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- CAT12.8.1 r2040: 1/1: ./sub-0025901/ses-1/sub-0025901_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 30s
- Internal resampling (1.33x1.00x1.00mm > 1.00x1.00x1.00mm): 1s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 6s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 38s
- Correct center-of-mass 3s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 16s
- Use initial fine affine registration. 64s
- SPM preprocessing 1 (estimate 2): 68s
- SPM preprocessing 2 (write):
- Write Segmentation 17s
- Update Segmentation 17s
- Update Skull-Stripping 42s
- Update probability maps 9s
- 85s
- Global intensity correction: 18s
- SANLM denoising after intensity normalization (medium): 22s
- Fast Optimized Shooting registration 34s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 4s
- Prepare segments (LASmod = 1.11) 12s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 25s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 41s
- 107s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 10s
- Blood vessel detection 7s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 19s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 5s
- 55s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 30s
- 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
- 9s
- 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 | 0.0792 0.0000 0.0792 | 32.0000
- 2 | 2.50 | 0.0769 0.0011 0.0780 | 29.4886
- 3 | 2.50 | 0.0762 0.0016 0.0779 | 26.9772
- 4 | 2.50 | 0.0759 0.0018 0.0777 | 24.6107
- 5 | 2.50 | 0.0757 0.0019 0.0776 | 22.6548
- 6 | 2.50 | 0.0754 0.0020 0.0774 | 20.6989
- 7 | 2.50 | 0.0752 0.0021 0.0773 | 18.9688
- 8 | 2.50 | 0.0750 0.0022 0.0771 | 17.4455
- 9 | 2.50 | 0.0747 0.0022 0.0769 | 15.9223
- 10 | 2.50 | 0.0744 0.0023 0.0767 | 14.6627
- 11 | 2.50 | 0.0742 0.0024 0.0765 | 13.4764
- 12 | 2.50 | 0.0739 0.0024 0.0763 | 12.3015
- 13 | 2.50 | 0.0736 0.0025 0.0761 | 11.3776
- 14 | 2.50 | 0.0734 0.0025 0.0759 | 10.4537
- 15 | 2.25 | 0.0708 0.0026 0.0734 | 9.5920
- 16 | 2.25 | 0.0683 0.0038 0.0721 | 8.8725
- 29 | 2.00 | 0.0693 0.0017 0.0710 | 3.3283
- 30 | 2.00 | 0.0643 0.0037 0.0680 | 3.1221
- 31 | 2.00 | 0.0626 0.0045 0.0671 | 2.9160
- 43 | 1.75 | 0.0615 0.0026 0.0641 | 1.5785
- 44 | 1.75 | 0.0577 0.0046 0.0623 | 1.5194
- 45 | 1.75 | 0.0565 0.0053 0.0617 | 1.4626
- 57 | 1.50 | 0.0548 0.0038 0.0587 | 1.0900
- 58 | 1.50 | 0.0521 0.0056 0.0577 | 1.0730
- Shooting registration with 2.50:-0.25:1.50 mm takes: 143s
- Prepare output 10s
- 153s
- Jacobian determinant (RMS): 0.010 0.035 0.050 0.071 0.092 | 0.096665
- Template Matching: 0.079 0.205 0.188 0.169 0.156 | 0.156441
- Write result maps: 60s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 22s
- CSF distance: 13s
- PBT2x thickness: 39s
- 78s
- Create initial surface 75s
- Topology correction: 72s
- Surface refinement: 79s
- Reduction of surface collisions with optimization: 56s
- Spherical mapping with areal smoothing 71s
- Spherical registration 290s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 19s
- CSF distance: 12s
- PBT2x thickness: 36s
- 73s
- Create initial surface 70s
- Topology correction: 70s
- Surface refinement: 75s
- Reduction of surface collisions with optimization: 55s
- Spherical mapping with areal smoothing 69s
- Spherical registration 284s
- Final surface processing results:
- Average thickness (FS): 2.5823 0.6414 mm
- Surface intensity / position RMSE: 0.0691 / 0.0709
- Euler number / defect number / defect size: 16.0 / 11.5 / 0.49%
- Display thickness: /var/lib/condor/execute/dir_1014522/ds/BNU_1/sub-0025901/ses-1/surf/lh.thickness.sub-0025901_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1014522/ds/BNU_1/sub-0025901/ses-1/surf/rh.thickness.sub-0025901_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1014522/ds/BNU_1/sub-0025901/ses-1/sub-0025901_ses-1_run-1_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1511s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 33s
- ROI estimation of 'lpba40' atlas 9s
- ROI estimation of 'hammers' atlas 23s
- 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 26s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 62s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 103s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 10s
- Write results 11s
- 399s
- Quality check: 12s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1014522/ds/BNU_1/sub-0025901/ses-1/report/catreport_sub-0025901_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 46 minute(s) and 45 second(s).
- Image Quality Rating (IQR): 82.47% (B-)
- GM volume (GMV): 52.78% (625.66 / 1185.46 ml)
- GM thickness (GMT): 2.58 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1014522/ds/BNU_1/sub-0025901/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_1014522/ds/BNU_1/sub-0025901/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_1014522/ds/BNU_1/sub-0025901/ses-1/label
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