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- CAT12.8.1 r2040: 1/1: ./sub-0025629/ses-2/sub-0025629_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 80s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 7s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 39s
- Correct center-of-mass 2s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 68s
- SPM preprocessing 1 (estimate 2): 62s
- SPM preprocessing 2 (write):
- Write Segmentation 16s
- Update Segmentation 18s
- Update Skull-Stripping 41s
- Update probability maps 8s
- 83s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 24s
- Fast Optimized Shooting registration 31s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.14) 13s
- Estimate local tissue thresholds (WM) 17s
- Estimate local tissue thresholds (GM) 24s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 44s
- 108s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 12s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.08) 23s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 62s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 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 | 0.0850 0.0000 0.0850 | 32.0000
- 2 | 2.50 | 0.0823 0.0012 0.0835 | 29.4886
- 3 | 2.50 | 0.0815 0.0019 0.0833 | 26.9772
- 4 | 2.50 | 0.0810 0.0021 0.0832 | 24.6107
- 5 | 2.50 | 0.0807 0.0023 0.0830 | 22.6548
- 6 | 2.50 | 0.0804 0.0024 0.0828 | 20.6989
- 7 | 2.50 | 0.0801 0.0025 0.0826 | 18.9688
- 8 | 2.50 | 0.0798 0.0026 0.0824 | 17.4455
- 9 | 2.50 | 0.0795 0.0027 0.0822 | 15.9223
- 10 | 2.50 | 0.0792 0.0028 0.0820 | 14.6627
- 11 | 2.50 | 0.0788 0.0029 0.0817 | 13.4764
- 12 | 2.50 | 0.0785 0.0030 0.0815 | 12.3015
- 13 | 2.50 | 0.0781 0.0031 0.0812 | 11.3776
- 14 | 2.50 | 0.0778 0.0032 0.0810 | 10.4537
- 15 | 2.25 | 0.0772 0.0033 0.0805 | 9.5920
- 16 | 2.25 | 0.0740 0.0049 0.0789 | 8.8725
- 29 | 2.00 | 0.0748 0.0022 0.0770 | 3.3283
- 30 | 2.00 | 0.0678 0.0050 0.0728 | 3.1221
- 31 | 2.00 | 0.0654 0.0061 0.0716 | 2.9160
- 43 | 1.75 | 0.0640 0.0035 0.0675 | 1.5785
- 44 | 1.75 | 0.0596 0.0058 0.0654 | 1.5194
- 45 | 1.75 | 0.0581 0.0066 0.0647 | 1.4626
- 57 | 1.50 | 0.0563 0.0048 0.0612 | 1.0900
- 58 | 1.50 | 0.0534 0.0067 0.0602 | 1.0730
- 59 | 1.50 | 0.0525 0.0073 0.0598 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 168s
- Prepare output 10s
- 178s
- Jacobian determinant (RMS): 0.011 0.041 0.063 0.089 0.111 | 0.118077
- Template Matching: 0.085 0.222 0.196 0.174 0.157 | 0.157410
- Write result maps: 33s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 47s
- CSF distance: 14s
- PBT2x thickness: 40s
- 107s
- Create initial surface 80s
- Topology correction: 74s
- Surface refinement: 95s
- Reduction of surface collisions with optimization: 60s
- Spherical mapping with areal smoothing 79s
- Spherical registration 305s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 30s
- CSF distance: 14s
- PBT2x thickness: 39s
- 88s
- Create initial surface 77s
- Topology correction: 72s
- Surface refinement: 82s
- Reduction of surface collisions with optimization: 56s
- Spherical mapping with areal smoothing 69s
- Spherical registration 285s
- Final surface processing results:
- Average thickness (FS): 2.5114 0.6183 mm
- Surface intensity / position RMSE: 0.0615 / 0.0596
- Euler number / defect number / defect size: 12.0 / 10.5 / 0.25%
- Display thickness: /var/lib/condor/execute/dir_937471/ds/SWU_4/sub-0025629/ses-2/surf/lh.thickness.sub-0025629_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_937471/ds/SWU_4/sub-0025629/ses-2/surf/rh.thickness.sub-0025629_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_937471/ds/SWU_4/sub-0025629/ses-2/sub-0025629_ses-2_run-1_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1620s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 8s
- ROI estimation of 'neuromorphometrics' atlas 29s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 20s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 12s
- ROI estimation of 'mori' atlas 17s
- ROI estimation of 'anatomy3' atlas 25s
- ROI estimation of 'julichbrain' atlas 33s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 13s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 24s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 54s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 82s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s
- Write results 8s
- 344s
- Quality check: 11s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_937471/ds/SWU_4/sub-0025629/ses-2/report/catreport_sub-0025629_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 48 minute(s) and 43 second(s).
- Image Quality Rating (IQR): 83.51% (B)
- GM volume (GMV): 45.07% (629.29 / 1396.37 ml)
- GM thickness (GMT): 2.51 0.62 mm
- Segmentations are saved in /var/lib/condor/execute/dir_937471/ds/SWU_4/sub-0025629/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_937471/ds/SWU_4/sub-0025629/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_937471/ds/SWU_4/sub-0025629/ses-2/label
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