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- CAT12.8.1 r2040: 1/1: ./sub-0025238/ses-2/sub-0025238_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 4s
- Affine registration 9s
- SPM preprocessing 1 (estimate 1 - TPM registration): 88s
- SPM preprocessing 1 (estimate 2): 89s
- SPM preprocessing 2 (write):
- Write Segmentation 18s
- Update Segmentation 21s
- Update Skull-Stripping 42s
- Update probability maps 8s
- 90s
- Global intensity correction: 15s
- SANLM denoising after intensity normalization (medium): 39s
- Fast Optimized Shooting registration 38s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 18s
- Estimate local tissue thresholds (WM) 22s
- Estimate local tissue thresholds (GM) 36s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 46s
- 131s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 17s
- Blood vessel detection 13s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 35s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 4s
- 87s
- 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 | 0.0818 0.0000 0.0818 | 32.0000
- 2 | 2.50 | 0.0791 0.0012 0.0803 | 29.4886
- 3 | 2.50 | 0.0783 0.0018 0.0801 | 26.9772
- 4 | 2.50 | 0.0779 0.0020 0.0799 | 24.6107
- 5 | 2.50 | 0.0776 0.0022 0.0798 | 22.6548
- 6 | 2.50 | 0.0773 0.0023 0.0796 | 20.6989
- 7 | 2.50 | 0.0771 0.0024 0.0794 | 18.9688
- 8 | 2.50 | 0.0768 0.0025 0.0792 | 17.4455
- 9 | 2.50 | 0.0765 0.0025 0.0790 | 15.9223
- 10 | 2.50 | 0.0762 0.0026 0.0788 | 14.6627
- 11 | 2.50 | 0.0759 0.0027 0.0786 | 13.4764
- 12 | 2.50 | 0.0756 0.0028 0.0783 | 12.3015
- 13 | 2.50 | 0.0752 0.0029 0.0781 | 11.3776
- 14 | 2.50 | 0.0749 0.0029 0.0779 | 10.4537
- 15 | 2.25 | 0.0742 0.0030 0.0771 | 9.5920
- 16 | 2.25 | 0.0713 0.0044 0.0757 | 8.8725
- 29 | 2.00 | 0.0728 0.0020 0.0748 | 3.3283
- 30 | 2.00 | 0.0668 0.0044 0.0712 | 3.1221
- 31 | 2.00 | 0.0648 0.0054 0.0702 | 2.9160
- 43 | 1.75 | 0.0639 0.0031 0.0670 | 1.5785
- 44 | 1.75 | 0.0595 0.0054 0.0649 | 1.5194
- 45 | 1.75 | 0.0580 0.0062 0.0642 | 1.4626
- 57 | 1.50 | 0.0566 0.0045 0.0611 | 1.0900
- 58 | 1.50 | 0.0534 0.0066 0.0600 | 1.0730
- 59 | 1.50 | 0.0524 0.0072 0.0596 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 204s
- Prepare output 13s
- 217s
- Jacobian determinant (RMS): 0.011 0.038 0.058 0.083 0.108 | 0.114759
- Template Matching: 0.082 0.214 0.194 0.174 0.157 | 0.157173
- Write result maps: 40s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 37s
- CSF distance: 22s
- PBT2x thickness: 65s
- 131s
- Create initial surface 112s
- Topology correction: 122s
- Surface refinement: 124s
- Reduction of surface collisions with optimization: 96s
- Spherical mapping with areal smoothing 115s
- Spherical registration 362s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 39s
- CSF distance: 21s
- PBT2x thickness: 65s
- 132s
- Create initial surface 111s
- Topology correction: 121s
- Surface refinement: 83s
- Reduction of surface collisions with optimization: 94s
- Spherical mapping with areal smoothing 113s
- Spherical registration 367s
- Final surface processing results:
- Average thickness (FS): 2.7591 0.6570 mm
- Surface intensity / position RMSE: 0.0735 / 0.0742
- Euler number / defect number / defect size: 16.0 / 12.0 / 0.65%
- Display thickness: /var/lib/condor/execute/dir_3468898/ds/UPSM_1/sub-0025238/ses-2/surf/lh.thickness.sub-0025238_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3468898/ds/UPSM_1/sub-0025238/ses-2/surf/rh.thickness.sub-0025238_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3468898/ds/UPSM_1/sub-0025238/ses-2/sub-0025238_ses-2_run-1_T1w.nii
- Surface ROI estimation: 12s
- Surface and thickness estimation takes: 2208s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 32s
- ROI estimation of 'lpba40' atlas 10s
- ROI estimation of 'hammers' atlas 23s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 9s
- ROI estimation of 'aal3' atlas 15s
- ROI estimation of 'mori' atlas 22s
- ROI estimation of 'anatomy3' atlas 28s
- ROI estimation of 'julichbrain' atlas 36s
- 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 56s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 81s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s
- Write results 8s
- 369s
- Quality check: 13s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3468898/ds/UPSM_1/sub-0025238/ses-2/report/catreport_sub-0025238_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 61 minute(s) and 28 second(s).
- Image Quality Rating (IQR): 82.84% (B-)
- GM volume (GMV): 53.93% (800.28 / 1484.03 ml)
- GM thickness (GMT): 2.76 0.66 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3468898/ds/UPSM_1/sub-0025238/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_3468898/ds/UPSM_1/sub-0025238/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_3468898/ds/UPSM_1/sub-0025238/ses-2/label
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