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- CAT12.8.1 r2040: 1/1: ./sub-0025788/ses-1/sub-0025788_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 45s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 5s
- Initial correction 5s
- Refine background 3s
- Final correction 5s
- Final scaling 4s
- 34s
- Correct center-of-mass 3s
- Affine registration 8s
- SPM preprocessing 1 (estimate 1 - TPM registration): 6s
- Use initial fine affine registration. 57s
- SPM preprocessing 1 (estimate 2): 57s
- SPM preprocessing 2 (write):
- Write Segmentation 16s
- Update Segmentation 17s
- Update Skull-Stripping 40s
- Update probability maps 8s
- 82s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 25s
- Fast Optimized Shooting registration 32s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.10) 13s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 27s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 48s
- 116s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 12s
- Blood vessel detection 9s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.05) 24s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 3s
- Final corrections 4s
- 64s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 32s
- 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
- 10s
- 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 | 0.0833 0.0000 0.0833 | 32.0000
- 2 | 2.50 | 0.0811 0.0011 0.0822 | 29.4886
- 3 | 2.50 | 0.0805 0.0016 0.0821 | 26.9772
- 4 | 2.50 | 0.0802 0.0018 0.0819 | 24.6107
- 5 | 2.50 | 0.0799 0.0019 0.0818 | 22.6548
- 6 | 2.50 | 0.0797 0.0020 0.0817 | 20.6989
- 7 | 2.50 | 0.0795 0.0020 0.0815 | 18.9688
- 8 | 2.50 | 0.0792 0.0021 0.0814 | 17.4455
- 9 | 2.50 | 0.0790 0.0022 0.0812 | 15.9223
- 10 | 2.50 | 0.0787 0.0023 0.0810 | 14.6627
- 11 | 2.50 | 0.0785 0.0023 0.0808 | 13.4764
- 12 | 2.50 | 0.0782 0.0024 0.0806 | 12.3015
- 13 | 2.50 | 0.0780 0.0025 0.0804 | 11.3776
- 14 | 2.50 | 0.0777 0.0025 0.0802 | 10.4537
- 15 | 2.25 | 0.0768 0.0025 0.0794 | 9.5920
- 16 | 2.25 | 0.0742 0.0038 0.0781 | 8.8725
- 29 | 2.00 | 0.0763 0.0017 0.0781 | 3.3283
- 30 | 2.00 | 0.0703 0.0041 0.0745 | 3.1221
- 31 | 2.00 | 0.0684 0.0051 0.0735 | 2.9160
- 43 | 1.75 | 0.0677 0.0029 0.0706 | 1.5785
- 44 | 1.75 | 0.0632 0.0053 0.0685 | 1.5194
- 45 | 1.75 | 0.0617 0.0061 0.0679 | 1.4626
- 57 | 1.50 | 0.0605 0.0044 0.0649 | 1.0900
- 58 | 1.50 | 0.0571 0.0066 0.0637 | 1.0730
- 59 | 1.50 | 0.0560 0.0073 0.0633 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 168s
- Prepare output 10s
- 178s
- Jacobian determinant (RMS): 0.009 0.033 0.051 0.076 0.099 | 0.105214
- Template Matching: 0.083 0.223 0.205 0.185 0.168 | 0.168018
- Write result maps: 33s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 30s
- CSF distance: 15s
- PBT2x thickness: 46s
- 97s
- Create initial surface 84s
- Topology correction: 100s
- Surface refinement: 91s
- Reduction of surface collisions with optimization: 75s
- Spherical mapping with areal smoothing 82s
- Spherical registration 296s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 30s
- CSF distance: 15s
- PBT2x thickness: 43s
- 94s
- Create initial surface 80s
- Topology correction: 94s
- Surface refinement: 106s
- Reduction of surface collisions with optimization: 75s
- Spherical mapping with areal smoothing 95s
- Spherical registration 312s
- Final surface processing results:
- Average thickness (FS): 2.5317 0.6569 mm
- Surface intensity / position RMSE: 0.0785 / 0.0993
- Euler number / defect number / defect size: 26.0 / 16.0 / 1.91%
- Display thickness: /var/lib/condor/execute/dir_931949/ds/SWU_4/sub-0025788/ses-1/surf/lh.thickness.sub-0025788_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_931949/ds/SWU_4/sub-0025788/ses-1/surf/rh.thickness.sub-0025788_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_931949/ds/SWU_4/sub-0025788/ses-1/sub-0025788_ses-1_run-1_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 1778s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 32s
- 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 40s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 27s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 58s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 84s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s
- Write results 8s
- 378s
- Quality check: 11s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_931949/ds/SWU_4/sub-0025788/ses-1/report/catreport_sub-0025788_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 51 minute(s) and 52 second(s).
- Image Quality Rating (IQR): 84.67% (B)
- GM volume (GMV): 49.37% (713.50 / 1445.26 ml)
- GM thickness (GMT): 2.53 0.66 mm
- Segmentations are saved in /var/lib/condor/execute/dir_931949/ds/SWU_4/sub-0025788/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_931949/ds/SWU_4/sub-0025788/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_931949/ds/SWU_4/sub-0025788/ses-1/label
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