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- CAT12.8.1 r2040: 1/1: ./sub-0025932/ses-2/sub-0025932_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 46s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 6s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 36s
- Correct center-of-mass 3s
- Affine registration 9s
- SPM preprocessing 1 (estimate 1 - TPM registration): 86s
- SPM preprocessing 1 (estimate 2): 75s
- SPM preprocessing 2 (write):
- Write Segmentation 17s
- Update Segmentation 18s
- Update Skull-Stripping 41s
- Update probability maps 8s
- 84s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 26s
- Fast Optimized Shooting registration 33s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.05) 14s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 26s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 40s
- 108s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 15s
- Blood vessel detection 9s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.03) 23s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 3s
- Final corrections 4s
- 66s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 34s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.07,0.990.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 3s
- 11s
- 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 | 0.0873 0.0000 0.0873 | 32.0000
- 2 | 2.50 | 0.0836 0.0015 0.0851 | 29.4886
- 3 | 2.50 | 0.0824 0.0023 0.0847 | 26.9772
- 4 | 2.50 | 0.0818 0.0026 0.0845 | 24.6107
- 5 | 2.50 | 0.0814 0.0029 0.0842 | 22.6548
- 6 | 2.50 | 0.0810 0.0030 0.0839 | 20.6989
- 7 | 2.50 | 0.0805 0.0031 0.0837 | 18.9688
- 8 | 2.50 | 0.0801 0.0033 0.0834 | 17.4455
- 9 | 2.50 | 0.0797 0.0034 0.0831 | 15.9223
- 10 | 2.50 | 0.0792 0.0035 0.0828 | 14.6627
- 11 | 2.50 | 0.0788 0.0037 0.0824 | 13.4764
- 12 | 2.50 | 0.0783 0.0038 0.0821 | 12.3015
- 13 | 2.50 | 0.0778 0.0039 0.0817 | 11.3776
- 14 | 2.50 | 0.0774 0.0040 0.0814 | 10.4537
- 15 | 2.25 | 0.0777 0.0041 0.0818 | 9.5920
- 16 | 2.25 | 0.0743 0.0058 0.0801 | 8.8725
- 29 | 2.00 | 0.0753 0.0026 0.0779 | 3.3283
- 30 | 2.00 | 0.0684 0.0054 0.0738 | 3.1221
- 31 | 2.00 | 0.0659 0.0065 0.0724 | 2.9160
- 43 | 1.75 | 0.0646 0.0038 0.0684 | 1.5785
- 44 | 1.75 | 0.0602 0.0061 0.0663 | 1.5194
- 45 | 1.75 | 0.0587 0.0069 0.0655 | 1.4626
- 57 | 1.50 | 0.0571 0.0051 0.0622 | 1.0900
- 58 | 1.50 | 0.0540 0.0071 0.0611 | 1.0730
- 59 | 1.50 | 0.0529 0.0077 0.0607 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 171s
- Prepare output 11s
- 182s
- Jacobian determinant (RMS): 0.013 0.049 0.074 0.101 0.125 | 0.131460
- Template Matching: 0.087 0.223 0.198 0.176 0.159 | 0.158805
- Write result maps: 35s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 30s
- CSF distance: 16s
- PBT2x thickness: 44s
- 96s
- Create initial surface 86s
- Topology correction: 94s
- Surface refinement: 76s
- Reduction of surface collisions with optimization: 70s
- Spherical mapping with areal smoothing 78s
- Spherical registration 300s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 34s
- CSF distance: 14s
- PBT2x thickness: 43s
- 97s
- Create initial surface 86s
- Topology correction: 93s
- Surface refinement: 107s
- Reduction of surface collisions with optimization: 69s
- Spherical mapping with areal smoothing 81s
- Spherical registration 300s
- Final surface processing results:
- Average thickness (FS): 2.5239 0.6208 mm
- Surface intensity / position RMSE: 0.0683 / 0.0681
- Euler number / defect number / defect size: 24.0 / 11.5 / 0.73%
- Display thickness: /var/lib/condor/execute/dir_566017/ds/BNU_2/sub-0025932/ses-2/surf/lh.thickness.sub-0025932_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_566017/ds/BNU_2/sub-0025932/ses-2/surf/rh.thickness.sub-0025932_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_566017/ds/BNU_2/sub-0025932/ses-2/sub-0025932_ses-2_run-1_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1730s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 8s
- ROI estimation of 'neuromorphometrics' atlas 30s
- 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 28s
- ROI estimation of 'julichbrain' atlas 38s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 16s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 27s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 64s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 139s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 12s
- Write results 14s
- 435s
- Quality check: 14s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_566017/ds/BNU_2/sub-0025932/ses-2/report/catreport_sub-0025932_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 52 minute(s) and 13 second(s).
- Image Quality Rating (IQR): 80.22% (B-)
- GM volume (GMV): 49.73% (701.26 / 1410.04 ml)
- GM thickness (GMT): 2.52 0.62 mm
- Segmentations are saved in /var/lib/condor/execute/dir_566017/ds/BNU_2/sub-0025932/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_566017/ds/BNU_2/sub-0025932/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_566017/ds/BNU_2/sub-0025932/ses-2/label
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