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- CAT12.8.1 r2040: 1/1: ./sub-0026184/ses-2/sub-0026184_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 55s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 7s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 39s
- Correct center-of-mass 5s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 84s
- SPM preprocessing 1 (estimate 2): 79s
- SPM preprocessing 2 (write):
- Write Segmentation 18s
- Update Segmentation 19s
- Update Skull-Stripping 44s
- Update probability maps 9s
- 90s
- Global intensity correction: 17s
- SANLM denoising after intensity normalization (medium): 28s
- Fast Optimized Shooting registration 39s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.11) 14s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 29s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 46s
- 117s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 15s
- Blood vessel detection 10s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.40) 26s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 3s
- Final corrections 4s
- 71s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 33s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.04]
- 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 | 0.1018 0.0000 0.1018 | 32.0000
- 2 | 2.50 | 0.0978 0.0016 0.0994 | 29.4886
- 3 | 2.50 | 0.0965 0.0025 0.0991 | 26.9772
- 4 | 2.50 | 0.0959 0.0029 0.0988 | 24.6107
- 5 | 2.50 | 0.0953 0.0032 0.0985 | 22.6548
- 6 | 2.50 | 0.0949 0.0033 0.0982 | 20.6989
- 7 | 2.50 | 0.0944 0.0035 0.0979 | 18.9688
- 8 | 2.50 | 0.0939 0.0037 0.0976 | 17.4455
- 9 | 2.50 | 0.0934 0.0039 0.0972 | 15.9223
- 10 | 2.50 | 0.0928 0.0041 0.0969 | 14.6627
- 11 | 2.50 | 0.0923 0.0043 0.0965 | 13.4764
- 12 | 2.50 | 0.0917 0.0044 0.0961 | 12.3015
- 13 | 2.50 | 0.0911 0.0046 0.0957 | 11.3776
- 14 | 2.50 | 0.0905 0.0048 0.0953 | 10.4537
- 15 | 2.25 | 0.0954 0.0050 0.1004 | 9.5920
- 16 | 2.25 | 0.0902 0.0077 0.0979 | 8.8725
- 17 | 2.25 | 0.0880 0.0087 0.0967 | 8.1530
- 18 | 2.25 | 0.0865 0.0092 0.0958 | 7.5234
- 19 | 2.25 | 0.0853 0.0095 0.0949 | 6.9630
- 20 | 2.25 | 0.0843 0.0097 0.0939 | 6.4027
- 21 | 2.25 | 0.0832 0.0099 0.0931 | 5.9447
- 22 | 2.25 | 0.0823 0.0100 0.0922 | 5.5083
- 23 | 2.25 | 0.0814 0.0100 0.0914 | 5.0803
- 24 | 2.25 | 0.0805 0.0101 0.0906 | 4.7404
- 25 | 2.25 | 0.0797 0.0100 0.0898 | 4.4005
- 26 | 2.25 | 0.0789 0.0100 0.0890 | 4.0868
- 27 | 2.25 | 0.0782 0.0101 0.0882 | 3.8221
- 28 | 2.25 | 0.0775 0.0100 0.0875 | 3.5574
- 29 | 2.00 | 0.0796 0.0096 0.0892 | 3.3283
- 30 | 2.00 | 0.0765 0.0109 0.0874 | 3.1221
- 31 | 2.00 | 0.0751 0.0112 0.0864 | 2.9160
- 32 | 2.00 | 0.0741 0.0114 0.0856 | 2.7495
- 43 | 1.75 | 0.0734 0.0066 0.0800 | 1.5785
- 44 | 1.75 | 0.0677 0.0099 0.0776 | 1.5194
- 45 | 1.75 | 0.0659 0.0108 0.0768 | 1.4626
- 57 | 1.50 | 0.0644 0.0080 0.0725 | 1.0900
- 58 | 1.50 | 0.0602 0.0109 0.0711 | 1.0730
- 59 | 1.50 | 0.0589 0.0117 0.0706 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 233s
- Prepare output 12s
- 245s
- Jacobian determinant (RMS): 0.014 0.058 0.116 0.157 0.197 | 0.209021
- Template Matching: 0.102 0.095 0.222 0.198 0.177 | 0.176761
- Write result maps: 36s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 44s
- CSF distance: 16s
- PBT2x thickness: 44s
- 111s
- Create initial surface 84s
- Topology correction: 76s
- Surface refinement: 68s
- Reduction of surface collisions with optimization: 52s
- Spherical mapping with areal smoothing 78s
- Spherical registration 320s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 28s
- CSF distance: 16s
- PBT2x thickness: 44s
- 94s
- Create initial surface 81s
- Topology correction: 77s
- Surface refinement: 90s
- Reduction of surface collisions with optimization: 52s
- Spherical mapping with areal smoothing 84s
- Spherical registration 333s
- Final surface processing results:
- Average thickness (FS): 2.3110 0.6081 mm
- Surface intensity / position RMSE: 0.0564 / 0.0526
- Euler number / defect number / defect size: 6.0 / 6.0 / 0.15%
- Display thickness: /var/lib/condor/execute/dir_2217288/ds/UM/sub-0026184/ses-2/surf/lh.thickness.sub-0026184_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2217288/ds/UM/sub-0026184/ses-2/surf/rh.thickness.sub-0026184_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2217288/ds/UM/sub-0026184/ses-2/sub-0026184_ses-2_run-1_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1691s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 32s
- ROI estimation of 'lpba40' atlas 9s
- ROI estimation of 'hammers' atlas 22s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 8s
- ROI estimation of 'aal3' atlas 13s
- ROI estimation of 'mori' atlas 19s
- ROI estimation of 'anatomy3' atlas 27s
- ROI estimation of 'julichbrain' atlas 36s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 14s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 25s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 58s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 86s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s
- Write results 9s
- 369s
- Quality check: 12s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2217288/ds/UM/sub-0026184/ses-2/report/catreport_sub-0026184_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 51 minute(s) and 58 second(s).
- Image Quality Rating (IQR): 83.62% (B)
- GM volume (GMV): 41.54% (517.18 / 1245.00 ml)
- GM thickness (GMT): 2.31 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2217288/ds/UM/sub-0026184/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_2217288/ds/UM/sub-0026184/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_2217288/ds/UM/sub-0026184/ses-2/label
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