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- CAT12.8.1 r2040: 1/1: ./sub-0025245/ses-3/sub-0025245_ses-3_run-1_T1w.n
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- SANLM denoising (medium): 66s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 7s
- Initial correction 7s
- Refine background 3s
- Final correction 6s
- Final scaling 7s
- 44s
- Correct center-of-mass 5s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 96s
- SPM preprocessing 1 (estimate 2): 68s
- SPM preprocessing 2 (write):
- Write Segmentation 19s
- Update Segmentation 23s
- Update Skull-Stripping 44s
- Update probability maps 9s
- 95s
- 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) 22s
- Estimate local tissue thresholds (GM) 36s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 46s
- 132s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 19s
- 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
- 88s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 40s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- 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 | 0.0799 0.0000 0.0799 | 32.0000
- 2 | 2.50 | 0.0775 0.0011 0.0786 | 29.4886
- 3 | 2.50 | 0.0768 0.0017 0.0785 | 26.9772
- 4 | 2.50 | 0.0764 0.0019 0.0783 | 24.6107
- 5 | 2.50 | 0.0762 0.0020 0.0782 | 22.6548
- 6 | 2.50 | 0.0759 0.0021 0.0780 | 20.6989
- 7 | 2.50 | 0.0756 0.0022 0.0779 | 18.9688
- 8 | 2.50 | 0.0754 0.0023 0.0777 | 17.4455
- 9 | 2.50 | 0.0751 0.0024 0.0775 | 15.9223
- 10 | 2.50 | 0.0748 0.0025 0.0773 | 14.6627
- 11 | 2.50 | 0.0745 0.0026 0.0771 | 13.4764
- 12 | 2.50 | 0.0743 0.0026 0.0769 | 12.3015
- 13 | 2.50 | 0.0740 0.0027 0.0767 | 11.3776
- 14 | 2.50 | 0.0737 0.0028 0.0764 | 10.4537
- 15 | 2.25 | 0.0718 0.0029 0.0747 | 9.5920
- 16 | 2.25 | 0.0691 0.0042 0.0733 | 8.8725
- 29 | 2.00 | 0.0696 0.0019 0.0715 | 3.3283
- 30 | 2.00 | 0.0643 0.0040 0.0683 | 3.1221
- 31 | 2.00 | 0.0625 0.0049 0.0674 | 2.9160
- 43 | 1.75 | 0.0616 0.0028 0.0644 | 1.5785
- 44 | 1.75 | 0.0577 0.0048 0.0625 | 1.5194
- 45 | 1.75 | 0.0564 0.0056 0.0620 | 1.4626
- 57 | 1.50 | 0.0549 0.0040 0.0590 | 1.0900
- 58 | 1.50 | 0.0521 0.0059 0.0580 | 1.0730
- 59 | 1.50 | 0.0511 0.0065 0.0576 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 210s
- Prepare output 14s
- 224s
- Jacobian determinant (RMS): 0.012 0.042 0.060 0.082 0.104 | 0.110345
- Template Matching: 0.080 0.207 0.188 0.169 0.153 | 0.153418
- Write result maps: 44s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 39s
- CSF distance: 22s
- PBT2x thickness: 66s
- 135s
- Create initial surface 113s
- Topology correction: 128s
- Surface refinement: 127s
- Reduction of surface collisions with optimization: 98s
- Spherical mapping with areal smoothing 116s
- Spherical registration 342s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 41s
- CSF distance: 21s
- PBT2x thickness: 66s
- 135s
- Create initial surface 114s
- Topology correction: 124s
- Surface refinement: 133s
- Reduction of surface collisions with optimization: 94s
- Spherical mapping with areal smoothing 127s
- Spherical registration 368s
- Final surface processing results:
- Average thickness (FS): 2.6922 0.6470 mm
- Surface intensity / position RMSE: 0.0749 / 0.0829
- Euler number / defect number / defect size: 42.0 / 23.0 / 1.20%
- Display thickness: /var/lib/condor/execute/dir_1701799/ds/UPSM_1/sub-0025245/ses-3/surf/lh.thickness.sub-0025245_ses-3_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1701799/ds/UPSM_1/sub-0025245/ses-3/surf/rh.thickness.sub-0025245_ses-3_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1701799/ds/UPSM_1/sub-0025245/ses-3/sub-0025245_ses-3_run-1_T1w.nii
- Surface ROI estimation: 12s
- Surface and thickness estimation takes: 2283s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 30s
- ROI estimation of 'lpba40' atlas 9s
- ROI estimation of 'hammers' atlas 22s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 8s
- ROI estimation of 'aal3' atlas 13s
- ROI estimation of 'mori' atlas 19s
- ROI estimation of 'anatomy3' atlas 28s
- ROI estimation of 'julichbrain' atlas 37s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 32s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 62s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 92s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s
- Write results 9s
- 386s
- Quality check: 14s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1701799/ds/UPSM_1/sub-0025245/ses-3/report/catreport_sub-0025245_ses-3_run-1_T1w.pdf
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- CAT preprocessing takes 63 minute(s) and 17 second(s).
- Image Quality Rating (IQR): 81.91% (B-)
- GM volume (GMV): 52.41% (814.92 / 1554.87 ml)
- GM thickness (GMT): 2.69 0.65 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1701799/ds/UPSM_1/sub-0025245/ses-3/mri
- Reports are saved in /var/lib/condor/execute/dir_1701799/ds/UPSM_1/sub-0025245/ses-3/report
- Labels are saved in /var/lib/condor/execute/dir_1701799/ds/UPSM_1/sub-0025245/ses-3/label
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