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- CAT12.8.1 r2040: 1/1: ./sub-0025267/ses-2/sub-0025267_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 71s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 7s
- Initial correction 9s
- Refine background 3s
- Final correction 6s
- Final scaling 6s
- 44s
- Correct center-of-mass 4s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 100s
- SPM preprocessing 1 (estimate 2): 101s
- SPM preprocessing 2 (write):
- Write Segmentation 20s
- Update Segmentation 23s
- Update Skull-Stripping 46s
- Update probability maps 9s
- 98s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 35s
- Fast Optimized Shooting registration 39s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 18s
- Estimate local tissue thresholds (WM) 23s
- Estimate local tissue thresholds (GM) 36s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 47s
- 134s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 5s
- Ventricle detection 20s
- Blood vessel detection 13s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 32s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 4s
- 89s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 44s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 6s
- Level 1 cleanup (brain masking) 4s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 4s
- 15s
- 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 | 0.0836 0.0000 0.0836 | 32.0000
- 2 | 2.50 | 0.0806 0.0013 0.0819 | 29.4886
- 3 | 2.50 | 0.0797 0.0019 0.0817 | 26.9772
- 4 | 2.50 | 0.0793 0.0022 0.0815 | 24.6107
- 5 | 2.50 | 0.0790 0.0023 0.0813 | 22.6548
- 6 | 2.50 | 0.0787 0.0024 0.0811 | 20.6989
- 7 | 2.50 | 0.0783 0.0025 0.0809 | 18.9688
- 8 | 2.50 | 0.0780 0.0027 0.0807 | 17.4455
- 9 | 2.50 | 0.0777 0.0027 0.0804 | 15.9223
- 10 | 2.50 | 0.0773 0.0028 0.0802 | 14.6627
- 11 | 2.50 | 0.0770 0.0029 0.0799 | 13.4764
- 12 | 2.50 | 0.0766 0.0030 0.0796 | 12.3015
- 13 | 2.50 | 0.0762 0.0031 0.0793 | 11.3776
- 14 | 2.50 | 0.0759 0.0032 0.0791 | 10.4537
- 15 | 2.25 | 0.0744 0.0033 0.0777 | 9.5920
- 16 | 2.25 | 0.0713 0.0048 0.0762 | 8.8725
- 29 | 2.00 | 0.0718 0.0022 0.0740 | 3.3283
- 30 | 2.00 | 0.0659 0.0045 0.0705 | 3.1221
- 31 | 2.00 | 0.0640 0.0055 0.0695 | 2.9160
- 43 | 1.75 | 0.0628 0.0032 0.0660 | 1.5785
- 44 | 1.75 | 0.0590 0.0052 0.0642 | 1.5194
- 45 | 1.75 | 0.0577 0.0059 0.0636 | 1.4626
- 57 | 1.50 | 0.0561 0.0043 0.0604 | 1.0900
- 58 | 1.50 | 0.0533 0.0061 0.0594 | 1.0730
- Shooting registration with 2.50:-0.25:1.50 mm takes: 185s
- Prepare output 14s
- 199s
- Jacobian determinant (RMS): 0.011 0.041 0.060 0.083 0.103 | 0.107200
- Template Matching: 0.084 0.214 0.192 0.173 0.160 | 0.159917
- Write result maps: 50s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 44s
- CSF distance: 22s
- PBT2x thickness: 69s
- 143s
- Create initial surface 117s
- Topology correction: 129s
- Surface refinement: 137s
- Reduction of surface collisions with optimization: 111s
- Spherical mapping with areal smoothing 125s
- Spherical registration 352s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 55s
- CSF distance: 22s
- PBT2x thickness: 67s
- 151s
- Create initial surface 115s
- Topology correction: 128s
- Surface refinement: 149s
- Reduction of surface collisions with optimization: 106s
- Spherical mapping with areal smoothing 133s
- Spherical registration 381s
- Final surface processing results:
- Average thickness (FS): 2.6750 0.6543 mm
- Surface intensity / position RMSE: 0.0731 / 0.0736
- Euler number / defect number / defect size: 20.0 / 17.5 / 0.75%
- Display thickness: /var/lib/condor/execute/dir_3468819/ds/UPSM_1/sub-0025267/ses-2/surf/lh.thickness.sub-0025267_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3468819/ds/UPSM_1/sub-0025267/ses-2/surf/rh.thickness.sub-0025267_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3468819/ds/UPSM_1/sub-0025267/ses-2/sub-0025267_ses-2_run-1_T1w.nii
- Surface ROI estimation: 14s
- Surface and thickness estimation takes: 2412s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 13s
- ROI estimation of 'neuromorphometrics' atlas 46s
- ROI estimation of 'lpba40' atlas 14s
- ROI estimation of 'hammers' atlas 33s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 12s
- ROI estimation of 'aal3' atlas 20s
- ROI estimation of 'mori' atlas 27s
- ROI estimation of 'anatomy3' atlas 37s
- ROI estimation of 'julichbrain' atlas 47s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 23s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 39s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 67s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 87s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s
- Write results 8s
- 477s
- Quality check: 14s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3468819/ds/UPSM_1/sub-0025267/ses-2/report/catreport_sub-0025267_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 67 minute(s) and 31 second(s).
- Image Quality Rating (IQR): 80.02% (B-)
- GM volume (GMV): 50.26% (828.73 / 1648.80 ml)
- GM thickness (GMT): 2.67 0.66 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3468819/ds/UPSM_1/sub-0025267/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_3468819/ds/UPSM_1/sub-0025267/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_3468819/ds/UPSM_1/sub-0025267/ses-2/label
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