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- CAT12.8.1 r2040: 1/1: ./sub-0026138/ses-2/sub-0026138_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 34s
- APP: Rough bias correction:
- Initialize 4s
- Estimate background 4s
- Initial correction 4s
- Refine background 2s
- Final correction 3s
- Final scaling 3s
- 23s
- Correct center-of-mass 2s
- Affine registration 6s
- SPM preprocessing 1 (estimate 1 - TPM registration): 48s
- SPM preprocessing 1 (estimate 2): 56s
- SPM preprocessing 2 (write):
- Write Segmentation 11s
- Update Segmentation 13s
- Update Skull-Stripping 28s
- Update probability maps 6s
- 58s
- Global intensity correction: 10s
- SANLM denoising after intensity normalization (medium): 17s
- Fast Optimized Shooting registration 23s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 2s
- Prepare partitions 1s
- Prepare segments (LASmod = 1.00) 9s
- Estimate local tissue thresholds (WM) 11s
- Estimate local tissue thresholds (GM) 16s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 26s
- 69s
- ROI segmentation (partitioning):
- Atlas -> subject space 5s
- Major structures 2s
- Ventricle detection 7s
- Blood vessel detection 5s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.07) 13s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 3s
- 38s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 22s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.990.04]
- 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
- 7s
- 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 | 0.0865 0.0000 0.0865 | 32.0000
- 2 | 2.50 | 0.0834 0.0013 0.0848 | 29.4886
- 3 | 2.50 | 0.0825 0.0021 0.0846 | 26.9772
- 4 | 2.50 | 0.0820 0.0024 0.0844 | 24.6107
- 5 | 2.50 | 0.0816 0.0025 0.0842 | 22.6548
- 6 | 2.50 | 0.0813 0.0027 0.0839 | 20.6989
- 7 | 2.50 | 0.0809 0.0028 0.0837 | 18.9688
- 8 | 2.50 | 0.0806 0.0029 0.0835 | 17.4455
- 9 | 2.50 | 0.0802 0.0030 0.0832 | 15.9223
- 10 | 2.50 | 0.0798 0.0032 0.0830 | 14.6627
- 11 | 2.50 | 0.0794 0.0033 0.0827 | 13.4764
- 12 | 2.50 | 0.0790 0.0034 0.0824 | 12.3015
- 13 | 2.50 | 0.0786 0.0035 0.0821 | 11.3776
- 14 | 2.50 | 0.0782 0.0036 0.0818 | 10.4537
- 15 | 2.25 | 0.0777 0.0037 0.0814 | 9.5920
- 16 | 2.25 | 0.0745 0.0053 0.0798 | 8.8725
- 29 | 2.00 | 0.0756 0.0024 0.0780 | 3.3283
- 30 | 2.00 | 0.0691 0.0050 0.0741 | 3.1221
- 31 | 2.00 | 0.0669 0.0060 0.0729 | 2.9160
- 43 | 1.75 | 0.0655 0.0035 0.0690 | 1.5785
- 44 | 1.75 | 0.0613 0.0057 0.0671 | 1.5194
- 45 | 1.75 | 0.0599 0.0065 0.0664 | 1.4626
- 57 | 1.50 | 0.0584 0.0048 0.0632 | 1.0900
- 58 | 1.50 | 0.0553 0.0068 0.0621 | 1.0730
- 59 | 1.50 | 0.0542 0.0075 0.0617 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 115s
- Prepare output 7s
- 122s
- Jacobian determinant (RMS): 0.013 0.048 0.071 0.097 0.121 | 0.128752
- Template Matching: 0.087 0.224 0.201 0.180 0.163 | 0.162644
- Write result maps: 24s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 17s
- CSF distance: 9s
- PBT2x thickness: 26s
- 55s
- Create initial surface 47s
- Topology correction: 49s
- Surface refinement: 44s
- Reduction of surface collisions with optimization: 36s
- Spherical mapping with areal smoothing 51s
- Spherical registration 197s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 16s
- CSF distance: 9s
- PBT2x thickness: 26s
- 55s
- Create initial surface 46s
- Topology correction: 50s
- Surface refinement: 44s
- Reduction of surface collisions with optimization: 37s
- Spherical mapping with areal smoothing 51s
- Spherical registration 203s
- Final surface processing results:
- Average thickness (FS): 2.4512 0.6307 mm
- Surface intensity / position RMSE: 0.0653 / 0.0619
- Euler number / defect number / defect size: 8.0 / 8.5 / 0.09%
- Display thickness: /var/lib/condor/execute/dir_3618454/ds/UM/sub-0026138/ses-2/surf/lh.thickness.sub-0026138_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3618454/ds/UM/sub-0026138/ses-2/surf/rh.thickness.sub-0026138_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3618454/ds/UM/sub-0026138/ses-2/sub-0026138_ses-2_run-1_T1w.nii
- Surface ROI estimation: 6s
- Surface and thickness estimation takes: 1026s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 27s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 19s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 11s
- ROI estimation of 'mori' atlas 18s
- 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 50s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 70s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s
- Write results 7s
- 320s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3618454/ds/UM/sub-0026138/ses-2/report/catreport_sub-0026138_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 32 minute(s) and 54 second(s).
- Image Quality Rating (IQR): 78.88% (C+)
- GM volume (GMV): 46.15% (592.25 / 1283.26 ml)
- GM thickness (GMT): 2.45 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3618454/ds/UM/sub-0026138/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_3618454/ds/UM/sub-0026138/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_3618454/ds/UM/sub-0026138/ses-2/label
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