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- CAT12.8.1 r2040: 1/1: ./sub-0025723/ses-1/sub-0025723_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 49s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 6s
- Initial correction 5s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 36s
- Correct center-of-mass 3s
- Affine registration 8s
- SPM preprocessing 1 (estimate 1 - TPM registration): 74s
- SPM preprocessing 1 (estimate 2): 59s
- SPM preprocessing 2 (write):
- Write Segmentation 17s
- Update Segmentation 19s
- Update Skull-Stripping 41s
- Update probability maps 8s
- 85s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 29s
- Fast Optimized Shooting registration 32s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.13) 15s
- Estimate local tissue thresholds (WM) 19s
- Estimate local tissue thresholds (GM) 27s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 50s
- 120s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 4s
- Ventricle detection 17s
- Blood vessel detection 10s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.02) 27s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 4s
- 74s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 34s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- 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 | 0.0824 0.0000 0.0824 | 32.0000
- 2 | 2.50 | 0.0799 0.0011 0.0810 | 29.4886
- 3 | 2.50 | 0.0791 0.0017 0.0808 | 26.9772
- 4 | 2.50 | 0.0788 0.0019 0.0807 | 24.6107
- 5 | 2.50 | 0.0785 0.0021 0.0805 | 22.6548
- 6 | 2.50 | 0.0782 0.0021 0.0803 | 20.6989
- 7 | 2.50 | 0.0779 0.0022 0.0802 | 18.9688
- 8 | 2.50 | 0.0777 0.0023 0.0800 | 17.4455
- 9 | 2.50 | 0.0774 0.0024 0.0798 | 15.9223
- 10 | 2.50 | 0.0771 0.0025 0.0796 | 14.6627
- 11 | 2.50 | 0.0768 0.0026 0.0793 | 13.4764
- 12 | 2.50 | 0.0765 0.0026 0.0791 | 12.3015
- 13 | 2.50 | 0.0762 0.0027 0.0789 | 11.3776
- 14 | 2.50 | 0.0759 0.0028 0.0786 | 10.4537
- 15 | 2.25 | 0.0750 0.0029 0.0779 | 9.5920
- 16 | 2.25 | 0.0723 0.0042 0.0765 | 8.8725
- 29 | 2.00 | 0.0739 0.0019 0.0758 | 3.3283
- 30 | 2.00 | 0.0681 0.0043 0.0724 | 3.1221
- 31 | 2.00 | 0.0661 0.0053 0.0714 | 2.9160
- 43 | 1.75 | 0.0653 0.0030 0.0683 | 1.5785
- 44 | 1.75 | 0.0610 0.0053 0.0663 | 1.5194
- 45 | 1.75 | 0.0595 0.0061 0.0656 | 1.4626
- 57 | 1.50 | 0.0581 0.0044 0.0625 | 1.0900
- 58 | 1.50 | 0.0548 0.0065 0.0614 | 1.0730
- 59 | 1.50 | 0.0537 0.0072 0.0609 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 162s
- Prepare output 10s
- 171s
- Jacobian determinant (RMS): 0.010 0.038 0.056 0.079 0.103 | 0.110386
- Template Matching: 0.082 0.217 0.198 0.178 0.161 | 0.161119
- Write result maps: 33s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 41s
- CSF distance: 15s
- PBT2x thickness: 46s
- 108s
- Create initial surface 88s
- Topology correction: 96s
- Surface refinement: 89s
- Reduction of surface collisions with optimization: 74s
- Spherical mapping with areal smoothing 82s
- Spherical registration 291s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 31s
- CSF distance: 15s
- PBT2x thickness: 47s
- 99s
- Create initial surface 90s
- Topology correction: 99s
- Surface refinement: 114s
- Reduction of surface collisions with optimization: 75s
- Spherical mapping with areal smoothing 92s
- Spherical registration 338s
- Final surface processing results:
- Average thickness (FS): 2.5735 0.6054 mm
- Surface intensity / position RMSE: 0.0669 / 0.0658
- Euler number / defect number / defect size: 20.0 / 12.5 / 0.60%
- Display thickness: /var/lib/condor/execute/dir_3065028/ds/SWU_4/sub-0025723/ses-1/surf/lh.thickness.sub-0025723_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3065028/ds/SWU_4/sub-0025723/ses-1/surf/rh.thickness.sub-0025723_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3065028/ds/SWU_4/sub-0025723/ses-1/sub-0025723_ses-1_run-1_T1w.nii
- Surface ROI estimation: 12s
- Surface and thickness estimation takes: 1841s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 13s
- ROI estimation of 'neuromorphometrics' atlas 45s
- ROI estimation of 'lpba40' atlas 11s
- ROI estimation of 'hammers' atlas 34s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 9s
- ROI estimation of 'aal3' atlas 16s
- ROI estimation of 'mori' atlas 20s
- ROI estimation of 'anatomy3' atlas 29s
- ROI estimation of 'julichbrain' atlas 37s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 26s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 57s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 88s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s
- Write results 8s
- 413s
- Quality check: 12s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3065028/ds/SWU_4/sub-0025723/ses-1/report/catreport_sub-0025723_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 53 minute(s) and 33 second(s).
- Image Quality Rating (IQR): 83.61% (B)
- GM volume (GMV): 47.61% (749.21 / 1573.62 ml)
- GM thickness (GMT): 2.57 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3065028/ds/SWU_4/sub-0025723/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_3065028/ds/SWU_4/sub-0025723/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_3065028/ds/SWU_4/sub-0025723/ses-1/label
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