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- CAT12.8.1 r2040: 1/1: ./sub-0025272/ses-3/sub-0025272_ses-3_run-1_T1w.n
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- SANLM denoising (medium): 60s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 7s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 39s
- Correct center-of-mass 4s
- Affine registration 9s
- SPM preprocessing 1 (estimate 1 - TPM registration): 79s
- SPM preprocessing 1 (estimate 2): 72s
- SPM preprocessing 2 (write):
- Write Segmentation 18s
- Update Segmentation 20s
- Update Skull-Stripping 42s
- Update probability maps 8s
- 88s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 31s
- Fast Optimized Shooting registration 40s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 16s
- Estimate local tissue thresholds (WM) 21s
- Estimate local tissue thresholds (GM) 31s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 43s
- 120s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 4s
- Ventricle detection 13s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 25s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 4s
- 70s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 34s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.07,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 5s
- 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 | 0.0808 0.0000 0.0808 | 32.0000
- 2 | 2.50 | 0.0785 0.0011 0.0796 | 29.4886
- 3 | 2.50 | 0.0778 0.0016 0.0794 | 26.9772
- 4 | 2.50 | 0.0775 0.0018 0.0793 | 24.6107
- 5 | 2.50 | 0.0772 0.0020 0.0792 | 22.6548
- 6 | 2.50 | 0.0770 0.0020 0.0790 | 20.6989
- 7 | 2.50 | 0.0767 0.0021 0.0788 | 18.9688
- 8 | 2.50 | 0.0765 0.0022 0.0787 | 17.4455
- 9 | 2.50 | 0.0762 0.0023 0.0785 | 15.9223
- 10 | 2.50 | 0.0759 0.0024 0.0783 | 14.6627
- 11 | 2.50 | 0.0757 0.0024 0.0781 | 13.4764
- 12 | 2.50 | 0.0754 0.0025 0.0779 | 12.3015
- 13 | 2.50 | 0.0751 0.0026 0.0777 | 11.3776
- 14 | 2.50 | 0.0748 0.0026 0.0775 | 10.4537
- 15 | 2.25 | 0.0728 0.0027 0.0755 | 9.5920
- 16 | 2.25 | 0.0701 0.0040 0.0741 | 8.8725
- 29 | 2.00 | 0.0708 0.0018 0.0726 | 3.3283
- 30 | 2.00 | 0.0652 0.0040 0.0692 | 3.1221
- 31 | 2.00 | 0.0633 0.0049 0.0682 | 2.9160
- 43 | 1.75 | 0.0621 0.0028 0.0649 | 1.5785
- 44 | 1.75 | 0.0583 0.0049 0.0631 | 1.5194
- 45 | 1.75 | 0.0570 0.0056 0.0626 | 1.4626
- 57 | 1.50 | 0.0554 0.0040 0.0594 | 1.0900
- 58 | 1.50 | 0.0526 0.0059 0.0585 | 1.0730
- Shooting registration with 2.50:-0.25:1.50 mm takes: 163s
- Prepare output 12s
- 175s
- Jacobian determinant (RMS): 0.011 0.038 0.056 0.077 0.098 | 0.103121
- Template Matching: 0.081 0.210 0.190 0.171 0.158 | 0.157804
- Write result maps: 33s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 36s
- CSF distance: 16s
- PBT2x thickness: 49s
- 107s
- Create initial surface 85s
- Topology correction: 81s
- Surface refinement: 75s
- Reduction of surface collisions with optimization: 62s
- Spherical mapping with areal smoothing 87s
- Spherical registration 321s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 31s
- CSF distance: 16s
- PBT2x thickness: 49s
- 103s
- Create initial surface 84s
- Topology correction: 83s
- Surface refinement: 88s
- Reduction of surface collisions with optimization: 63s
- Spherical mapping with areal smoothing 85s
- Spherical registration 316s
- Final surface processing results:
- Average thickness (FS): 2.6660 0.6253 mm
- Surface intensity / position RMSE: 0.0667 / 0.0648
- Euler number / defect number / defect size: 12.0 / 12.0 / 0.25%
- Display thickness: /var/lib/condor/execute/dir_1702337/ds/UPSM_1/sub-0025272/ses-3/surf/lh.thickness.sub-0025272_ses-3_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1702337/ds/UPSM_1/sub-0025272/ses-3/surf/rh.thickness.sub-0025272_ses-3_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1702337/ds/UPSM_1/sub-0025272/ses-3/sub-0025272_ses-3_run-1_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1736s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 26s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 18s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 11s
- ROI estimation of 'mori' atlas 16s
- ROI estimation of 'anatomy3' atlas 24s
- ROI estimation of 'julichbrain' atlas 31s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 49s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 73s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s
- Write results 8s
- 313s
- Quality check: 11s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1702337/ds/UPSM_1/sub-0025272/ses-3/report/catreport_sub-0025272_ses-3_run-1_T1w.pdf
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- CAT preprocessing takes 50 minute(s) and 14 second(s).
- Image Quality Rating (IQR): 81.67% (B-)
- GM volume (GMV): 50.04% (656.08 / 1311.20 ml)
- GM thickness (GMT): 2.67 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1702337/ds/UPSM_1/sub-0025272/ses-3/mri
- Reports are saved in /var/lib/condor/execute/dir_1702337/ds/UPSM_1/sub-0025272/ses-3/report
- Labels are saved in /var/lib/condor/execute/dir_1702337/ds/UPSM_1/sub-0025272/ses-3/label
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