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- CAT12.8.1 r2040: 1/1: ./sub-0025316/ses-2/sub-0025316_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 67s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 7s
- Initial correction 7s
- Refine background 3s
- Final correction 6s
- Final scaling 6s
- 41s
- Correct center-of-mass 5s
- Affine registration 9s
- SPM preprocessing 1 (estimate 1 - TPM registration): 13s
- Use initial fine affine registration. 88s
- SPM preprocessing 1 (estimate 2): 80s
- SPM preprocessing 2 (write):
- Write Segmentation 19s
- Update Segmentation 22s
- Update Skull-Stripping 45s
- Update probability maps 8s
- 94s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 37s
- Fast Optimized Shooting registration 39s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- 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) 44s
- 132s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 19s
- Blood vessel detection 12s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 30s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 4s
- 85s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 39s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.07,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 5s
- 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 | 0.0804 0.0000 0.0804 | 32.0000
- 2 | 2.50 | 0.0785 0.0009 0.0794 | 29.4886
- 3 | 2.50 | 0.0780 0.0014 0.0794 | 26.9772
- 4 | 2.50 | 0.0777 0.0015 0.0793 | 24.6107
- 5 | 2.50 | 0.0775 0.0016 0.0792 | 22.6548
- 6 | 2.50 | 0.0773 0.0017 0.0790 | 20.6989
- 7 | 2.50 | 0.0772 0.0018 0.0789 | 18.9688
- 8 | 2.50 | 0.0770 0.0018 0.0788 | 17.4455
- 9 | 2.50 | 0.0768 0.0019 0.0786 | 15.9223
- 10 | 2.50 | 0.0765 0.0020 0.0785 | 14.6627
- 11 | 2.50 | 0.0763 0.0020 0.0784 | 13.4764
- 12 | 2.50 | 0.0761 0.0021 0.0782 | 12.3015
- 13 | 2.50 | 0.0759 0.0021 0.0780 | 11.3776
- 14 | 2.50 | 0.0757 0.0022 0.0778 | 10.4537
- 15 | 2.25 | 0.0742 0.0022 0.0764 | 9.5920
- 16 | 2.25 | 0.0716 0.0035 0.0751 | 8.8725
- 29 | 2.00 | 0.0731 0.0016 0.0747 | 3.3283
- 30 | 2.00 | 0.0674 0.0039 0.0713 | 3.1221
- 31 | 2.00 | 0.0656 0.0048 0.0704 | 2.9160
- 43 | 1.75 | 0.0649 0.0028 0.0676 | 1.5785
- 44 | 1.75 | 0.0605 0.0051 0.0656 | 1.5194
- 45 | 1.75 | 0.0591 0.0059 0.0650 | 1.4626
- 57 | 1.50 | 0.0577 0.0042 0.0619 | 1.0900
- 58 | 1.50 | 0.0545 0.0063 0.0608 | 1.0730
- 59 | 1.50 | 0.0535 0.0069 0.0605 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 215s
- Prepare output 14s
- 229s
- Jacobian determinant (RMS): 0.008 0.030 0.049 0.078 0.105 | 0.111969
- Template Matching: 0.080 0.215 0.197 0.177 0.161 | 0.160621
- Write result maps: 42s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 37s
- CSF distance: 22s
- PBT2x thickness: 66s
- 133s
- Create initial surface 109s
- Topology correction: 124s
- Surface refinement: 102s
- Reduction of surface collisions with optimization: 102s
- Spherical mapping with areal smoothing 118s
- Spherical registration 337s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 36s
- CSF distance: 21s
- PBT2x thickness: 64s
- 129s
- Create initial surface 107s
- Topology correction: 123s
- Surface refinement: 104s
- Reduction of surface collisions with optimization: 98s
- Spherical mapping with areal smoothing 121s
- Spherical registration 363s
- Final surface processing results:
- Average thickness (FS): 2.8386 0.6475 mm
- Surface intensity / position RMSE: 0.0742 / 0.0712
- Euler number / defect number / defect size: 18.0 / 16.0 / 0.98%
- Display thickness: /var/lib/condor/execute/dir_1702769/ds/UPSM_1/sub-0025316/ses-2/surf/lh.thickness.sub-0025316_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1702769/ds/UPSM_1/sub-0025316/ses-2/surf/rh.thickness.sub-0025316_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1702769/ds/UPSM_1/sub-0025316/ses-2/sub-0025316_ses-2_run-1_T1w.nii
- Surface ROI estimation: 12s
- Surface and thickness estimation takes: 2198s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 34s
- ROI estimation of 'lpba40' atlas 10s
- ROI estimation of 'hammers' atlas 23s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 8s
- ROI estimation of 'aal3' atlas 14s
- ROI estimation of 'mori' atlas 20s
- ROI estimation of 'anatomy3' atlas 26s
- ROI estimation of 'julichbrain' atlas 35s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 14s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 24s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 57s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 85s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s
- Write results 9s
- 368s
- Quality check: 14s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1702769/ds/UPSM_1/sub-0025316/ses-2/report/catreport_sub-0025316_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 61 minute(s) and 41 second(s).
- Image Quality Rating (IQR): 84.72% (B)
- GM volume (GMV): 54.97% (846.14 / 1539.21 ml)
- GM thickness (GMT): 2.84 0.65 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1702769/ds/UPSM_1/sub-0025316/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_1702769/ds/UPSM_1/sub-0025316/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_1702769/ds/UPSM_1/sub-0025316/ses-2/label
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