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- CAT12.8.1 r2040: 1/1: ./sub-0026031/ses-2/sub-0026031_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 357s
- Internal resampling (1.20x0.50x0.50mm > 0.80x0.80x0.80mm): 3s
- APP: Rough bias correction:
- Initialize 16s
- Estimate background 12s
- Initial correction 16s
- Refine background 7s
- Final correction 14s
- Final scaling 12s
- 93s
- Correct center-of-mass 5s
- Affine registration 20s
- SPM preprocessing 1 (estimate 1 - TPM registration): 170s
- SPM preprocessing 1 (estimate 2): 90s
- SPM preprocessing 2 (write):
- Write Segmentation 42s
- Update Segmentation 49s
- Update Skull-Stripping 119s
- Update probability maps 25s
- 235s
- Global intensity correction: 44s
- SANLM denoising after intensity normalization (medium): 75s
- Fast Optimized Shooting registration 66s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 10s
- Prepare partitions 8s
- Prepare segments (LASmod = 1.00) 40s
- Estimate local tissue thresholds (WM) 54s
- Estimate local tissue thresholds (GM) 87s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 110s
- 319s
- ROI segmentation (partitioning):
- Atlas -> subject space 21s
- Major structures 10s
- Ventricle detection 50s
- Blood vessel detection 32s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.01) 70s
- Manual stroke lesion detection 0s
- Closing of deep structures 5s
- Side alignment 10s
- Final corrections 10s
- 208s
- Blood vessel correction (BVCstr=0.50): 4s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 75s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 12s
- Level 1 cleanup (brain masking) 6s
- Level 2 cleanup (CSF correction) 3s
- Level 3 cleanup (CSF/WM PVE) 7s
- 29s
- 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 | 0.0869 0.0000 0.0869 | 32.0000
- 2 | 2.50 | 0.0846 0.0011 0.0857 | 29.4886
- 3 | 2.50 | 0.0840 0.0016 0.0856 | 26.9772
- 4 | 2.50 | 0.0837 0.0018 0.0854 | 24.6107
- 5 | 2.50 | 0.0834 0.0019 0.0853 | 22.6548
- 6 | 2.50 | 0.0832 0.0020 0.0851 | 20.6989
- 7 | 2.50 | 0.0830 0.0020 0.0850 | 18.9688
- 8 | 2.50 | 0.0827 0.0021 0.0848 | 17.4455
- 9 | 2.50 | 0.0825 0.0022 0.0846 | 15.9223
- 10 | 2.50 | 0.0822 0.0023 0.0845 | 14.6627
- 11 | 2.50 | 0.0819 0.0023 0.0843 | 13.4764
- 12 | 2.50 | 0.0817 0.0024 0.0840 | 12.3015
- 13 | 2.50 | 0.0814 0.0025 0.0838 | 11.3776
- 14 | 2.50 | 0.0811 0.0025 0.0836 | 10.4537
- 15 | 2.25 | 0.0823 0.0025 0.0848 | 9.5920
- 16 | 2.25 | 0.0790 0.0041 0.0831 | 8.8725
- 17 | 2.25 | 0.0777 0.0047 0.0824 | 8.1530
- 18 | 2.25 | 0.0770 0.0049 0.0819 | 7.5234
- 19 | 2.25 | 0.0764 0.0050 0.0814 | 6.9630
- 20 | 2.25 | 0.0759 0.0051 0.0810 | 6.4027
- 21 | 2.25 | 0.0754 0.0051 0.0805 | 5.9447
- 22 | 2.25 | 0.0749 0.0052 0.0801 | 5.5083
- 29 | 2.00 | 0.0780 0.0032 0.0812 | 3.3283
- 30 | 2.00 | 0.0736 0.0054 0.0789 | 3.1221
- 31 | 2.00 | 0.0721 0.0061 0.0781 | 2.9160
- 43 | 1.75 | 0.0720 0.0034 0.0754 | 1.5785
- 44 | 1.75 | 0.0668 0.0062 0.0731 | 1.5194
- 45 | 1.75 | 0.0652 0.0071 0.0723 | 1.4626
- 57 | 1.50 | 0.0643 0.0051 0.0694 | 1.0900
- 58 | 1.50 | 0.0603 0.0078 0.0681 | 1.0730
- 59 | 1.50 | 0.0591 0.0085 0.0676 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 224s
- Prepare output 22s
- 247s
- Jacobian determinant (RMS): 0.009 0.034 0.062 0.097 0.138 | 0.142405
- Template Matching: 0.087 0.225 0.216 0.196 0.177 | 0.177396
- Write result maps: 260s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 49s
- CSF distance: 24s
- PBT2x thickness: 68s
- 148s
- Create initial surface 112s
- Topology correction: 123s
- Surface refinement: 147s
- Reduction of surface collisions with optimization: 100s
- Spherical mapping with areal smoothing 121s
- Spherical registration 335s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 52s
- CSF distance: 23s
- PBT2x thickness: 71s
- 154s
- Create initial surface 117s
- Topology correction: 127s
- Surface refinement: 121s
- Reduction of surface collisions with optimization: 106s
- Spherical mapping with areal smoothing 119s
- Spherical registration 337s
- Final surface processing results:
- Average thickness (FS): 2.6553 0.6258 mm
- Surface intensity / position RMSE: 0.0814 / 0.0773
- Euler number / defect number / defect size: 44.0 / 30.5 / 0.82%
- Display thickness: /var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-2/surf/lh.thickness.sub-0026031_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-2/surf/rh.thickness.sub-0026031_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-2/sub-0026031_ses-2_run-1_T1w.nii
- Surface ROI estimation: 11s
- Surface and thickness estimation takes: 2367s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 20s
- ROI estimation of 'neuromorphometrics' atlas 72s
- ROI estimation of 'lpba40' atlas 21s
- ROI estimation of 'hammers' atlas 51s
- ROI estimation of 'thalamus' atlas 4s
- ROI estimation of 'ibsr' atlas 18s
- ROI estimation of 'aal3' atlas 28s
- ROI estimation of 'mori' atlas 41s
- ROI estimation of 'anatomy3' atlas 59s
- ROI estimation of 'julichbrain' atlas 79s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 32s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 54s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 128s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 192s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 16s
- Write results 18s
- 817s
- Quality check: 67s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-2/report/catreport_sub-0026031_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 94 minute(s) and 30 second(s).
- Image Quality Rating (IQR): 70.52% (C-)
- GM volume (GMV): 52.88% (886.70 / 1676.80 ml)
- GM thickness (GMT): 2.66 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-2/label
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