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- CAT12.8.1 r2040: 1/1: ./sub-0026032/ses-1/sub-0026032_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 327s
- Internal resampling (1.20x0.50x0.50mm > 0.80x0.50x0.50mm): 5s
- APP: Rough bias correction:
- Initialize 11s
- Estimate background 10s
- Initial correction 24s
- Refine background 5s
- Final correction 14s
- Final scaling 30s
- 132s
- Correct center-of-mass 6s
- Affine registration 42s
- SPM preprocessing 1 (estimate 1 - TPM registration): 86s
- SPM preprocessing 1 (estimate 2): 74s
- SPM preprocessing 2 (write):
- Write Segmentation 102s
- Update Segmentation 118s
- Update Skull-Stripping 379s
- Update probability maps 105s
- 704s
- Global intensity correction: 91s
- SANLM denoising after intensity normalization (medium): 307s
- Fast Optimized Shooting registration 105s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 21s
- Prepare partitions 17s
- Prepare segments (LASmod = 1.00) 110s
- Estimate local tissue thresholds (WM) 70s
- Estimate local tissue thresholds (GM) 85s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 346s
- 671s
- ROI segmentation (partitioning):
- Atlas -> subject space 28s
- Major structures 5s
- Ventricle detection 23s
- Blood vessel detection 16s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.02) 41s
- Manual stroke lesion detection 0s
- Closing of deep structures 3s
- Side alignment 6s
- Final corrections 26s
- 148s
- Blood vessel correction (BVCstr=0.50): 10s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 159s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 28s
- Level 1 cleanup (brain masking) 15s
- Level 2 cleanup (CSF correction) 8s
- Level 3 cleanup (CSF/WM PVE) 19s
- 71s
- 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 | 0.0836 0.0014 0.0850 | 29.4886
- 3 | 2.50 | 0.0826 0.0021 0.0847 | 26.9772
- 4 | 2.50 | 0.0821 0.0024 0.0845 | 24.6107
- 5 | 2.50 | 0.0817 0.0026 0.0843 | 22.6548
- 6 | 2.50 | 0.0814 0.0027 0.0841 | 20.6989
- 7 | 2.50 | 0.0810 0.0028 0.0839 | 18.9688
- 8 | 2.50 | 0.0806 0.0030 0.0836 | 17.4455
- 9 | 2.50 | 0.0803 0.0031 0.0833 | 15.9223
- 10 | 2.50 | 0.0799 0.0032 0.0831 | 14.6627
- 11 | 2.50 | 0.0795 0.0033 0.0828 | 13.4764
- 12 | 2.50 | 0.0791 0.0034 0.0825 | 12.3015
- 13 | 2.50 | 0.0787 0.0035 0.0822 | 11.3776
- 14 | 2.50 | 0.0783 0.0036 0.0819 | 10.4537
- 15 | 2.25 | 0.0786 0.0037 0.0823 | 9.5920
- 16 | 2.25 | 0.0751 0.0054 0.0805 | 8.8725
- 17 | 2.25 | 0.0737 0.0060 0.0797 | 8.1530
- 29 | 2.00 | 0.0752 0.0028 0.0779 | 3.3283
- 30 | 2.00 | 0.0691 0.0053 0.0744 | 3.1221
- 31 | 2.00 | 0.0669 0.0064 0.0733 | 2.9160
- 43 | 1.75 | 0.0660 0.0037 0.0697 | 1.5785
- 44 | 1.75 | 0.0614 0.0061 0.0675 | 1.5194
- 45 | 1.75 | 0.0599 0.0069 0.0668 | 1.4626
- 57 | 1.50 | 0.0583 0.0051 0.0634 | 1.0900
- 58 | 1.50 | 0.0550 0.0072 0.0622 | 1.0730
- 59 | 1.50 | 0.0539 0.0079 0.0618 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 214s
- Prepare output 43s
- 257s
- Jacobian determinant (RMS): 0.013 0.049 0.074 0.101 0.124 | 0.130948
- Template Matching: 0.087 0.221 0.201 0.180 0.162 | 0.161551
- Write result maps: 363s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 54s
- CSF distance: 22s
- PBT2x thickness: 65s
- 150s
- Create initial surface 119s
- Topology correction: 130s
- Surface refinement: 121s
- Reduction of surface collisions with optimization: 105s
- Spherical mapping with areal smoothing 125s
- Spherical registration 343s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 46s
- CSF distance: 22s
- PBT2x thickness: 65s
- 141s
- Create initial surface 117s
- Topology correction: 131s
- Surface refinement: 121s
- Reduction of surface collisions with optimization: 102s
- Spherical mapping with areal smoothing 116s
- Spherical registration 342s
- Final surface processing results:
- Average thickness (FS): 2.4392 0.5875 mm
- Surface intensity / position RMSE: 0.0744 / 0.0704
- Euler number / defect number / defect size: 18.0 / 18.5 / 0.44%
- Display thickness: /var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-1/surf/lh.thickness.sub-0026032_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-1/surf/rh.thickness.sub-0026032_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-1/sub-0026032_ses-1_run-1_T1w.nii
- Surface ROI estimation: 11s
- Surface and thickness estimation takes: 2433s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 51s
- ROI estimation of 'neuromorphometrics' atlas 183s
- ROI estimation of 'lpba40' atlas 52s
- ROI estimation of 'hammers' atlas 125s
- ROI estimation of 'thalamus' atlas 10s
- ROI estimation of 'ibsr' atlas 44s
- ROI estimation of 'aal3' atlas 70s
- ROI estimation of 'mori' atlas 106s
- ROI estimation of 'anatomy3' atlas 151s
- ROI estimation of 'julichbrain' atlas 198s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 79s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 136s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 310s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 476s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 39s
- Write results 40s
- 2031s
- Quality check: 57s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-1/report/catreport_sub-0026032_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 138 minute(s) and 47 second(s).
- Image Quality Rating (IQR): 75.65% (C)
- GM volume (GMV): 48.57% (781.60 / 1609.29 ml)
- GM thickness (GMT): 2.44 0.59 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-1/label
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