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- CAT12.8.1 r1980: 1/1: ./dir_19436/ds/sub-009/sub-009_ses-t0_T1w.n
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- SANLM denoising (medium): 18s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 6s
- Initial correction 6s
- Refine background 3s
- Final correction 4s
- Final scaling 5s
- 35s
- Correct center-of-mass 4s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 70s
- SPM preprocessing 1 (estimate 2): 59s
- SPM preprocessing 2 (write):
- Write Segmentation 15s
- Update Segmentation 17s
- Update Skull-Stripping 39s
- Update probability maps 8s
- 79s
- Global intensity correction: 14s
- SANLM denoising after intensity normalization (medium): 17s
- Fast Optimized Shooting registration 33s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.12) 13s
- Estimate local tissue thresholds (WM) 15s
- Estimate local tissue thresholds (GM) 19s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 24s
- 80s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 11s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.04) 24s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 62s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 31s
- 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 | 0.0855 0.0000 0.0855 | 32.0000
- 2 | 2.50 | 0.0822 0.0014 0.0836 | 29.4886
- 3 | 2.50 | 0.0812 0.0021 0.0833 | 26.9772
- 4 | 2.50 | 0.0807 0.0024 0.0831 | 24.6107
- 5 | 2.50 | 0.0803 0.0026 0.0829 | 22.6548
- 6 | 2.50 | 0.0799 0.0027 0.0827 | 20.6989
- 7 | 2.50 | 0.0796 0.0029 0.0824 | 18.9688
- 8 | 2.50 | 0.0792 0.0030 0.0822 | 17.4455
- 9 | 2.50 | 0.0788 0.0031 0.0819 | 15.9223
- 10 | 2.50 | 0.0784 0.0032 0.0816 | 14.6627
- 11 | 2.50 | 0.0780 0.0034 0.0813 | 13.4764
- 12 | 2.50 | 0.0775 0.0034 0.0810 | 12.3015
- 13 | 2.50 | 0.0771 0.0036 0.0807 | 11.3776
- 14 | 2.50 | 0.0767 0.0037 0.0803 | 10.4537
- 15 | 2.25 | 0.0761 0.0038 0.0799 | 9.5920
- 16 | 2.25 | 0.0728 0.0055 0.0783 | 8.8725
- 29 | 2.00 | 0.0733 0.0025 0.0758 | 3.3283
- 30 | 2.00 | 0.0664 0.0053 0.0717 | 3.1221
- 31 | 2.00 | 0.0640 0.0064 0.0704 | 2.9160
- 43 | 1.75 | 0.0624 0.0037 0.0661 | 1.5785
- 44 | 1.75 | 0.0581 0.0059 0.0640 | 1.5194
- 45 | 1.75 | 0.0566 0.0067 0.0633 | 1.4626
- 57 | 1.50 | 0.0549 0.0050 0.0599 | 1.0900
- 58 | 1.50 | 0.0520 0.0068 0.0588 | 1.0730
- 59 | 1.50 | 0.0511 0.0074 0.0585 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 163s
- Prepare output 10s
- 173s
- Jacobian determinant (RMS): 0.013 0.050 0.075 0.103 0.125 | 0.131886
- Template Matching: 0.086 0.218 0.192 0.170 0.153 | 0.153215
- Write result maps: 22s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 56s
- CSF distance: 13s
- PBT2x thickness: 38s
- 112s
- Create initial surface 77s
- Topology correction: 69s
- Surface refinement: 55s
- Reduction of surface collisions with optimization: 50s
- Spherical mapping with areal smoothing 65s
- Spherical registration 293s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 28s
- CSF distance: 12s
- PBT2x thickness: 35s
- 81s
- Create initial surface 74s
- Topology correction: 68s
- Surface refinement: 65s
- Reduction of surface collisions with optimization: 51s
- Spherical mapping with areal smoothing 66s
- Spherical registration 287s
- Final surface processing results:
- Average thickness (FS): 2.4845 0.6111 mm
- Surface intensity / position RMSE: 0.0632 / 0.0630
- Euler number / defect number / defect size: 10.0 / 7.0 / 0.48%
- Display thickness: /var/lib/condor/execute/dir_19436/ds/sub-009/surf/lh.thickness.sub-009_ses-t0_T1w
- Display thickness: /var/lib/condor/execute/dir_19436/ds/sub-009/surf/rh.thickness.sub-009_ses-t0_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_19436/ds/sub-009/sub-009_ses-t0_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1492s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 25s
- ROI estimation of 'lpba40' atlas 7s
- ROI estimation of 'hammers' atlas 18s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 6s
- ROI estimation of 'aal3' atlas 10s
- ROI estimation of 'mori' atlas 15s
- ROI estimation of 'anatomy3' atlas 22s
- ROI estimation of 'julichbrain' atlas 29s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 49s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 82s
- Write results 84s
- 306s
- Quality check: 5s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_19436/ds/sub-009/report/catreport_sub-009_ses-t0_T1w.pdf
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- CAT preprocessing takes 43 minute(s) and 33 second(s).
- Image Quality Rating (IQR): 82.80% (B-)
- GM volume (GMV): 45.25% (574.13 / 1268.90 ml)
- GM thickness (GMT): 2.48 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_19436/ds/sub-009/mri
- Reports are saved in /var/lib/condor/execute/dir_19436/ds/sub-009/report
- Labels are saved in /var/lib/condor/execute/dir_19436/ds/sub-009/label
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