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- CAT12.8.1 r2040: 1/1: ./sub-0027368/ses-2/sub-0027368_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 44s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 6s
- Initial correction 8s
- Refine background 4s
- Final correction 6s
- Final scaling 5s
- 45s
- Correct center-of-mass 4s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 12s
- Use initial fine affine registration. 74s
- SPM preprocessing 1 (estimate 2): 81s
- SPM preprocessing 2 (write):
- Write Segmentation 20s
- Update Segmentation 20s
- Update Skull-Stripping 50s
- Update probability maps 11s
- 102s
- Global intensity correction: 20s
- SANLM denoising after intensity normalization (medium): 26s
- Fast Optimized Shooting registration 35s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.00) 14s
- Estimate local tissue thresholds (WM) 21s
- Estimate local tissue thresholds (GM) 30s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 47s
- 124s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 3s
- Ventricle detection 13s
- Blood vessel detection 9s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 24s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 3s
- Final corrections 5s
- 68s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 33s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.670.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 3s
- 12s
- 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 | 0.0826 0.0000 0.0826 | 32.0000
- 2 | 2.50 | 0.0800 0.0012 0.0811 | 29.4886
- 3 | 2.50 | 0.0792 0.0018 0.0810 | 26.9772
- 4 | 2.50 | 0.0788 0.0020 0.0808 | 24.6107
- 5 | 2.50 | 0.0785 0.0022 0.0807 | 22.6548
- 6 | 2.50 | 0.0782 0.0023 0.0805 | 20.6989
- 7 | 2.50 | 0.0780 0.0024 0.0803 | 18.9688
- 8 | 2.50 | 0.0777 0.0025 0.0801 | 17.4455
- 9 | 2.50 | 0.0774 0.0026 0.0799 | 15.9223
- 10 | 2.50 | 0.0770 0.0027 0.0797 | 14.6627
- 11 | 2.50 | 0.0767 0.0028 0.0795 | 13.4764
- 12 | 2.50 | 0.0764 0.0028 0.0793 | 12.3015
- 13 | 2.50 | 0.0761 0.0030 0.0790 | 11.3776
- 14 | 2.50 | 0.0758 0.0030 0.0788 | 10.4537
- 15 | 2.25 | 0.0758 0.0031 0.0789 | 9.5920
- 16 | 2.25 | 0.0728 0.0046 0.0774 | 8.8725
- 29 | 2.00 | 0.0743 0.0021 0.0764 | 3.3283
- 30 | 2.00 | 0.0679 0.0046 0.0726 | 3.1221
- 31 | 2.00 | 0.0657 0.0057 0.0714 | 2.9160
- 43 | 1.75 | 0.0647 0.0033 0.0680 | 1.5785
- 44 | 1.75 | 0.0603 0.0056 0.0659 | 1.5194
- 45 | 1.75 | 0.0588 0.0065 0.0652 | 1.4626
- 57 | 1.50 | 0.0574 0.0047 0.0621 | 1.0900
- 58 | 1.50 | 0.0542 0.0068 0.0610 | 1.0730
- 59 | 1.50 | 0.0531 0.0075 0.0606 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 172s
- Prepare output 11s
- 184s
- Jacobian determinant (RMS): 0.012 0.044 0.066 0.094 0.122 | 0.130017
- Template Matching: 0.083 0.218 0.197 0.176 0.159 | 0.159303
- Write result maps: 46s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 28s
- CSF distance: 14s
- PBT2x thickness: 41s
- 88s
- Create initial surface 77s
- Topology correction: 86s
- Surface refinement: 75s
- Reduction of surface collisions with optimization: 64s
- Spherical mapping with areal smoothing 76s
- Spherical registration 280s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 23s
- CSF distance: 13s
- PBT2x thickness: 39s
- 80s
- Create initial surface 76s
- Topology correction: 88s
- Surface refinement: 79s
- Reduction of surface collisions with optimization: 64s
- Spherical mapping with areal smoothing 75s
- Spherical registration 295s
- Final surface processing results:
- Average thickness (FS): 2.4895 0.5882 mm
- Surface intensity / position RMSE: 0.0705 / 0.0765
- Euler number / defect number / defect size: 18.0 / 11.0 / 0.91%
- Display thickness: /var/lib/condor/execute/dir_3676058/ds/DC_1/sub-0027368/ses-2/surf/lh.thickness.sub-0027368_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3676058/ds/DC_1/sub-0027368/ses-2/surf/rh.thickness.sub-0027368_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3676058/ds/DC_1/sub-0027368/ses-2/sub-0027368_ses-2_run-1_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1601s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 10s
- ROI estimation of 'neuromorphometrics' atlas 37s
- ROI estimation of 'lpba40' atlas 13s
- ROI estimation of 'hammers' atlas 34s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 13s
- ROI estimation of 'aal3' atlas 21s
- ROI estimation of 'mori' atlas 33s
- ROI estimation of 'anatomy3' atlas 49s
- ROI estimation of 'julichbrain' atlas 79s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 36s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 74s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 154s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 194s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 16s
- Write results 17s
- 766s
- Quality check: 15s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3676058/ds/DC_1/sub-0027368/ses-2/report/catreport_sub-0027368_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 56 minute(s) and 40 second(s).
- Image Quality Rating (IQR): 76.25% (C)
- GM volume (GMV): 52.20% (665.48 / 1274.97 ml)
- GM thickness (GMT): 2.49 0.59 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3676058/ds/DC_1/sub-0027368/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_3676058/ds/DC_1/sub-0027368/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_3676058/ds/DC_1/sub-0027368/ses-2/label
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