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- CAT12.8.1 r1980: 1/1: ./sub-season211_ses-3_acq-MPrageHiRes_T1w.n
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- SANLM denoising (medium): 107s
- APP: Rough bias correction:
- Initialize 11s
- Estimate background 12s
- Initial correction 16s
- Refine background 6s
- Final correction 13s
- Final scaling 12s
- 81s
- Correct center-of-mass 12s
- Affine registration 19s
- SPM preprocessing 1 (estimate 1 - TPM registration): 122s
- SPM preprocessing 1 (estimate 2): 161s
- SPM preprocessing 2 (write):
- Write Segmentation 26s
- Update Segmentation 31s
- Update Skull-Stripping 68s
- Update probability maps 14s
- 139s
- Global intensity correction: 27s
- SANLM denoising after intensity normalization (medium): 14s
- Fast Optimized Shooting registration 49s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 8s
- Prepare partitions 5s
- Prepare segments (LASmod = 1.00) 24s
- Estimate local tissue thresholds (WM) 28s
- Estimate local tissue thresholds (GM) 35s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 38s
- 144s
- ROI segmentation (partitioning):
- Atlas -> subject space 15s
- Major structures 6s
- Ventricle detection 19s
- Blood vessel detection 14s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 42s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 6s
- Final corrections 8s
- 111s
- Blood vessel correction (BVCstr=0.50): 3s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 58s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 7s
- Level 1 cleanup (brain masking) 5s
- Level 2 cleanup (CSF correction) 3s
- Level 3 cleanup (CSF/WM PVE) 5s
- 19s
- 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 | 0.0812 0.0000 0.0812 | 32.0000
- 2 | 2.50 | 0.0779 0.0014 0.0793 | 29.4886
- 3 | 2.50 | 0.0769 0.0021 0.0791 | 26.9772
- 4 | 2.50 | 0.0765 0.0024 0.0789 | 24.6107
- 5 | 2.50 | 0.0761 0.0026 0.0787 | 22.6548
- 6 | 2.50 | 0.0757 0.0027 0.0784 | 20.6989
- 7 | 2.50 | 0.0754 0.0028 0.0782 | 18.9688
- 8 | 2.50 | 0.0750 0.0029 0.0780 | 17.4455
- 9 | 2.50 | 0.0746 0.0030 0.0777 | 15.9223
- 10 | 2.50 | 0.0742 0.0032 0.0774 | 14.6627
- 11 | 2.50 | 0.0739 0.0033 0.0771 | 13.4764
- 12 | 2.50 | 0.0735 0.0034 0.0768 | 12.3015
- 13 | 2.50 | 0.0730 0.0035 0.0765 | 11.3776
- 14 | 2.50 | 0.0726 0.0036 0.0762 | 10.4537
- 15 | 2.25 | 0.0709 0.0037 0.0745 | 9.5920
- 16 | 2.25 | 0.0677 0.0052 0.0730 | 8.8725
- 29 | 2.00 | 0.0677 0.0024 0.0701 | 3.3283
- 30 | 2.00 | 0.0619 0.0047 0.0666 | 3.1221
- 31 | 2.00 | 0.0600 0.0056 0.0655 | 2.9160
- 43 | 1.75 | 0.0586 0.0033 0.0619 | 1.5785
- 44 | 1.75 | 0.0551 0.0051 0.0602 | 1.5194
- 45 | 1.75 | 0.0539 0.0058 0.0596 | 1.4626
- 57 | 1.50 | 0.0523 0.0042 0.0565 | 1.0900
- 58 | 1.50 | 0.0497 0.0059 0.0556 | 1.0730
- Shooting registration with 2.50:-0.25:1.50 mm takes: 196s
- Prepare output 14s
- 210s
- Jacobian determinant (RMS): 0.014 0.049 0.072 0.095 0.116 | 0.120043
- Template Matching: 0.081 0.203 0.180 0.162 0.149 | 0.149060
- Write result maps: 47s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 33s
- CSF distance: 17s
- PBT2x thickness: 51s
- 110s
- Create initial surface 95s
- Topology correction: 105s
- Surface refinement: 91s
- Reduction of surface collisions with optimization: 82s
- Spherical mapping with areal smoothing 94s
- Spherical registration 267s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 31s
- CSF distance: 17s
- PBT2x thickness: 51s
- 106s
- Create initial surface 90s
- Topology correction: 106s
- Surface refinement: 94s
- Reduction of surface collisions with optimization: 84s
- Spherical mapping with areal smoothing 96s
- Spherical registration 278s
- Final surface processing results:
- Average thickness (FS): 2.4584 0.5665 mm
- Surface intensity / position RMSE: 0.0742 / 0.0712
- Euler number / defect number / defect size: 12.0 / 9.0 / 0.16%
- Display thickness: /var/lib/condor/execute/dir_2516/ds/sub-season211/surf/lh.thickness.sub-season211_ses-3_acq-MPrageHiRes_T1w
- Display thickness: /var/lib/condor/execute/dir_2516/ds/sub-season211/surf/rh.thickness.sub-season211_ses-3_acq-MPrageHiRes_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2516/ds/sub-season211/sub-season211_ses-3_acq-MPrageHiRes_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1813s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 21s
- ROI estimation of 'neuromorphometrics' atlas 74s
- ROI estimation of 'lpba40' atlas 22s
- ROI estimation of 'hammers' atlas 47s
- ROI estimation of 'thalamus' atlas 4s
- ROI estimation of 'ibsr' atlas 17s
- ROI estimation of 'aal3' atlas 27s
- ROI estimation of 'mori' atlas 41s
- ROI estimation of 'anatomy3' atlas 61s
- ROI estimation of 'julichbrain' atlas 79s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 31s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 35s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 121s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 180s
- Write results 181s
- 762s
- Quality check: 7s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2516/ds/sub-season211/report/catreport_sub-season211_ses-3_acq-MPrageHiRes_T1w.pdf
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- CAT preprocessing takes 69 minute(s) and 5 second(s).
- Image Quality Rating (IQR): 86.51% (B)
- GM volume (GMV): 50.79% (630.09 / 1240.46 ml)
- GM thickness (GMT): 2.46 0.57 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2516/ds/sub-season211/mri
- Reports are saved in /var/lib/condor/execute/dir_2516/ds/sub-season211/report
- Labels are saved in /var/lib/condor/execute/dir_2516/ds/sub-season211/label
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