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- CAT12.8.1 r2040: 1/1: ./sub-0025977/ses-2/sub-0025977_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 55s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 6s
- Initial correction 7s
- Refine background 3s
- Final correction 6s
- Final scaling 5s
- 42s
- Correct center-of-mass 3s
- Affine registration 11s
- SPM preprocessing 1 (estimate 1 - TPM registration): 92s
- SPM preprocessing 1 (estimate 2): 110s
- SPM preprocessing 2 (write):
- Write Segmentation 21s
- Update Segmentation 22s
- Update Skull-Stripping 49s
- Update probability maps 10s
- 103s
- Global intensity correction: 19s
- SANLM denoising after intensity normalization (medium): 30s
- Fast Optimized Shooting registration 43s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.00) 16s
- Estimate local tissue thresholds (WM) 24s
- Estimate local tissue thresholds (GM) 36s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 52s
- 138s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 4s
- Ventricle detection 15s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 27s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 3s
- Final corrections 5s
- 77s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 36s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.990.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 5s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 3s
- 13s
- 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 | 0.0814 0.0000 0.0814 | 32.0000
- 2 | 2.50 | 0.0787 0.0012 0.0799 | 29.4886
- 3 | 2.50 | 0.0779 0.0018 0.0797 | 26.9772
- 4 | 2.50 | 0.0775 0.0021 0.0796 | 24.6107
- 5 | 2.50 | 0.0772 0.0022 0.0794 | 22.6548
- 6 | 2.50 | 0.0769 0.0023 0.0792 | 20.6989
- 7 | 2.50 | 0.0766 0.0024 0.0790 | 18.9688
- 8 | 2.50 | 0.0762 0.0026 0.0788 | 17.4455
- 9 | 2.50 | 0.0759 0.0026 0.0786 | 15.9223
- 10 | 2.50 | 0.0756 0.0028 0.0784 | 14.6627
- 11 | 2.50 | 0.0753 0.0028 0.0781 | 13.4764
- 12 | 2.50 | 0.0750 0.0029 0.0779 | 12.3015
- 13 | 2.50 | 0.0746 0.0030 0.0776 | 11.3776
- 14 | 2.50 | 0.0743 0.0031 0.0774 | 10.4537
- 15 | 2.25 | 0.0733 0.0032 0.0765 | 9.5920
- 16 | 2.25 | 0.0704 0.0046 0.0750 | 8.8725
- 29 | 2.00 | 0.0715 0.0021 0.0736 | 3.3283
- 30 | 2.00 | 0.0654 0.0045 0.0698 | 3.1221
- 31 | 2.00 | 0.0632 0.0054 0.0687 | 2.9160
- 43 | 1.75 | 0.0622 0.0032 0.0654 | 1.5785
- 44 | 1.75 | 0.0581 0.0053 0.0634 | 1.5194
- 45 | 1.75 | 0.0567 0.0061 0.0627 | 1.4626
- 57 | 1.50 | 0.0552 0.0044 0.0596 | 1.0900
- 58 | 1.50 | 0.0523 0.0063 0.0586 | 1.0730
- 59 | 1.50 | 0.0513 0.0069 0.0582 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 206s
- Prepare output 14s
- 220s
- Jacobian determinant (RMS): 0.011 0.040 0.059 0.081 0.103 | 0.109847
- Template Matching: 0.081 0.211 0.190 0.170 0.154 | 0.153896
- Write result maps: 47s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 39s
- CSF distance: 21s
- PBT2x thickness: 58s
- 125s
- Create initial surface 102s
- Topology correction: 114s
- Surface refinement: 119s
- Reduction of surface collisions with optimization: 85s
- Spherical mapping with areal smoothing 107s
- Spherical registration 363s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 33s
- CSF distance: 19s
- PBT2x thickness: 56s
- 115s
- Create initial surface 101s
- Topology correction: 112s
- Surface refinement: 91s
- Reduction of surface collisions with optimization: 79s
- Spherical mapping with areal smoothing 105s
- Spherical registration 336s
- Final surface processing results:
- Average thickness (FS): 2.5806 0.6359 mm
- Surface intensity / position RMSE: 0.0710 / 0.0748
- Euler number / defect number / defect size: 20.0 / 17.0 / 0.78%
- Display thickness: /var/lib/condor/execute/dir_3468518/ds/BNU_2/sub-0025977/ses-2/surf/lh.thickness.sub-0025977_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3468518/ds/BNU_2/sub-0025977/ses-2/surf/rh.thickness.sub-0025977_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3468518/ds/BNU_2/sub-0025977/ses-2/sub-0025977_ses-2_run-1_T1w.nii
- Surface ROI estimation: 11s
- Surface and thickness estimation takes: 2075s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 14s
- ROI estimation of 'neuromorphometrics' atlas 52s
- ROI estimation of 'lpba40' atlas 15s
- ROI estimation of 'hammers' atlas 35s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 13s
- ROI estimation of 'aal3' atlas 20s
- ROI estimation of 'mori' atlas 33s
- ROI estimation of 'anatomy3' atlas 46s
- ROI estimation of 'julichbrain' atlas 60s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 26s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 54s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 109s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 150s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 14s
- Write results 16s
- 646s
- Quality check: 16s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3468518/ds/BNU_2/sub-0025977/ses-2/report/catreport_sub-0025977_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 64 minute(s) and 55 second(s).
- Image Quality Rating (IQR): 83.75% (B)
- GM volume (GMV): 50.97% (699.63 / 1372.65 ml)
- GM thickness (GMT): 2.58 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3468518/ds/BNU_2/sub-0025977/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_3468518/ds/BNU_2/sub-0025977/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_3468518/ds/BNU_2/sub-0025977/ses-2/label
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