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- CAT12.8.1 r1980: 1/1: ./execute/dir_44936/ds/sub-003/sub-003_T1w.n
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- SANLM denoising (medium): 169s
- APP: Rough bias correction:
- Initialize 13s
- Estimate background 14s
- Initial correction 13s
- Refine background 7s
- Final correction 13s
- Final scaling 21s
- 93s
- Correct center-of-mass 7s
- Affine registration 18s
- SPM preprocessing 1 (estimate 1 - TPM registration): 164s
- SPM preprocessing 1 (estimate 2): 89s
- SPM preprocessing 2 (write):
- Write Segmentation 33s
- Update Segmentation 44s
- Update Skull-Stripping 90s
- Update probability maps 17s
- 185s
- Global intensity correction: 31s
- SANLM denoising after intensity normalization (medium): 37s
- Fast Optimized Shooting registration 56s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 12s
- Prepare partitions 5s
- Prepare segments (LASmod = 1.00) 38s
- Estimate local tissue thresholds (WM) 36s
- Estimate local tissue thresholds (GM) 51s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 51s
- 200s
- ROI segmentation (partitioning):
- Atlas -> subject space 19s
- Major structures 9s
- Ventricle detection 35s
- Blood vessel detection 25s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.09) 69s
- Manual stroke lesion detection 0s
- Closing of deep structures 5s
- Side alignment 11s
- Final corrections 9s
- 184s
- Blood vessel correction (BVCstr=0.50): 3s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 87s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 12s
- Level 1 cleanup (brain masking) 6s
- Level 2 cleanup (CSF correction) 4s
- Level 3 cleanup (CSF/WM PVE) 7s
- 29s
- 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 | 0.0863 0.0000 0.0863 | 32.0000
- 2 | 2.50 | 0.0828 0.0014 0.0842 | 29.4886
- 3 | 2.50 | 0.0817 0.0022 0.0839 | 26.9772
- 4 | 2.50 | 0.0812 0.0025 0.0837 | 24.6107
- 5 | 2.50 | 0.0808 0.0027 0.0835 | 22.6548
- 6 | 2.50 | 0.0804 0.0028 0.0832 | 20.6989
- 7 | 2.50 | 0.0801 0.0029 0.0830 | 18.9688
- 8 | 2.50 | 0.0797 0.0030 0.0827 | 17.4455
- 9 | 2.50 | 0.0793 0.0031 0.0824 | 15.9223
- 10 | 2.50 | 0.0789 0.0033 0.0821 | 14.6627
- 11 | 2.50 | 0.0785 0.0034 0.0818 | 13.4764
- 12 | 2.50 | 0.0781 0.0034 0.0815 | 12.3015
- 13 | 2.50 | 0.0777 0.0036 0.0812 | 11.3776
- 14 | 2.50 | 0.0773 0.0036 0.0809 | 10.4537
- 15 | 2.25 | 0.0768 0.0037 0.0805 | 9.5920
- 16 | 2.25 | 0.0734 0.0054 0.0788 | 8.8725
- 29 | 2.00 | 0.0746 0.0024 0.0770 | 3.3283
- 30 | 2.00 | 0.0682 0.0050 0.0732 | 3.1221
- 31 | 2.00 | 0.0660 0.0060 0.0720 | 2.9160
- 43 | 1.75 | 0.0651 0.0035 0.0685 | 1.5785
- 44 | 1.75 | 0.0607 0.0058 0.0664 | 1.5194
- 45 | 1.75 | 0.0592 0.0066 0.0657 | 1.4626
- 57 | 1.50 | 0.0576 0.0048 0.0624 | 1.0900
- 58 | 1.50 | 0.0543 0.0069 0.0612 | 1.0730
- 59 | 1.50 | 0.0532 0.0076 0.0608 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 247s
- Prepare output 18s
- 264s
- Jacobian determinant (RMS): 0.012 0.044 0.064 0.087 0.109 | 0.115363
- Template Matching: 0.086 0.220 0.198 0.177 0.160 | 0.159723
- Write result maps: 49s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 68s
- CSF distance: 21s
- PBT2x thickness: 63s
- 160s
- Create initial surface 108s
- Topology correction: 126s
- Surface refinement: 106s
- Reduction of surface collisions with optimization: 97s
- Spherical mapping with areal smoothing 111s
- Spherical registration 300s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 75s
- CSF distance: 21s
- PBT2x thickness: 62s
- 167s
- Create initial surface 106s
- Topology correction: 125s
- Surface refinement: 106s
- Reduction of surface collisions with optimization: 96s
- Spherical mapping with areal smoothing 109s
- Spherical registration 291s
- Final surface processing results:
- Average thickness (FS): 2.4883 0.5767 mm
- Surface intensity / position RMSE: 0.0634 / 0.0603
- Euler number / defect number / defect size: 10.0 / 5.0 / 0.17%
- Display thickness: /var/lib/condor/execute/dir_44936/ds/sub-003/surf/lh.thickness.sub-003_T1w
- Display thickness: /var/lib/condor/execute/dir_44936/ds/sub-003/surf/rh.thickness.sub-003_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_44936/ds/sub-003/sub-003_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 2142s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 23s
- ROI estimation of 'neuromorphometrics' atlas 83s
- ROI estimation of 'lpba40' atlas 24s
- ROI estimation of 'hammers' atlas 58s
- ROI estimation of 'thalamus' atlas 4s
- ROI estimation of 'ibsr' atlas 20s
- ROI estimation of 'aal3' atlas 34s
- ROI estimation of 'mori' atlas 51s
- ROI estimation of 'anatomy3' atlas 72s
- ROI estimation of 'julichbrain' atlas 96s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 35s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 45s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 154s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 230s
- Write results 231s
- 930s
- Quality check: 11s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_44936/ds/sub-003/report/catreport_sub-003_T1w.pdf
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- CAT preprocessing takes 82 minute(s) and 14 second(s).
- Image Quality Rating (IQR): 87.69% (B+)
- GM volume (GMV): 47.00% (699.57 / 1488.37 ml)
- GM thickness (GMT): 2.49 0.58 mm
- Segmentations are saved in /var/lib/condor/execute/dir_44936/ds/sub-003/mri
- Reports are saved in /var/lib/condor/execute/dir_44936/ds/sub-003/report
- Labels are saved in /var/lib/condor/execute/dir_44936/ds/sub-003/label
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