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- CAT12.8.1 r1980: 1/1: ./sub-wlsubj062_ses-anat_acq-highres_run-01_T1w.n
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- SANLM denoising (medium): 68s
- APP: Rough bias correction:
- Initialize 13s
- Estimate background 11s
- Initial correction 13s
- Refine background 7s
- Final correction 12s
- Final scaling 13s
- 82s
- Correct center-of-mass 4s
- Affine registration 17s
- SPM preprocessing 1 (estimate 1 - TPM registration): 157s
- SPM preprocessing 1 (estimate 2): 67s
- SPM preprocessing 2 (write):
- Write Segmentation 34s
- Update Segmentation 44s
- Update Skull-Stripping 99s
- Update probability maps 18s
- 196s
- Global intensity correction: 33s
- SANLM denoising after intensity normalization (medium): 23s
- Fast Optimized Shooting registration 63s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 11s
- Prepare partitions 5s
- Prepare segments (LASmod = 1.01) 33s
- Estimate local tissue thresholds (WM) 38s
- Estimate local tissue thresholds (GM) 54s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 53s
- 202s
- ROI segmentation (partitioning):
- Atlas -> subject space 21s
- Major structures 9s
- Ventricle detection 27s
- Blood vessel detection 26s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.12) 70s
- Manual stroke lesion detection 0s
- Closing of deep structures 5s
- Side alignment 10s
- Final corrections 10s
- 177s
- Blood vessel correction (BVCstr=0.50): 3s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 59s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 10s
- Level 1 cleanup (brain masking) 6s
- Level 2 cleanup (CSF correction) 3s
- Level 3 cleanup (CSF/WM PVE) 6s
- 25s
- 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 | 0.0839 0.0000 0.0839 | 32.0000
- 2 | 2.50 | 0.0810 0.0013 0.0822 | 29.4886
- 3 | 2.50 | 0.0801 0.0019 0.0821 | 26.9772
- 4 | 2.50 | 0.0797 0.0021 0.0819 | 24.6107
- 5 | 2.50 | 0.0794 0.0023 0.0817 | 22.6548
- 6 | 2.50 | 0.0791 0.0024 0.0815 | 20.6989
- 7 | 2.50 | 0.0788 0.0025 0.0813 | 18.9688
- 8 | 2.50 | 0.0785 0.0026 0.0811 | 17.4455
- 9 | 2.50 | 0.0782 0.0027 0.0809 | 15.9223
- 10 | 2.50 | 0.0778 0.0028 0.0807 | 14.6627
- 11 | 2.50 | 0.0775 0.0029 0.0804 | 13.4764
- 12 | 2.50 | 0.0772 0.0030 0.0801 | 12.3015
- 13 | 2.50 | 0.0768 0.0031 0.0799 | 11.3776
- 14 | 2.50 | 0.0765 0.0031 0.0796 | 10.4537
- 15 | 2.25 | 0.0750 0.0032 0.0782 | 9.5920
- 16 | 2.25 | 0.0720 0.0047 0.0767 | 8.8725
- 29 | 2.00 | 0.0723 0.0021 0.0744 | 3.3283
- 30 | 2.00 | 0.0662 0.0045 0.0707 | 3.1221
- 31 | 2.00 | 0.0642 0.0055 0.0697 | 2.9160
- 43 | 1.75 | 0.0629 0.0032 0.0660 | 1.5785
- 44 | 1.75 | 0.0589 0.0053 0.0641 | 1.5194
- 45 | 1.75 | 0.0575 0.0060 0.0636 | 1.4626
- 57 | 1.50 | 0.0557 0.0044 0.0601 | 1.0900
- 58 | 1.50 | 0.0528 0.0062 0.0591 | 1.0730
- 59 | 1.50 | 0.0519 0.0068 0.0588 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 242s
- Prepare output 17s
- 259s
- Jacobian determinant (RMS): 0.012 0.044 0.064 0.088 0.109 | 0.115624
- Template Matching: 0.084 0.216 0.192 0.173 0.156 | 0.155717
- Write result maps: 56s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 60s
- CSF distance: 22s
- PBT2x thickness: 63s
- 153s
- Create initial surface 96s
- Topology correction: 111s
- Surface refinement: 93s
- Reduction of surface collisions with optimization: 73s
- Spherical mapping with areal smoothing 104s
- Spherical registration 304s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 69s
- CSF distance: 21s
- PBT2x thickness: 59s
- 158s
- Create initial surface 98s
- Topology correction: 110s
- Surface refinement: 128s
- Reduction of surface collisions with optimization: 72s
- Spherical mapping with areal smoothing 103s
- Spherical registration 290s
- Final surface processing results:
- Average thickness (FS): 2.4958 0.5984 mm
- Surface intensity / position RMSE: 0.0656 / 0.0609
- Euler number / defect number / defect size: 8.0 / 9.0 / 0.11%
- Display thickness: /var/lib/condor/execute/dir_2937729/ds/sub-wlsubj062/surf/lh.thickness.sub-wlsubj062_ses-anat_acq-highres_run-01_T1w
- Display thickness: /var/lib/condor/execute/dir_2937729/ds/sub-wlsubj062/surf/rh.thickness.sub-wlsubj062_ses-anat_acq-highres_run-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2937729/ds/sub-wlsubj062/sub-wlsubj062_ses-anat_acq-highres_run-01_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 2036s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 28s
- ROI estimation of 'neuromorphometrics' atlas 106s
- ROI estimation of 'lpba40' atlas 31s
- ROI estimation of 'hammers' atlas 75s
- ROI estimation of 'thalamus' atlas 5s
- ROI estimation of 'ibsr' atlas 26s
- ROI estimation of 'aal3' atlas 41s
- ROI estimation of 'mori' atlas 62s
- ROI estimation of 'anatomy3' atlas 90s
- ROI estimation of 'julichbrain' atlas 118s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 44s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 60s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 194s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 284s
- Write results 285s
- 1167s
- Quality check: 11s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2937729/ds/sub-wlsubj062/report/catreport_sub-wlsubj062_ses-anat_acq-highres_run-01_T1w.pdf
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- CAT preprocessing takes 81 minute(s) and 17 second(s).
- Image Quality Rating (IQR): 86.80% (B+)
- GM volume (GMV): 44.75% (692.37 / 1547.18 ml)
- GM thickness (GMT): 2.50 0.60 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2937729/ds/sub-wlsubj062/mri
- Reports are saved in /var/lib/condor/execute/dir_2937729/ds/sub-wlsubj062/report
- Labels are saved in /var/lib/condor/execute/dir_2937729/ds/sub-wlsubj062/label
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