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- CAT12.8.1 r2040: 1/1: ./sub-0027271/ses-2/sub-0027271_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 50s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 5s
- Initial correction 5s
- Refine background 3s
- Final correction 4s
- Final scaling 4s
- 31s
- Correct center-of-mass 5s
- Affine registration 7s
- SPM preprocessing 1 (estimate 1 - TPM registration): 67s
- SPM preprocessing 1 (estimate 2): 41s
- SPM preprocessing 2 (write):
- Write Segmentation 14s
- Update Segmentation 16s
- Update Skull-Stripping 34s
- Update probability maps 7s
- 72s
- Global intensity correction: 13s
- SANLM denoising after intensity normalization (medium): 22s
- Fast Optimized Shooting registration 29s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 12s
- Estimate local tissue thresholds (WM) 15s
- Estimate local tissue thresholds (GM) 23s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 35s
- 92s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 3s
- Ventricle detection 11s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.06) 19s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 55s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 28s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 2s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 9s
- 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 | 0.0873 0.0000 0.0873 | 32.0000
- 2 | 2.50 | 0.0838 0.0014 0.0853 | 29.4886
- 3 | 2.50 | 0.0828 0.0022 0.0850 | 26.9772
- 4 | 2.50 | 0.0823 0.0025 0.0848 | 24.6107
- 5 | 2.50 | 0.0819 0.0027 0.0846 | 22.6548
- 6 | 2.50 | 0.0815 0.0028 0.0843 | 20.6989
- 7 | 2.50 | 0.0812 0.0029 0.0841 | 18.9688
- 8 | 2.50 | 0.0808 0.0030 0.0838 | 17.4455
- 9 | 2.50 | 0.0804 0.0031 0.0835 | 15.9223
- 10 | 2.50 | 0.0800 0.0032 0.0833 | 14.6627
- 11 | 2.50 | 0.0796 0.0033 0.0830 | 13.4764
- 12 | 2.50 | 0.0793 0.0034 0.0827 | 12.3015
- 13 | 2.50 | 0.0788 0.0035 0.0824 | 11.3776
- 14 | 2.50 | 0.0784 0.0036 0.0820 | 10.4537
- 15 | 2.25 | 0.0774 0.0037 0.0811 | 9.5920
- 16 | 2.25 | 0.0742 0.0053 0.0794 | 8.8725
- 29 | 2.00 | 0.0750 0.0024 0.0773 | 3.3283
- 30 | 2.00 | 0.0689 0.0048 0.0737 | 3.1221
- 31 | 2.00 | 0.0669 0.0057 0.0726 | 2.9160
- 43 | 1.75 | 0.0656 0.0033 0.0690 | 1.5785
- 44 | 1.75 | 0.0616 0.0054 0.0670 | 1.5194
- 45 | 1.75 | 0.0602 0.0062 0.0664 | 1.4626
- 57 | 1.50 | 0.0586 0.0045 0.0631 | 1.0900
- 58 | 1.50 | 0.0556 0.0064 0.0620 | 1.0730
- Shooting registration with 2.50:-0.25:1.50 mm takes: 145s
- Prepare output 10s
- 155s
- Jacobian determinant (RMS): 0.013 0.047 0.068 0.092 0.115 | 0.119704
- Template Matching: 0.087 0.223 0.201 0.181 0.167 | 0.166762
- Write result maps: 31s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 29s
- CSF distance: 14s
- PBT2x thickness: 41s
- 90s
- Create initial surface 79s
- Topology correction: 75s
- Surface refinement: 88s
- Reduction of surface collisions with optimization: 60s
- Spherical mapping with areal smoothing 85s
- Spherical registration 305s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 27s
- CSF distance: 14s
- PBT2x thickness: 39s
- 85s
- Create initial surface 76s
- Topology correction: 71s
- Surface refinement: 90s
- Reduction of surface collisions with optimization: 56s
- Spherical mapping with areal smoothing 68s
- Spherical registration 291s
- Final surface processing results:
- Average thickness (FS): 2.4641 0.6105 mm
- Surface intensity / position RMSE: 0.0677 / 0.0649
- Euler number / defect number / defect size: 18.0 / 11.5 / 0.40%
- Display thickness: /var/lib/condor/execute/dir_612028/ds/UWM/sub-0027271/ses-2/surf/lh.thickness.sub-0027271_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_612028/ds/UWM/sub-0027271/ses-2/surf/rh.thickness.sub-0027271_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_612028/ds/UWM/sub-0027271/ses-2/sub-0027271_ses-2_run-1_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1607s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 8s
- ROI estimation of 'neuromorphometrics' atlas 28s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 19s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 10s
- ROI estimation of 'mori' atlas 16s
- 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 46s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 70s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s
- Write results 7s
- 304s
- Quality check: 10s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_612028/ds/UWM/sub-0027271/ses-2/report/catreport_sub-0027271_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 44 minute(s) and 53 second(s).
- Image Quality Rating (IQR): 83.31% (B-)
- GM volume (GMV): 49.58% (627.09 / 1264.89 ml)
- GM thickness (GMT): 2.46 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_612028/ds/UWM/sub-0027271/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_612028/ds/UWM/sub-0027271/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_612028/ds/UWM/sub-0027271/ses-2/label
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