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- CAT12.8.1 r2040: 1/1: ./sub-0003034/ses-1/sub-0003034_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 74s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 4s
- Initial correction 5s
- Refine background 3s
- Final correction 4s
- Final scaling 4s
- 31s
- Correct center-of-mass 3s
- Affine registration 8s
- SPM preprocessing 1 (estimate 1 - TPM registration): 61s
- SPM preprocessing 1 (estimate 2): 52s
- SPM preprocessing 2 (write):
- Write Segmentation 14s
- Update Segmentation 16s
- Update Skull-Stripping 36s
- Update probability maps 8s
- 74s
- Global intensity correction: 13s
- SANLM denoising after intensity normalization (medium): 20s
- Fast Optimized Shooting registration 27s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 11s
- Estimate local tissue thresholds (WM) 14s
- Estimate local tissue thresholds (GM) 21s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 37s
- 92s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 2s
- Ventricle detection 8s
- Blood vessel detection 7s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.26) 17s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 49s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 27s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 3s
- 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 | 0.0871 0.0000 0.0871 | 32.0000
- 2 | 2.50 | 0.0848 0.0011 0.0859 | 29.4886
- 3 | 2.50 | 0.0841 0.0017 0.0858 | 26.9772
- 4 | 2.50 | 0.0838 0.0019 0.0857 | 24.6107
- 5 | 2.50 | 0.0835 0.0020 0.0855 | 22.6548
- 6 | 2.50 | 0.0832 0.0021 0.0853 | 20.6989
- 7 | 2.50 | 0.0830 0.0022 0.0852 | 18.9688
- 8 | 2.50 | 0.0827 0.0023 0.0850 | 17.4455
- 9 | 2.50 | 0.0824 0.0024 0.0848 | 15.9223
- 10 | 2.50 | 0.0821 0.0025 0.0846 | 14.6627
- 11 | 2.50 | 0.0818 0.0026 0.0844 | 13.4764
- 12 | 2.50 | 0.0815 0.0027 0.0842 | 12.3015
- 13 | 2.50 | 0.0812 0.0028 0.0840 | 11.3776
- 14 | 2.50 | 0.0809 0.0028 0.0837 | 10.4537
- 15 | 2.25 | 0.0810 0.0029 0.0839 | 9.5920
- 16 | 2.25 | 0.0778 0.0045 0.0822 | 8.8725
- 17 | 2.25 | 0.0765 0.0051 0.0815 | 8.1530
- 18 | 2.25 | 0.0756 0.0053 0.0810 | 7.5234
- 19 | 2.25 | 0.0750 0.0055 0.0805 | 6.9630
- 29 | 2.00 | 0.0769 0.0028 0.0797 | 3.3283
- 30 | 2.00 | 0.0713 0.0052 0.0766 | 3.1221
- 31 | 2.00 | 0.0695 0.0062 0.0757 | 2.9160
- 43 | 1.75 | 0.0684 0.0035 0.0719 | 1.5785
- 44 | 1.75 | 0.0638 0.0060 0.0697 | 1.5194
- 45 | 1.75 | 0.0623 0.0068 0.0691 | 1.4626
- 57 | 1.50 | 0.0606 0.0049 0.0656 | 1.0900
- 58 | 1.50 | 0.0574 0.0071 0.0645 | 1.0730
- 59 | 1.50 | 0.0563 0.0078 0.0641 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 164s
- Prepare output 8s
- 171s
- Jacobian determinant (RMS): 0.011 0.042 0.068 0.096 0.123 | 0.130699
- Template Matching: 0.087 0.225 0.209 0.187 0.169 | 0.168930
- Write result maps: 43s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 23s
- CSF distance: 11s
- PBT2x thickness: 31s
- 70s
- Create initial surface 56s
- Topology correction: 66s
- Surface refinement: 57s
- Reduction of surface collisions with optimization: 43s
- Spherical mapping with areal smoothing 56s
- Spherical registration 218s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 29s
- CSF distance: 11s
- PBT2x thickness: 31s
- 75s
- Create initial surface 56s
- Topology correction: 66s
- Surface refinement: 51s
- Reduction of surface collisions with optimization: 45s
- Spherical mapping with areal smoothing 58s
- Spherical registration 211s
- Final surface processing results:
- Average thickness (FS): 2.4582 0.6897 mm
- Surface intensity / position RMSE: 0.0652 / 0.0676
- Euler number / defect number / defect size: 18.0 / 11.0 / 0.57%
- Display thickness: /var/lib/condor/execute/dir_103637/ds/BMB_1/sub-0003034/ses-1/surf/lh.thickness.sub-0003034_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_103637/ds/BMB_1/sub-0003034/ses-1/surf/rh.thickness.sub-0003034_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_103637/ds/BMB_1/sub-0003034/ses-1/sub-0003034_ses-1_run-1_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1204s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 15s
- ROI estimation of 'neuromorphometrics' atlas 70s
- ROI estimation of 'lpba40' atlas 25s
- ROI estimation of 'hammers' atlas 60s
- ROI estimation of 'thalamus' atlas 5s
- ROI estimation of 'ibsr' atlas 22s
- ROI estimation of 'aal3' atlas 37s
- ROI estimation of 'mori' atlas 55s
- ROI estimation of 'anatomy3' atlas 80s
- ROI estimation of 'julichbrain' atlas 103s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 41s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 80s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 142s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 137s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 10s
- Write results 11s
- 882s
- Quality check: 9s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_103637/ds/BMB_1/sub-0003034/ses-1/report/catreport_sub-0003034_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 49 minute(s) and 50 second(s).
- Image Quality Rating (IQR): 81.39% (B-)
- GM volume (GMV): 44.81% (644.82 / 1439.09 ml)
- GM thickness (GMT): 2.46 0.69 mm
- Segmentations are saved in /var/lib/condor/execute/dir_103637/ds/BMB_1/sub-0003034/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_103637/ds/BMB_1/sub-0003034/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_103637/ds/BMB_1/sub-0003034/ses-1/label
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