0.0811 | 8.8725
- 17 | 2.25 | 0.0742 0.0061 0.0803 | 8.1530
- 29 | 2.00 | 0.0761 0.0028 0.0789 | 3.3283
- 30 | 2.00 | 0.0699 0.0054 0.0753 | 3.1221
- 31 | 2.00 | 0.0677 0.0064 0.0741 | 2.9160
- 43 | 1.75 | 0.0670 0.0037 0.0707 | 1.5785
- 44 | 1.75 | 0.0624 0.0062 0.0685 | 1.5194
- 45 | 1.75 | 0.0608 0.0070 0.0678 | 1.4626
- 57 | 1.50 | 0.0595 0.0051 0.0647 | 1.0900
- 58 | 1.50 | 0.0561 0.0074 0.0635 | 1.0730
- 59 | 1.50 | 0.0549 0.0081 0.0630 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 190s
- Prepare output 19s
- 209s
- Jacobian determinant (RMS): 0.012 0.046 0.070 0.096 0.122 | 0.128951
- Template Matching: 0.087 0.223 0.203 0.182 0.165 | 0.164730
- Write result maps: 43s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 50s
- CSF distance: 24s
- PBT2x thickness: 67s
- 150s
- Create initial surface 119s
- Topology correction: 118s
- Surface refinement: 113s
- Reduction of surface collisions with optimization: 94s
- Spherical mapping with areal smoothing 98s
- Spherical registration 287s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 64s
- CSF distance: 21s
- PBT2x thickness: 59s
- 150s
- Create initial surface 101s
- Topology correction: 115s
- Surface refinement: 105s
- Reduction of surface collisions with optimization: 91s
- Spherical mapping with areal smoothing 98s
- Spherical registration 298s
- Final surface processing results:
- Average thickness (FS): 2.5847 0.6008 mm
- Surface intensity / position RMSE: 0.0674 / 0.0690
- Euler number / defect number / defect size: 26.0 / 13.5 / 0.84%
- Display thickness: /var/lib/condor/execute/dir_59863/ds/sub-011/surf/lh.thickness.sub-011_T1w
- Display thickness: /var/lib/condor/execute/dir_59863/ds/sub-011/surf/rh.thickness.sub-011_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_59863/ds/sub-011/sub-011_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 2069s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 16s
- ROI estimation of 'neuromorphometrics' atlas 58s
- ROI estimation of 'lpba40' atlas 18s
- ROI estimation of 'hammers' atlas 39s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 14s
- ROI estimation of 'aal3' atlas 24s
- ROI estimation of 'mori' atlas 33s
- ROI estimation of 'anatomy3' atlas 47s
- ROI estimation of 'julichbrain' atlas 63s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 26s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 46s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 93s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 135s
- Write results 136s
- 617s
- Quality check: 10s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_59863/ds/sub-011/report/catreport_sub-011_T1w.pdf
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- CAT preprocessing takes 70 minute(s) and 56 second(s).
- Image Quality Rating (IQR): 86.50% (B)
- GM volume (GMV): 49.06% (851.08 / 1734.90 ml)
- GM thickness (GMT): 2.58 0.60 mm
- Segmentations are saved in /var/lib/condor/execute/dir_59863/ds/sub-011/mri
- Reports are saved in /var/lib/condor/execute/dir_59863/ds/sub-011/report
- Labels are saved in /var/lib/condor/execute/dir_59863/ds/sub-011/label
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