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- CAT12.8.1 r2040: 1/1: ./sub-0026019/ses-1/sub-0026019_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 173s
- Internal resampling (1.20x0.50x0.50mm > 0.80x0.80x0.80mm): 2s
- APP: Rough bias correction:
- Initialize 9s
- Estimate background 6s
- Initial correction 7s
- Refine background 4s
- Final correction 6s
- Final scaling 6s
- 46s
- Correct center-of-mass 2s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 81s
- SPM preprocessing 1 (estimate 2): 36s
- SPM preprocessing 2 (write):
- Write Segmentation 22s
- Update Segmentation 23s
- Update Skull-Stripping 54s
- Update probability maps 12s
- 111s
- Global intensity correction: 21s
- SANLM denoising after intensity normalization (medium): 37s
- Fast Optimized Shooting registration 32s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.00) 18s
- Estimate local tissue thresholds (WM) 24s
- Estimate local tissue thresholds (GM) 34s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 52s
- 141s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 4s
- Ventricle detection 11s
- Blood vessel detection 12s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 24s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 6s
- 72s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 35s
- 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) 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 | 0.0836 0.0000 0.0836 | 32.0000
- 2 | 2.50 | 0.0799 0.0014 0.0813 | 29.4886
- 3 | 2.50 | 0.0788 0.0022 0.0810 | 26.9772
- 4 | 2.50 | 0.0783 0.0025 0.0808 | 24.6107
- 5 | 2.50 | 0.0779 0.0027 0.0805 | 22.6548
- 6 | 2.50 | 0.0775 0.0028 0.0803 | 20.6989
- 7 | 2.50 | 0.0772 0.0029 0.0800 | 18.9688
- 8 | 2.50 | 0.0768 0.0030 0.0798 | 17.4455
- 9 | 2.50 | 0.0764 0.0031 0.0795 | 15.9223
- 10 | 2.50 | 0.0760 0.0032 0.0792 | 14.6627
- 11 | 2.50 | 0.0756 0.0033 0.0789 | 13.4764
- 12 | 2.50 | 0.0753 0.0033 0.0786 | 12.3015
- 13 | 2.50 | 0.0749 0.0034 0.0783 | 11.3776
- 14 | 2.50 | 0.0745 0.0035 0.0780 | 10.4537
- 15 | 2.25 | 0.0740 0.0036 0.0776 | 9.5920
- 16 | 2.25 | 0.0706 0.0053 0.0758 | 8.8725
- 29 | 2.00 | 0.0716 0.0024 0.0740 | 3.3283
- 30 | 2.00 | 0.0652 0.0049 0.0701 | 3.1221
- 31 | 2.00 | 0.0630 0.0059 0.0689 | 2.9160
- 43 | 1.75 | 0.0620 0.0034 0.0654 | 1.5785
- 44 | 1.75 | 0.0578 0.0056 0.0635 | 1.5194
- 45 | 1.75 | 0.0564 0.0064 0.0628 | 1.4626
- 57 | 1.50 | 0.0551 0.0047 0.0597 | 1.0900
- 58 | 1.50 | 0.0520 0.0066 0.0586 | 1.0730
- 59 | 1.50 | 0.0510 0.0073 0.0582 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 107s
- Prepare output 10s
- 117s
- Jacobian determinant (RMS): 0.012 0.045 0.066 0.091 0.114 | 0.120575
- Template Matching: 0.084 0.212 0.189 0.169 0.153 | 0.152895
- Write result maps: 140s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 18s
- CSF distance: 9s
- PBT2x thickness: 27s
- 59s
- Create initial surface 49s
- Topology correction: 60s
- Surface refinement: 42s
- Reduction of surface collisions with optimization: 41s
- Spherical mapping with areal smoothing 52s
- Spherical registration 186s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 17s
- CSF distance: 9s
- PBT2x thickness: 28s
- 58s
- Create initial surface 51s
- Topology correction: 64s
- Surface refinement: 54s
- Reduction of surface collisions with optimization: 46s
- Spherical mapping with areal smoothing 56s
- Spherical registration 194s
- Final surface processing results:
- Average thickness (FS): 2.6372 0.6384 mm
- Surface intensity / position RMSE: 0.0750 / 0.0724
- Euler number / defect number / defect size: 26.0 / 20.0 / 0.80%
- Display thickness: /var/lib/condor/execute/dir_1912318/ds/Utah_1/sub-0026019/ses-1/surf/lh.thickness.sub-0026019_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1912318/ds/Utah_1/sub-0026019/ses-1/surf/rh.thickness.sub-0026019_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1912318/ds/Utah_1/sub-0026019/ses-1/sub-0026019_ses-1_run-1_T1w.nii
- Surface ROI estimation: 6s
- Surface and thickness estimation takes: 1115s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 12s
- ROI estimation of 'neuromorphometrics' atlas 44s
- ROI estimation of 'lpba40' atlas 13s
- ROI estimation of 'hammers' atlas 31s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 11s
- ROI estimation of 'aal3' atlas 16s
- ROI estimation of 'mori' atlas 24s
- ROI estimation of 'anatomy3' atlas 34s
- ROI estimation of 'julichbrain' atlas 46s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 18s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 31s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 71s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 106s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 9s
- Write results 10s
- 471s
- Quality check: 35s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1912318/ds/Utah_1/sub-0026019/ses-1/report/catreport_sub-0026019_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 45 minute(s) and 55 second(s).
- Image Quality Rating (IQR): 81.46% (B-)
- GM volume (GMV): 52.30% (699.14 / 1336.78 ml)
- GM thickness (GMT): 2.64 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1912318/ds/Utah_1/sub-0026019/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_1912318/ds/Utah_1/sub-0026019/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_1912318/ds/Utah_1/sub-0026019/ses-1/label
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