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- CAT12.8.1 r2040: 1/1: ./sub-0026002/ses-5/sub-0026002_ses-5_run-1_T1w.n
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- SANLM denoising (medium): 48s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 6s
- Initial correction 7s
- Refine background 3s
- Final correction 5s
- Final scaling 6s
- 40s
- Correct center-of-mass 3s
- Affine registration 12s
- SPM preprocessing 1 (estimate 1 - TPM registration): 72s
- SPM preprocessing 1 (estimate 2): 60s
- SPM preprocessing 2 (write):
- Write Segmentation 17s
- Update Segmentation 19s
- Update Skull-Stripping 41s
- Update probability maps 9s
- 86s
- Global intensity correction: 17s
- SANLM denoising after intensity normalization (medium): 23s
- Fast Optimized Shooting registration 38s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.17) 13s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 23s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 39s
- 103s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 3s
- Ventricle detection 12s
- Blood vessel detection 9s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.11) 23s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 3s
- Final corrections 5s
- 66s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 27s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- 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 | 0.0831 0.0000 0.0831 | 32.0000
- 2 | 2.50 | 0.0810 0.0010 0.0821 | 29.4886
- 3 | 2.50 | 0.0804 0.0015 0.0820 | 26.9772
- 4 | 2.50 | 0.0801 0.0017 0.0818 | 24.6107
- 5 | 2.50 | 0.0799 0.0019 0.0817 | 22.6548
- 6 | 2.50 | 0.0796 0.0020 0.0816 | 20.6989
- 7 | 2.50 | 0.0794 0.0020 0.0814 | 18.9688
- 8 | 2.50 | 0.0792 0.0021 0.0813 | 17.4455
- 9 | 2.50 | 0.0789 0.0022 0.0811 | 15.9223
- 10 | 2.50 | 0.0787 0.0023 0.0810 | 14.6627
- 11 | 2.50 | 0.0784 0.0024 0.0808 | 13.4764
- 12 | 2.50 | 0.0782 0.0024 0.0806 | 12.3015
- 13 | 2.50 | 0.0779 0.0025 0.0804 | 11.3776
- 14 | 2.50 | 0.0776 0.0026 0.0802 | 10.4537
- 15 | 2.25 | 0.0766 0.0026 0.0793 | 9.5920
- 16 | 2.25 | 0.0740 0.0039 0.0779 | 8.8725
- 29 | 2.00 | 0.0756 0.0018 0.0774 | 3.3283
- 30 | 2.00 | 0.0693 0.0042 0.0735 | 3.1221
- 31 | 2.00 | 0.0672 0.0053 0.0724 | 2.9160
- 43 | 1.75 | 0.0660 0.0030 0.0690 | 1.5785
- 44 | 1.75 | 0.0615 0.0054 0.0669 | 1.5194
- 45 | 1.75 | 0.0600 0.0062 0.0662 | 1.4626
- 57 | 1.50 | 0.0584 0.0045 0.0629 | 1.0900
- 58 | 1.50 | 0.0553 0.0065 0.0618 | 1.0730
- 59 | 1.50 | 0.0543 0.0071 0.0614 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 188s
- Prepare output 10s
- 198s
- Jacobian determinant (RMS): 0.010 0.036 0.054 0.077 0.099 | 0.106238
- Template Matching: 0.083 0.222 0.201 0.180 0.163 | 0.162840
- Write result maps: 44s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 53s
- CSF distance: 15s
- PBT2x thickness: 47s
- 121s
- Create initial surface 75s
- Topology correction: 86s
- Surface refinement: 72s
- Reduction of surface collisions with optimization: 55s
- Spherical mapping with areal smoothing 77s
- Spherical registration 243s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 34s
- CSF distance: 16s
- PBT2x thickness: 47s
- 104s
- Create initial surface 76s
- Topology correction: 86s
- Surface refinement: 74s
- Reduction of surface collisions with optimization: 54s
- Spherical mapping with areal smoothing 77s
- Spherical registration 237s
- Final surface processing results:
- Average thickness (FS): 2.4614 0.6203 mm
- Surface intensity / position RMSE: 0.0624 / 0.0640
- Euler number / defect number / defect size: 16.0 / 9.0 / 0.63%
- Display thickness: /var/lib/condor/execute/dir_2737911/ds/XHCUMS/sub-0026002/ses-5/surf/lh.thickness.sub-0026002_ses-5_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2737911/ds/XHCUMS/sub-0026002/ses-5/surf/rh.thickness.sub-0026002_ses-5_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2737911/ds/XHCUMS/sub-0026002/ses-5/sub-0026002_ses-5_run-1_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1530s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 14s
- ROI estimation of 'neuromorphometrics' atlas 51s
- ROI estimation of 'lpba40' atlas 15s
- ROI estimation of 'hammers' atlas 36s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 13s
- ROI estimation of 'aal3' atlas 21s
- ROI estimation of 'mori' atlas 31s
- ROI estimation of 'anatomy3' atlas 45s
- ROI estimation of 'julichbrain' atlas 60s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 22s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 29s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 96s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 143s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 10s
- Write results 11s
- 588s
- Quality check: 12s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2737911/ds/XHCUMS/sub-0026002/ses-5/report/catreport_sub-0026002_ses-5_run-1_T1w.pdf
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- CAT preprocessing takes 51 minute(s) and 6 second(s).
- Image Quality Rating (IQR): 82.92% (B-)
- GM volume (GMV): 45.09% (641.57 / 1422.88 ml)
- GM thickness (GMT): 2.46 0.62 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2737911/ds/XHCUMS/sub-0026002/ses-5/mri
- Reports are saved in /var/lib/condor/execute/dir_2737911/ds/XHCUMS/sub-0026002/ses-5/report
- Labels are saved in /var/lib/condor/execute/dir_2737911/ds/XHCUMS/sub-0026002/ses-5/label
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