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- CAT12.8.1 r2040: 1/1: ./sub-0025995/ses-1/sub-0025995_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 31s
- APP: Rough bias correction:
- Initialize 4s
- Estimate background 3s
- Initial correction 3s
- Refine background 2s
- Final correction 3s
- Final scaling 3s
- 22s
- Correct center-of-mass 2s
- Affine registration 5s
- SPM preprocessing 1 (estimate 1 - TPM registration): 6s
- Use initial fine affine registration. 36s
- SPM preprocessing 1 (estimate 2): 36s
- SPM preprocessing 2 (write):
- Write Segmentation 11s
- Update Segmentation 12s
- Update Skull-Stripping 25s
- Update probability maps 6s
- 53s
- Global intensity correction: 10s
- SANLM denoising after intensity normalization (medium): 14s
- Fast Optimized Shooting registration 21s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 2s
- Prepare partitions 1s
- Prepare segments (LASmod = 1.00) 7s
- Estimate local tissue thresholds (WM) 11s
- Estimate local tissue thresholds (GM) 16s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 28s
- 67s
- ROI segmentation (partitioning):
- Atlas -> subject space 4s
- Major structures 2s
- Ventricle detection 5s
- Blood vessel detection 5s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.08) 11s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 3s
- 32s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 21s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 2s
- Level 1 cleanup (brain masking) 2s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 6s
- 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 | 0.0855 0.0000 0.0855 | 32.0000
- 2 | 2.50 | 0.0826 0.0013 0.0839 | 29.4886
- 3 | 2.50 | 0.0817 0.0019 0.0837 | 26.9772
- 4 | 2.50 | 0.0813 0.0022 0.0835 | 24.6107
- 5 | 2.50 | 0.0809 0.0024 0.0833 | 22.6548
- 6 | 2.50 | 0.0806 0.0025 0.0831 | 20.6989
- 7 | 2.50 | 0.0803 0.0026 0.0829 | 18.9688
- 8 | 2.50 | 0.0800 0.0027 0.0827 | 17.4455
- 9 | 2.50 | 0.0796 0.0028 0.0824 | 15.9223
- 10 | 2.50 | 0.0792 0.0029 0.0822 | 14.6627
- 11 | 2.50 | 0.0789 0.0030 0.0819 | 13.4764
- 12 | 2.50 | 0.0785 0.0031 0.0816 | 12.3015
- 13 | 2.50 | 0.0781 0.0032 0.0813 | 11.3776
- 14 | 2.50 | 0.0777 0.0033 0.0810 | 10.4537
- 15 | 2.25 | 0.0777 0.0034 0.0811 | 9.5920
- 16 | 2.25 | 0.0744 0.0050 0.0795 | 8.8725
- 29 | 2.00 | 0.0753 0.0023 0.0776 | 3.3283
- 30 | 2.00 | 0.0685 0.0050 0.0735 | 3.1221
- 31 | 2.00 | 0.0661 0.0061 0.0722 | 2.9160
- 43 | 1.75 | 0.0647 0.0035 0.0682 | 1.5785
- 44 | 1.75 | 0.0603 0.0059 0.0662 | 1.5194
- 45 | 1.75 | 0.0589 0.0067 0.0655 | 1.4626
- 57 | 1.50 | 0.0574 0.0049 0.0622 | 1.0900
- 58 | 1.50 | 0.0543 0.0069 0.0612 | 1.0730
- 59 | 1.50 | 0.0533 0.0075 0.0608 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 100s
- Prepare output 6s
- 106s
- Jacobian determinant (RMS): 0.012 0.043 0.064 0.089 0.112 | 0.116718
- Template Matching: 0.085 0.223 0.198 0.177 0.160 | 0.159798
- Write result maps: 21s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 19s
- CSF distance: 8s
- PBT2x thickness: 23s
- 53s
- Create initial surface 42s
- Topology correction: 47s
- Surface refinement: 41s
- Reduction of surface collisions with optimization: 34s
- Spherical mapping with areal smoothing 46s
- Spherical registration 176s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 18s
- CSF distance: 7s
- PBT2x thickness: 23s
- 51s
- Create initial surface 41s
- Topology correction: 54s
- Surface refinement: 42s
- Reduction of surface collisions with optimization: 33s
- Spherical mapping with areal smoothing 46s
- Spherical registration 177s
- Final surface processing results:
- Average thickness (FS): 2.3564 0.6350 mm
- Surface intensity / position RMSE: 0.0647 / 0.0665
- Euler number / defect number / defect size: 28.0 / 15.5 / 0.57%
- Display thickness: /var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-1/surf/lh.thickness.sub-0025995_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-1/surf/rh.thickness.sub-0025995_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-1/sub-0025995_ses-1_run-1_T1w.nii
- Surface ROI estimation: 5s
- Surface and thickness estimation takes: 935s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 6s
- ROI estimation of 'neuromorphometrics' atlas 21s
- ROI estimation of 'lpba40' atlas 6s
- ROI estimation of 'hammers' atlas 15s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 5s
- ROI estimation of 'aal3' atlas 8s
- ROI estimation of 'mori' atlas 11s
- ROI estimation of 'anatomy3' atlas 16s
- ROI estimation of 'julichbrain' atlas 21s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 9s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 16s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 35s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 52s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 5s
- Write results 5s
- 226s
- Quality check: 7s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-1/report/catreport_sub-0025995_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 28 minute(s) and 36 second(s).
- Image Quality Rating (IQR): 81.01% (B-)
- GM volume (GMV): 44.25% (574.60 / 1298.43 ml)
- GM thickness (GMT): 2.36 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-1/label
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