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- CAT12.8.1 r2040: 1/1: ./sub-0027222/ses-1/sub-0027222_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 54s
- APP: Rough bias correction:
- Initialize 4s
- Estimate background 5s
- Initial correction 7s
- Refine background 2s
- Final correction 5s
- Final scaling 4s
- 32s
- Correct center-of-mass 2s
- Affine registration 8s
- SPM preprocessing 1 (estimate 1 - TPM registration): 56s
- SPM preprocessing 1 (estimate 2): 45s
- SPM preprocessing 2 (write):
- Write Segmentation 12s
- Update Segmentation 15s
- Update Skull-Stripping 32s
- Update probability maps 6s
- 65s
- Global intensity correction: 11s
- SANLM denoising after intensity normalization (medium): 19s
- Fast Optimized Shooting registration 23s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.13) 11s
- Estimate local tissue thresholds (WM) 13s
- Estimate local tissue thresholds (GM) 19s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 32s
- 82s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 3s
- Ventricle detection 10s
- Blood vessel detection 7s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.10) 18s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 3s
- 51s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 26s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- 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
- 8s
- 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 | 0.0872 0.0000 0.0872 | 32.0000
- 2 | 2.50 | 0.0842 0.0013 0.0855 | 29.4886
- 3 | 2.50 | 0.0834 0.0019 0.0853 | 26.9772
- 4 | 2.50 | 0.0829 0.0022 0.0851 | 24.6107
- 5 | 2.50 | 0.0826 0.0023 0.0849 | 22.6548
- 6 | 2.50 | 0.0823 0.0024 0.0847 | 20.6989
- 7 | 2.50 | 0.0821 0.0025 0.0846 | 18.9688
- 8 | 2.50 | 0.0818 0.0026 0.0844 | 17.4455
- 9 | 2.50 | 0.0815 0.0027 0.0841 | 15.9223
- 10 | 2.50 | 0.0811 0.0028 0.0839 | 14.6627
- 11 | 2.50 | 0.0808 0.0028 0.0837 | 13.4764
- 12 | 2.50 | 0.0805 0.0029 0.0834 | 12.3015
- 13 | 2.50 | 0.0802 0.0030 0.0832 | 11.3776
- 14 | 2.50 | 0.0799 0.0030 0.0829 | 10.4537
- 15 | 2.25 | 0.0797 0.0031 0.0828 | 9.5920
- 16 | 2.25 | 0.0766 0.0046 0.0812 | 8.8725
- 17 | 2.25 | 0.0753 0.0052 0.0805 | 8.1530
- 18 | 2.25 | 0.0745 0.0054 0.0799 | 7.5234
- 29 | 2.00 | 0.0763 0.0026 0.0789 | 3.3283
- 30 | 2.00 | 0.0709 0.0049 0.0759 | 3.1221
- 31 | 2.00 | 0.0691 0.0058 0.0749 | 2.9160
- 43 | 1.75 | 0.0683 0.0033 0.0716 | 1.5785
- 44 | 1.75 | 0.0638 0.0057 0.0695 | 1.5194
- 45 | 1.75 | 0.0623 0.0065 0.0689 | 1.4626
- 57 | 1.50 | 0.0609 0.0047 0.0656 | 1.0900
- 58 | 1.50 | 0.0576 0.0069 0.0645 | 1.0730
- 59 | 1.50 | 0.0566 0.0076 0.0641 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 135s
- Prepare output 7s
- 142s
- Jacobian determinant (RMS): 0.010 0.035 0.056 0.080 0.107 | 0.114644
- Template Matching: 0.087 0.223 0.207 0.187 0.170 | 0.169660
- Write result maps: 26s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 28s
- CSF distance: 12s
- PBT2x thickness: 31s
- 76s
- Create initial surface 56s
- Topology correction: 68s
- Surface refinement: 51s
- Reduction of surface collisions with optimization: 47s
- Spherical mapping with areal smoothing 59s
- Spherical registration 192s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 30s
- CSF distance: 11s
- PBT2x thickness: 32s
- 77s
- Create initial surface 58s
- Topology correction: 67s
- Surface refinement: 55s
- Reduction of surface collisions with optimization: 47s
- Spherical mapping with areal smoothing 60s
- Spherical registration 206s
- Final surface processing results:
- Average thickness (FS): 2.5863 0.6477 mm
- Surface intensity / position RMSE: 0.0655 / 0.0655
- Euler number / defect number / defect size: 16.0 / 14.0 / 0.39%
- Display thickness: /var/lib/condor/execute/dir_2875243/ds/SWU_1/sub-0027222/ses-1/surf/lh.thickness.sub-0027222_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2875243/ds/SWU_1/sub-0027222/ses-1/surf/rh.thickness.sub-0027222_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2875243/ds/SWU_1/sub-0027222/ses-1/sub-0027222_ses-1_run-1_T1w.nii
- Surface ROI estimation: 6s
- Surface and thickness estimation takes: 1188s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 26s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 18s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 6s
- ROI estimation of 'aal3' atlas 10s
- ROI estimation of 'mori' atlas 15s
- ROI estimation of 'anatomy3' atlas 21s
- ROI estimation of 'julichbrain' atlas 28s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 44s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 63s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 5s
- Write results 6s
- 284s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2875243/ds/SWU_1/sub-0027222/ses-1/report/catreport_sub-0027222_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 36 minute(s) and 42 second(s).
- Image Quality Rating (IQR): 81.82% (B-)
- GM volume (GMV): 47.63% (734.69 / 1542.46 ml)
- GM thickness (GMT): 2.59 0.65 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2875243/ds/SWU_1/sub-0027222/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_2875243/ds/SWU_1/sub-0027222/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_2875243/ds/SWU_1/sub-0027222/ses-1/label
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