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- CAT12.8.1 r2040: 1/1: ./sub-0026006/ses-5/sub-0026006_ses-5_run-1_T1w.n
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- SANLM denoising (medium): 57s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 6s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 37s
- Correct center-of-mass 3s
- Affine registration 9s
- SPM preprocessing 1 (estimate 1 - TPM registration): 75s
- SPM preprocessing 1 (estimate 2): 62s
- SPM preprocessing 2 (write):
- Write Segmentation 17s
- Update Segmentation 22s
- Update Skull-Stripping 44s
- Update probability maps 9s
- 91s
- Global intensity correction: 17s
- SANLM denoising after intensity normalization (medium): 33s
- Fast Optimized Shooting registration 34s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.13) 17s
- Estimate local tissue thresholds (WM) 20s
- Estimate local tissue thresholds (GM) 28s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 53s
- 128s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 22s
- Blood vessel detection 12s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.15) 30s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 4s
- 85s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 38s
- AMAP peaks: [CSF,GM,WM] = [0.350.07,0.680.08,0.980.04]
- 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
- 13s
- 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 | 0.0851 0.0000 0.0851 | 32.0000
- 2 | 2.50 | 0.0830 0.0010 0.0841 | 29.4886
- 3 | 2.50 | 0.0824 0.0015 0.0839 | 26.9772
- 4 | 2.50 | 0.0821 0.0017 0.0838 | 24.6107
- 5 | 2.50 | 0.0818 0.0019 0.0837 | 22.6548
- 6 | 2.50 | 0.0816 0.0019 0.0835 | 20.6989
- 7 | 2.50 | 0.0814 0.0020 0.0834 | 18.9688
- 8 | 2.50 | 0.0811 0.0021 0.0832 | 17.4455
- 9 | 2.50 | 0.0809 0.0021 0.0830 | 15.9223
- 10 | 2.50 | 0.0806 0.0022 0.0828 | 14.6627
- 11 | 2.50 | 0.0804 0.0023 0.0826 | 13.4764
- 12 | 2.50 | 0.0801 0.0023 0.0824 | 12.3015
- 13 | 2.50 | 0.0799 0.0024 0.0823 | 11.3776
- 14 | 2.50 | 0.0796 0.0024 0.0820 | 10.4537
- 15 | 2.25 | 0.0798 0.0025 0.0823 | 9.5920
- 16 | 2.25 | 0.0772 0.0038 0.0809 | 8.8725
- 17 | 2.25 | 0.0762 0.0042 0.0804 | 8.1530
- 18 | 2.25 | 0.0756 0.0044 0.0799 | 7.5234
- 19 | 2.25 | 0.0751 0.0045 0.0795 | 6.9630
- 20 | 2.25 | 0.0746 0.0045 0.0791 | 6.4027
- 29 | 2.00 | 0.0771 0.0025 0.0795 | 3.3283
- 30 | 2.00 | 0.0723 0.0047 0.0769 | 3.1221
- 31 | 2.00 | 0.0707 0.0055 0.0762 | 2.9160
- 43 | 1.75 | 0.0700 0.0030 0.0731 | 1.5785
- 44 | 1.75 | 0.0653 0.0056 0.0710 | 1.5194
- 45 | 1.75 | 0.0639 0.0065 0.0703 | 1.4626
- 57 | 1.50 | 0.0628 0.0046 0.0674 | 1.0900
- 58 | 1.50 | 0.0592 0.0070 0.0663 | 1.0730
- 59 | 1.50 | 0.0582 0.0077 0.0659 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 193s
- Prepare output 11s
- 203s
- Jacobian determinant (RMS): 0.009 0.031 0.051 0.075 0.101 | 0.107033
- Template Matching: 0.085 0.224 0.212 0.192 0.174 | 0.174499
- Write result maps: 39s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 49s
- CSF distance: 18s
- PBT2x thickness: 51s
- 125s
- Create initial surface 95s
- Topology correction: 109s
- Surface refinement: 129s
- Reduction of surface collisions with optimization: 83s
- Spherical mapping with areal smoothing 99s
- Spherical registration 303s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 56s
- CSF distance: 19s
- PBT2x thickness: 51s
- 133s
- Create initial surface 94s
- Topology correction: 109s
- Surface refinement: 130s
- Reduction of surface collisions with optimization: 84s
- Spherical mapping with areal smoothing 102s
- Spherical registration 301s
- Final surface processing results:
- Average thickness (FS): 2.3286 0.6068 mm
- Surface intensity / position RMSE: 0.0617 / 0.0640
- Euler number / defect number / defect size: 18.0 / 13.5 / 0.56%
- Display thickness: /var/lib/condor/execute/dir_3298923/ds/XHCUMS/sub-0026006/ses-5/surf/lh.thickness.sub-0026006_ses-5_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3298923/ds/XHCUMS/sub-0026006/ses-5/surf/rh.thickness.sub-0026006_ses-5_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3298923/ds/XHCUMS/sub-0026006/ses-5/sub-0026006_ses-5_run-1_T1w.nii
- Surface ROI estimation: 12s
- Surface and thickness estimation takes: 2006s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 11s
- ROI estimation of 'neuromorphometrics' atlas 42s
- ROI estimation of 'lpba40' atlas 12s
- ROI estimation of 'hammers' atlas 30s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 11s
- ROI estimation of 'aal3' atlas 18s
- ROI estimation of 'mori' atlas 26s
- ROI estimation of 'anatomy3' atlas 36s
- ROI estimation of 'julichbrain' atlas 49s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 19s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 31s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 79s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 86s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s
- Write results 8s
- 460s
- Quality check: 12s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3298923/ds/XHCUMS/sub-0026006/ses-5/report/catreport_sub-0026006_ses-5_run-1_T1w.pdf
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- CAT preprocessing takes 58 minute(s) and 29 second(s).
- Image Quality Rating (IQR): 83.12% (B-)
- GM volume (GMV): 40.75% (737.13 / 1809.12 ml)
- GM thickness (GMT): 2.33 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3298923/ds/XHCUMS/sub-0026006/ses-5/mri
- Reports are saved in /var/lib/condor/execute/dir_3298923/ds/XHCUMS/sub-0026006/ses-5/report
- Labels are saved in /var/lib/condor/execute/dir_3298923/ds/XHCUMS/sub-0026006/ses-5/label
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