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- CAT12.8.1 r1980: 1/1: ./dir_50573/ds/sub-0375/sub-0375_ses-01_T1w.n
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- SANLM denoising (medium): 178s
- APP: Rough bias correction:
- Initialize 11s
- Estimate background 12s
- Initial correction 27s
- Refine background 5s
- Final correction 13s
- Final scaling 9s
- 88s
- Correct center-of-mass 4s
- Affine registration 21s
- SPM preprocessing 1 (estimate 1 - TPM registration): 118s
- SPM preprocessing 1 (estimate 2): 88s
- SPM preprocessing 2 (write):
- Write Segmentation 28s
- Update Segmentation 31s
- Update Skull-Stripping 68s
- Update probability maps 14s
- 141s
- Global intensity correction: 26s
- SANLM denoising after intensity normalization (medium): 23s
- Fast Optimized Shooting registration 47s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 6s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.00) 24s
- Estimate local tissue thresholds (WM) 33s
- Estimate local tissue thresholds (GM) 53s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 55s
- 181s
- ROI segmentation (partitioning):
- Atlas -> subject space 12s
- Major structures 6s
- Ventricle detection 24s
- Blood vessel detection 19s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 47s
- Manual stroke lesion detection 0s
- Closing of deep structures 3s
- Side alignment 6s
- Final corrections 7s
- 123s
- Blood vessel correction (BVCstr=0.50): 3s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 56s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 7s
- Level 1 cleanup (brain masking) 5s
- Level 2 cleanup (CSF correction) 3s
- Level 3 cleanup (CSF/WM PVE) 5s
- 19s
- 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 | 0.0856 0.0000 0.0856 | 32.0000
- 2 | 2.50 | 0.0838 0.0009 0.0847 | 29.4886
- 3 | 2.50 | 0.0833 0.0013 0.0847 | 26.9772
- 4 | 2.50 | 0.0831 0.0015 0.0846 | 24.6107
- 5 | 2.50 | 0.0829 0.0016 0.0845 | 22.6548
- 6 | 2.50 | 0.0828 0.0016 0.0844 | 20.6989
- 7 | 2.50 | 0.0826 0.0016 0.0842 | 18.9688
- 8 | 2.50 | 0.0824 0.0017 0.0841 | 17.4455
- 9 | 2.50 | 0.0822 0.0017 0.0840 | 15.9223
- 10 | 2.50 | 0.0820 0.0018 0.0838 | 14.6627
- 11 | 2.50 | 0.0819 0.0018 0.0837 | 13.4764
- 12 | 2.50 | 0.0817 0.0019 0.0835 | 12.3015
- 13 | 2.50 | 0.0814 0.0019 0.0834 | 11.3776
- 14 | 2.50 | 0.0813 0.0019 0.0832 | 10.4537
- 15 | 2.25 | 0.0824 0.0020 0.0844 | 9.5920
- 16 | 2.25 | 0.0798 0.0032 0.0830 | 8.8725
- 17 | 2.25 | 0.0789 0.0036 0.0825 | 8.1530
- 18 | 2.25 | 0.0783 0.0038 0.0821 | 7.5234
- 19 | 2.25 | 0.0779 0.0039 0.0818 | 6.9630
- 20 | 2.25 | 0.0775 0.0039 0.0814 | 6.4027
- 21 | 2.25 | 0.0771 0.0040 0.0811 | 5.9447
- 22 | 2.25 | 0.0767 0.0040 0.0807 | 5.5083
- 23 | 2.25 | 0.0763 0.0040 0.0804 | 5.0803
- 24 | 2.25 | 0.0760 0.0041 0.0801 | 4.7404
- 25 | 2.25 | 0.0756 0.0041 0.0797 | 4.4005
- 26 | 2.25 | 0.0753 0.0041 0.0794 | 4.0868
- 27 | 2.25 | 0.0749 0.0042 0.0791 | 3.8221
- 29 | 2.00 | 0.0778 0.0036 0.0814 | 3.3283
- 30 | 2.00 | 0.0749 0.0050 0.0799 | 3.1221
- 43 | 1.75 | 0.0747 0.0027 0.0774 | 1.5785
- 44 | 1.75 | 0.0693 0.0056 0.0749 | 1.5194
- 45 | 1.75 | 0.0677 0.0065 0.0742 | 1.4626
- 57 | 1.50 | 0.0671 0.0046 0.0717 | 1.0900
- 58 | 1.50 | 0.0633 0.0072 0.0705 | 1.0730
- 59 | 1.50 | 0.0621 0.0080 0.0701 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 227s
- Prepare output 17s
- 244s
- Jacobian determinant (RMS): 0.007 0.024 0.048 0.074 0.105 | 0.112051
- Template Matching: 0.086 0.225 0.225 0.203 0.186 | 0.186201
- Write result maps: 41s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 44s
- CSF distance: 26s
- PBT2x thickness: 72s
- 149s
- Create initial surface 122s
- Topology correction: 138s
- Surface refinement: 118s
- Reduction of surface collisions with optimization: 92s
- Spherical mapping with areal smoothing 110s
- Spherical registration 328s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 49s
- CSF distance: 25s
- PBT2x thickness: 72s
- 155s
- Create initial surface 127s
- Topology correction: 128s
- Surface refinement: 106s
- Reduction of surface collisions with optimization: 95s
- Spherical mapping with areal smoothing 113s
- Spherical registration 374s
- Final surface processing results:
- Average thickness (FS): 2.6916 0.6757 mm
- Surface intensity / position RMSE: 0.0838 / 0.0899
- Euler number / defect number / defect size: 52.0 / 31.0 / 1.36%
- Display thickness: /var/lib/condor/execute/dir_50573/ds/sub-0375/surf/lh.thickness.sub-0375_ses-01_T1w
- Display thickness: /var/lib/condor/execute/dir_50573/ds/sub-0375/surf/rh.thickness.sub-0375_ses-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_50573/ds/sub-0375/sub-0375_ses-01_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 2296s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 16s
- ROI estimation of 'neuromorphometrics' atlas 57s
- ROI estimation of 'lpba40' atlas 16s
- ROI estimation of 'hammers' atlas 39s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 13s
- ROI estimation of 'aal3' atlas 21s
- ROI estimation of 'mori' atlas 30s
- ROI estimation of 'anatomy3' atlas 43s
- ROI estimation of 'julichbrain' atlas 57s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 22s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 39s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 89s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 132s
- Write results 133s
- 579s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_50573/ds/sub-0375/report/catreport_sub-0375_ses-01_T1w.pdf
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- CAT preprocessing takes 74 minute(s) and 30 second(s).
- Image Quality Rating (IQR): 81.29% (B-)
- GM volume (GMV): 51.54% (866.00 / 1680.30 ml)
- GM thickness (GMT): 2.69 0.68 mm
- Segmentations are saved in /var/lib/condor/execute/dir_50573/ds/sub-0375/mri
- Reports are saved in /var/lib/condor/execute/dir_50573/ds/sub-0375/report
- Labels are saved in /var/lib/condor/execute/dir_50573/ds/sub-0375/label
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