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- CAT12.8.1 r2040: 1/1: ./sub-0027205/ses-2/sub-0027205_ses-2_run-2_T1w.n
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- SANLM denoising (medium): 32s
- APP: Rough bias correction:
- Initialize 4s
- Estimate background 3s
- Initial correction 5s
- Refine background 2s
- Final correction 4s
- Final scaling 3s
- 25s
- Correct center-of-mass 2s
- Affine registration 5s
- SPM preprocessing 1 (estimate 1 - TPM registration): 5s
- Use initial fine affine registration. 40s
- SPM preprocessing 1 (estimate 2): 38s
- SPM preprocessing 2 (write):
- Write Segmentation 11s
- Update Segmentation 12s
- Update Skull-Stripping 28s
- Update probability maps 6s
- 57s
- Global intensity correction: 11s
- SANLM denoising after intensity normalization (medium): 16s
- Fast Optimized Shooting registration 23s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 2s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.18) 9s
- Estimate local tissue thresholds (WM) 12s
- Estimate local tissue thresholds (GM) 18s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 31s
- 77s
- ROI segmentation (partitioning):
- Atlas -> subject space 5s
- Major structures 2s
- Ventricle detection 6s
- Blood vessel detection 6s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.01) 13s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 3s
- 38s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 23s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- 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
- 7s
- 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 | 0.0811 0.0000 0.0811 | 32.0000
- 2 | 2.50 | 0.0787 0.0011 0.0798 | 29.4886
- 3 | 2.50 | 0.0780 0.0017 0.0797 | 26.9772
- 4 | 2.50 | 0.0777 0.0019 0.0795 | 24.6107
- 5 | 2.50 | 0.0774 0.0020 0.0794 | 22.6548
- 6 | 2.50 | 0.0771 0.0021 0.0792 | 20.6989
- 7 | 2.50 | 0.0769 0.0022 0.0791 | 18.9688
- 8 | 2.50 | 0.0766 0.0023 0.0789 | 17.4455
- 9 | 2.50 | 0.0764 0.0023 0.0787 | 15.9223
- 10 | 2.50 | 0.0761 0.0024 0.0785 | 14.6627
- 11 | 2.50 | 0.0758 0.0025 0.0783 | 13.4764
- 12 | 2.50 | 0.0755 0.0025 0.0781 | 12.3015
- 13 | 2.50 | 0.0752 0.0026 0.0779 | 11.3776
- 14 | 2.50 | 0.0750 0.0027 0.0776 | 10.4537
- 15 | 2.25 | 0.0729 0.0027 0.0757 | 9.5920
- 16 | 2.25 | 0.0702 0.0041 0.0743 | 8.8725
- 29 | 2.00 | 0.0709 0.0018 0.0727 | 3.3283
- 30 | 2.00 | 0.0651 0.0041 0.0692 | 3.1221
- 31 | 2.00 | 0.0632 0.0050 0.0682 | 2.9160
- 43 | 1.75 | 0.0619 0.0029 0.0647 | 1.5785
- 44 | 1.75 | 0.0579 0.0049 0.0628 | 1.5194
- 45 | 1.75 | 0.0566 0.0056 0.0622 | 1.4626
- 57 | 1.50 | 0.0548 0.0041 0.0589 | 1.0900
- 58 | 1.50 | 0.0520 0.0059 0.0579 | 1.0730
- Shooting registration with 2.50:-0.25:1.50 mm takes: 94s
- Prepare output 7s
- 100s
- Jacobian determinant (RMS): 0.010 0.036 0.054 0.076 0.096 | 0.100520
- Template Matching: 0.081 0.211 0.190 0.170 0.156 | 0.156139
- Write result maps: 23s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 28s
- CSF distance: 10s
- PBT2x thickness: 28s
- 69s
- Create initial surface 49s
- Topology correction: 51s
- Surface refinement: 42s
- Reduction of surface collisions with optimization: 40s
- Spherical mapping with areal smoothing 55s
- Spherical registration 211s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 21s
- CSF distance: 10s
- PBT2x thickness: 28s
- 63s
- Create initial surface 50s
- Topology correction: 51s
- Surface refinement: 58s
- Reduction of surface collisions with optimization: 38s
- Spherical mapping with areal smoothing 51s
- Spherical registration 188s
- Final surface processing results:
- Average thickness (FS): 2.5392 0.6211 mm
- Surface intensity / position RMSE: 0.0631 / 0.0616
- Euler number / defect number / defect size: 8.0 / 6.5 / 0.36%
- Display thickness: /var/lib/condor/execute/dir_2875144/ds/SWU_1/sub-0027205/ses-2/surf/lh.thickness.sub-0027205_ses-2_run-2_T1w
- Display thickness: /var/lib/condor/execute/dir_2875144/ds/SWU_1/sub-0027205/ses-2/surf/rh.thickness.sub-0027205_ses-2_run-2_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2875144/ds/SWU_1/sub-0027205/ses-2/sub-0027205_ses-2_run-2_T1w.nii
- Surface ROI estimation: 6s
- Surface and thickness estimation takes: 1078s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 6s
- ROI estimation of 'neuromorphometrics' atlas 23s
- ROI estimation of 'lpba40' atlas 7s
- ROI estimation of 'hammers' atlas 16s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 6s
- ROI estimation of 'aal3' atlas 9s
- ROI estimation of 'mori' atlas 14s
- ROI estimation of 'anatomy3' atlas 19s
- ROI estimation of 'julichbrain' atlas 26s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 10s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 19s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 41s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 61s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 5s
- Write results 6s
- 263s
- Quality check: 7s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2875144/ds/SWU_1/sub-0027205/ses-2/report/catreport_sub-0027205_ses-2_run-2_T1w.pdf
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- CAT preprocessing takes 32 minute(s) and 17 second(s).
- Image Quality Rating (IQR): 83.57% (B)
- GM volume (GMV): 47.02% (619.07 / 1316.64 ml)
- GM thickness (GMT): 2.54 0.62 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2875144/ds/SWU_1/sub-0027205/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_2875144/ds/SWU_1/sub-0027205/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_2875144/ds/SWU_1/sub-0027205/ses-2/label
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