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- CAT12.8.1 r1980: 1/1: ./ds/sub-f5001ob/sub-f5001ob_ses-wave1bas_T1w.n
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- SANLM denoising (medium): 157s
- APP: Rough bias correction:
- Initialize 11s
- Estimate background 10s
- Initial correction 11s
- Refine background 5s
- Final correction 10s
- Final scaling 11s
- 69s
- Correct center-of-mass 5s
- Affine registration 18s
- SPM preprocessing 1 (estimate 1 - TPM registration): 122s
- SPM preprocessing 1 (estimate 2): 44s
- SPM preprocessing 2 (write):
- Write Segmentation 26s
- Update Segmentation 31s
- Update Skull-Stripping 68s
- Update probability maps 15s
- 141s
- Global intensity correction: 27s
- SANLM denoising after intensity normalization (medium): 35s
- Fast Optimized Shooting registration 41s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 7s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.00) 24s
- Estimate local tissue thresholds (WM) 31s
- Estimate local tissue thresholds (GM) 40s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 69s
- 182s
- ROI segmentation (partitioning):
- Atlas -> subject space 13s
- Major structures 6s
- Ventricle detection 26s
- Blood vessel detection 17s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 58s
- Manual stroke lesion detection 0s
- Closing of deep structures 3s
- Side alignment 7s
- Final corrections 7s
- 137s
- Blood vessel correction (BVCstr=0.50): 3s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 50s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 8s
- Level 1 cleanup (brain masking) 4s
- Level 2 cleanup (CSF correction) 2s
- 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 | 0.0838 0.0000 0.0838 | 32.0000
- 2 | 2.50 | 0.0800 0.0015 0.0815 | 29.4886
- 3 | 2.50 | 0.0788 0.0024 0.0812 | 26.9772
- 4 | 2.50 | 0.0783 0.0027 0.0809 | 24.6107
- 5 | 2.50 | 0.0778 0.0029 0.0807 | 22.6548
- 6 | 2.50 | 0.0774 0.0031 0.0805 | 20.6989
- 7 | 2.50 | 0.0770 0.0032 0.0802 | 18.9688
- 8 | 2.50 | 0.0766 0.0034 0.0799 | 17.4455
- 9 | 2.50 | 0.0761 0.0035 0.0796 | 15.9223
- 10 | 2.50 | 0.0757 0.0036 0.0793 | 14.6627
- 11 | 2.50 | 0.0752 0.0038 0.0790 | 13.4764
- 12 | 2.50 | 0.0748 0.0038 0.0786 | 12.3015
- 13 | 2.50 | 0.0743 0.0040 0.0783 | 11.3776
- 14 | 2.50 | 0.0738 0.0041 0.0779 | 10.4537
- 15 | 2.25 | 0.0732 0.0042 0.0774 | 9.5920
- 16 | 2.25 | 0.0693 0.0062 0.0755 | 8.8725
- 17 | 2.25 | 0.0677 0.0069 0.0746 | 8.1530
- 29 | 2.00 | 0.0681 0.0032 0.0713 | 3.3283
- 30 | 2.00 | 0.0617 0.0059 0.0675 | 3.1221
- 31 | 2.00 | 0.0595 0.0069 0.0664 | 2.9160
- 43 | 1.75 | 0.0581 0.0040 0.0621 | 1.5785
- 44 | 1.75 | 0.0539 0.0062 0.0601 | 1.5194
- 45 | 1.75 | 0.0526 0.0069 0.0595 | 1.4626
- 57 | 1.50 | 0.0508 0.0051 0.0559 | 1.0900
- 58 | 1.50 | 0.0480 0.0069 0.0549 | 1.0730
- 59 | 1.50 | 0.0471 0.0075 0.0546 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 158s
- Prepare output 14s
- 172s
- Jacobian determinant (RMS): 0.014 0.053 0.081 0.109 0.134 | 0.141637
- Template Matching: 0.084 0.203 0.179 0.158 0.141 | 0.141174
- Write result maps: 36s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 39s
- CSF distance: 13s
- PBT2x thickness: 39s
- 96s
- Create initial surface 75s
- Topology correction: 73s
- Surface refinement: 77s
- Reduction of surface collisions with optimization: 57s
- Spherical mapping with areal smoothing 82s
- Spherical registration 319s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 33s
- CSF distance: 13s
- PBT2x thickness: 40s
- 92s
- Create initial surface 75s
- Topology correction: 83s
- Surface refinement: 82s
- Reduction of surface collisions with optimization: 53s
- Spherical mapping with areal smoothing 67s
- Spherical registration 273s
- Final surface processing results:
- Average thickness (FS): 2.4808 0.6262 mm
- Surface intensity / position RMSE: 0.0659 / 0.0662
- Euler number / defect number / defect size: 14.0 / 12.0 / 0.58%
- Display thickness: /var/lib/condor/execute/dir_15318/ds/sub-f5001ob/surf/lh.thickness.sub-f5001ob_ses-wave1bas_T1w
- Display thickness: /var/lib/condor/execute/dir_15318/ds/sub-f5001ob/surf/rh.thickness.sub-f5001ob_ses-wave1bas_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_15318/ds/sub-f5001ob/sub-f5001ob_ses-wave1bas_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1607s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 13s
- ROI estimation of 'neuromorphometrics' atlas 50s
- ROI estimation of 'lpba40' atlas 15s
- ROI estimation of 'hammers' atlas 35s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 12s
- ROI estimation of 'aal3' atlas 20s
- ROI estimation of 'mori' atlas 30s
- ROI estimation of 'anatomy3' atlas 42s
- ROI estimation of 'julichbrain' atlas 58s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 23s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 40s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 94s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 130s
- Write results 131s
- 566s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_15318/ds/sub-f5001ob/report/catreport_sub-f5001ob_ses-wave1bas_T1w.pdf
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- CAT preprocessing takes 60 minute(s) and 10 second(s).
- Image Quality Rating (IQR): 86.38% (B)
- GM volume (GMV): 45.40% (602.69 / 1327.57 ml)
- GM thickness (GMT): 2.48 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_15318/ds/sub-f5001ob/mri
- Reports are saved in /var/lib/condor/execute/dir_15318/ds/sub-f5001ob/report
- Labels are saved in /var/lib/condor/execute/dir_15318/ds/sub-f5001ob/label
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