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- CAT12.8.1 r2040: 1/1: ./sub-0003059/ses-1/sub-0003059_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 87s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 6s
- Initial correction 5s
- Refine background 3s
- Final correction 4s
- Final scaling 5s
- 34s
- Correct center-of-mass 3s
- Affine registration 7s
- SPM preprocessing 1 (estimate 1 - TPM registration): 7s
- Use initial fine affine registration. 7s
- Use previous fine affine registration. 50s
- SPM preprocessing 1 (estimate 2): 57s
- SPM preprocessing 2 (write):
- Write Segmentation 14s
- Update Segmentation 16s
- Update Skull-Stripping 36s
- Update probability maps 7s
- 73s
- Global intensity correction: 13s
- SANLM denoising after intensity normalization (medium): 22s
- Fast Optimized Shooting registration 26s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 11s
- Estimate local tissue thresholds (WM) 15s
- Estimate local tissue thresholds (GM) 20s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 30s
- 84s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 3s
- Ventricle detection 9s
- Blood vessel detection 7s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.08) 18s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 51s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 28s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.07,0.990.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 3s
- Level 1 cleanup (brain masking) 3s
- 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 | 0.0825 0.0000 0.0825 | 32.0000
- 2 | 2.50 | 0.0799 0.0012 0.0811 | 29.4886
- 3 | 2.50 | 0.0791 0.0018 0.0809 | 26.9772
- 4 | 2.50 | 0.0787 0.0020 0.0807 | 24.6107
- 5 | 2.50 | 0.0783 0.0022 0.0806 | 22.6548
- 6 | 2.50 | 0.0781 0.0023 0.0804 | 20.6989
- 7 | 2.50 | 0.0778 0.0024 0.0802 | 18.9688
- 8 | 2.50 | 0.0775 0.0025 0.0800 | 17.4455
- 9 | 2.50 | 0.0772 0.0026 0.0798 | 15.9223
- 10 | 2.50 | 0.0768 0.0027 0.0795 | 14.6627
- 11 | 2.50 | 0.0765 0.0028 0.0793 | 13.4764
- 12 | 2.50 | 0.0762 0.0029 0.0790 | 12.3015
- 13 | 2.50 | 0.0758 0.0030 0.0788 | 11.3776
- 14 | 2.50 | 0.0755 0.0031 0.0785 | 10.4537
- 15 | 2.25 | 0.0742 0.0032 0.0773 | 9.5920
- 16 | 2.25 | 0.0712 0.0046 0.0758 | 8.8725
- 29 | 2.00 | 0.0717 0.0021 0.0738 | 3.3283
- 30 | 2.00 | 0.0654 0.0046 0.0700 | 3.1221
- 31 | 2.00 | 0.0632 0.0057 0.0689 | 2.9160
- 43 | 1.75 | 0.0618 0.0033 0.0651 | 1.5785
- 44 | 1.75 | 0.0577 0.0054 0.0631 | 1.5194
- 45 | 1.75 | 0.0563 0.0062 0.0625 | 1.4626
- 57 | 1.50 | 0.0546 0.0045 0.0591 | 1.0900
- 58 | 1.50 | 0.0517 0.0064 0.0581 | 1.0730
- 59 | 1.50 | 0.0508 0.0070 0.0578 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 160s
- Prepare output 8s
- 168s
- Jacobian determinant (RMS): 0.011 0.042 0.064 0.090 0.113 | 0.119785
- Template Matching: 0.083 0.213 0.190 0.169 0.152 | 0.152375
- Write result maps: 41s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 21s
- CSF distance: 12s
- PBT2x thickness: 34s
- 72s
- Create initial surface 64s
- Topology correction: 73s
- Surface refinement: 76s
- Reduction of surface collisions with optimization: 53s
- Spherical mapping with areal smoothing 63s
- Spherical registration 208s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 20s
- CSF distance: 11s
- PBT2x thickness: 32s
- 69s
- Create initial surface 60s
- Topology correction: 70s
- Surface refinement: 58s
- Reduction of surface collisions with optimization: 49s
- Spherical mapping with areal smoothing 61s
- Spherical registration 233s
- Final surface processing results:
- Average thickness (FS): 2.5433 0.6023 mm
- Surface intensity / position RMSE: 0.0626 / 0.0613
- Euler number / defect number / defect size: 16.0 / 12.0 / 0.35%
- Display thickness: /var/lib/condor/execute/dir_104054/ds/BMB_1/sub-0003059/ses-1/surf/lh.thickness.sub-0003059_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_104054/ds/BMB_1/sub-0003059/ses-1/surf/rh.thickness.sub-0003059_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_104054/ds/BMB_1/sub-0003059/ses-1/sub-0003059_ses-1_run-1_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1290s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 21s
- ROI estimation of 'neuromorphometrics' atlas 78s
- ROI estimation of 'lpba40' atlas 23s
- ROI estimation of 'hammers' atlas 55s
- ROI estimation of 'thalamus' atlas 4s
- ROI estimation of 'ibsr' atlas 20s
- ROI estimation of 'aal3' atlas 34s
- ROI estimation of 'mori' atlas 50s
- ROI estimation of 'anatomy3' atlas 72s
- ROI estimation of 'julichbrain' atlas 92s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 38s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 70s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 122s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 125s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 9s
- Write results 10s
- 815s
- Quality check: 10s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_104054/ds/BMB_1/sub-0003059/ses-1/report/catreport_sub-0003059_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 49 minute(s) and 44 second(s).
- Image Quality Rating (IQR): 84.45% (B)
- GM volume (GMV): 46.10% (696.68 / 1511.14 ml)
- GM thickness (GMT): 2.54 0.60 mm
- Segmentations are saved in /var/lib/condor/execute/dir_104054/ds/BMB_1/sub-0003059/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_104054/ds/BMB_1/sub-0003059/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_104054/ds/BMB_1/sub-0003059/ses-1/label
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