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- CAT12.8.1 r1980: 1/1: ./execute/dir_31788/ds/sub-045/sub-045_T1w.n
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- SANLM denoising (medium): 89s
- APP: Rough bias correction:
- Initialize 9s
- Estimate background 10s
- Initial correction 10s
- Refine background 5s
- Final correction 9s
- Final scaling 12s
- 64s
- Correct center-of-mass 4s
- Affine registration 13s
- SPM preprocessing 1 (estimate 1 - TPM registration): 124s
- SPM preprocessing 1 (estimate 2): 51s
- SPM preprocessing 2 (write):
- Write Segmentation 24s
- Update Segmentation 32s
- Update Skull-Stripping 73s
- Update probability maps 12s
- 141s
- Global intensity correction: 23s
- SANLM denoising after intensity normalization (medium): 24s
- Fast Optimized Shooting registration 37s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 8s
- Prepare partitions 5s
- Prepare segments (LASmod = 1.00) 28s
- Estimate local tissue thresholds (WM) 29s
- Estimate local tissue thresholds (GM) 44s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 41s
- 160s
- ROI segmentation (partitioning):
- Atlas -> subject space 13s
- Major structures 7s
- Ventricle detection 32s
- Blood vessel detection 20s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 57s
- Manual stroke lesion detection 0s
- Closing of deep structures 4s
- Side alignment 8s
- Final corrections 6s
- 147s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 61s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.04]
- 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) 6s
- 21s
- 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 | 0.0850 0.0000 0.0850 | 32.0000
- 2 | 2.50 | 0.0822 0.0012 0.0834 | 29.4886
- 3 | 2.50 | 0.0814 0.0018 0.0832 | 26.9772
- 4 | 2.50 | 0.0810 0.0021 0.0830 | 24.6107
- 5 | 2.50 | 0.0806 0.0022 0.0829 | 22.6548
- 6 | 2.50 | 0.0804 0.0023 0.0827 | 20.6989
- 7 | 2.50 | 0.0801 0.0024 0.0825 | 18.9688
- 8 | 2.50 | 0.0798 0.0026 0.0823 | 17.4455
- 9 | 2.50 | 0.0795 0.0026 0.0821 | 15.9223
- 10 | 2.50 | 0.0791 0.0028 0.0819 | 14.6627
- 11 | 2.50 | 0.0788 0.0028 0.0816 | 13.4764
- 12 | 2.50 | 0.0785 0.0029 0.0814 | 12.3015
- 13 | 2.50 | 0.0781 0.0030 0.0811 | 11.3776
- 14 | 2.50 | 0.0778 0.0031 0.0809 | 10.4537
- 15 | 2.25 | 0.0788 0.0032 0.0819 | 9.5920
- 16 | 2.25 | 0.0756 0.0047 0.0803 | 8.8725
- 17 | 2.25 | 0.0742 0.0053 0.0795 | 8.1530
- 29 | 2.00 | 0.0765 0.0024 0.0790 | 3.3283
- 30 | 2.00 | 0.0706 0.0049 0.0755 | 3.1221
- 31 | 2.00 | 0.0685 0.0059 0.0744 | 2.9160
- 43 | 1.75 | 0.0679 0.0034 0.0713 | 1.5785
- 44 | 1.75 | 0.0633 0.0058 0.0691 | 1.5194
- 45 | 1.75 | 0.0617 0.0067 0.0684 | 1.4626
- 57 | 1.50 | 0.0605 0.0049 0.0654 | 1.0900
- 58 | 1.50 | 0.0570 0.0072 0.0641 | 1.0730
- 59 | 1.50 | 0.0557 0.0079 0.0637 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 153s
- Prepare output 13s
- 166s
- Jacobian determinant (RMS): 0.012 0.044 0.067 0.093 0.118 | 0.125751
- Template Matching: 0.085 0.223 0.206 0.185 0.167 | 0.167233
- Write result maps: 32s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 30s
- CSF distance: 17s
- PBT2x thickness: 46s
- 100s
- Create initial surface 87s
- Topology correction: 97s
- Surface refinement: 81s
- Reduction of surface collisions with optimization: 78s
- Spherical mapping with areal smoothing 80s
- Spherical registration 303s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 33s
- CSF distance: 16s
- PBT2x thickness: 46s
- 101s
- Create initial surface 88s
- Topology correction: 97s
- Surface refinement: 114s
- Reduction of surface collisions with optimization: 82s
- Spherical mapping with areal smoothing 94s
- Spherical registration 291s
- Final surface processing results:
- Average thickness (FS): 2.5763 0.6037 mm
- Surface intensity / position RMSE: 0.0717 / 0.0668
- Euler number / defect number / defect size: 12.0 / 9.0 / 0.44%
- Display thickness: /var/lib/condor/execute/dir_31788/ds/sub-045/surf/lh.thickness.sub-045_T1w
- Display thickness: /var/lib/condor/execute/dir_31788/ds/sub-045/surf/rh.thickness.sub-045_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_31788/ds/sub-045/sub-045_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1799s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 11s
- ROI estimation of 'neuromorphometrics' atlas 39s
- ROI estimation of 'lpba40' atlas 11s
- ROI estimation of 'hammers' atlas 27s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 10s
- ROI estimation of 'aal3' atlas 15s
- ROI estimation of 'mori' atlas 22s
- ROI estimation of 'anatomy3' atlas 32s
- ROI estimation of 'julichbrain' atlas 42s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 30s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 66s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 98s
- Write results 98s
- 423s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_31788/ds/sub-045/report/catreport_sub-045_T1w.pdf
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- CAT preprocessing takes 58 minute(s) and 24 second(s).
- Image Quality Rating (IQR): 84.77% (B)
- GM volume (GMV): 50.48% (782.24 / 1549.59 ml)
- GM thickness (GMT): 2.58 0.60 mm
- Segmentations are saved in /var/lib/condor/execute/dir_31788/ds/sub-045/mri
- Reports are saved in /var/lib/condor/execute/dir_31788/ds/sub-045/report
- Labels are saved in /var/lib/condor/execute/dir_31788/ds/sub-045/label
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