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- CAT12.8.1 r2040: 1/1: ./sub-0026043/ses-1/sub-0026043_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 226s
- Internal resampling (1.20x0.50x0.50mm > 0.80x0.80x0.80mm): 2s
- APP: Rough bias correction:
- Initialize 9s
- Estimate background 7s
- Initial correction 8s
- Refine background 4s
- Final correction 7s
- Final scaling 7s
- 51s
- Correct center-of-mass 3s
- Affine registration 27s
- SPM preprocessing 1 (estimate 1 - TPM registration): 102s
- SPM preprocessing 1 (estimate 2): 38s
- SPM preprocessing 2 (write):
- Write Segmentation 23s
- Update Segmentation 28s
- Update Skull-Stripping 61s
- Update probability maps 12s
- 124s
- Global intensity correction: 22s
- SANLM denoising after intensity normalization (medium): 50s
- Fast Optimized Shooting registration 31s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 6s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.04) 23s
- Estimate local tissue thresholds (WM) 26s
- Estimate local tissue thresholds (GM) 38s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 56s
- 157s
- ROI segmentation (partitioning):
- Atlas -> subject space 10s
- Major structures 5s
- Ventricle detection 16s
- Blood vessel detection 16s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.16) 32s
- Manual stroke lesion detection 0s
- Closing of deep structures 3s
- Side alignment 6s
- Final corrections 6s
- 95s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 49s
- AMAP peaks: [CSF,GM,WM] = [0.370.05,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 6s
- Level 1 cleanup (brain masking) 4s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 4s
- 16s
- 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 | 0.0890 0.0000 0.0890 | 32.0000
- 2 | 2.50 | 0.0857 0.0014 0.0871 | 29.4886
- 3 | 2.50 | 0.0848 0.0021 0.0868 | 26.9772
- 4 | 2.50 | 0.0843 0.0023 0.0866 | 24.6107
- 5 | 2.50 | 0.0839 0.0025 0.0864 | 22.6548
- 6 | 2.50 | 0.0836 0.0026 0.0862 | 20.6989
- 7 | 2.50 | 0.0833 0.0027 0.0860 | 18.9688
- 8 | 2.50 | 0.0829 0.0028 0.0858 | 17.4455
- 9 | 2.50 | 0.0826 0.0029 0.0855 | 15.9223
- 10 | 2.50 | 0.0822 0.0030 0.0852 | 14.6627
- 11 | 2.50 | 0.0818 0.0031 0.0850 | 13.4764
- 12 | 2.50 | 0.0815 0.0032 0.0846 | 12.3015
- 13 | 2.50 | 0.0811 0.0033 0.0844 | 11.3776
- 14 | 2.50 | 0.0807 0.0033 0.0841 | 10.4537
- 15 | 2.25 | 0.0803 0.0034 0.0837 | 9.5920
- 16 | 2.25 | 0.0771 0.0049 0.0821 | 8.8725
- 17 | 2.25 | 0.0759 0.0054 0.0814 | 8.1530
- 18 | 2.25 | 0.0752 0.0056 0.0808 | 7.5234
- 19 | 2.25 | 0.0746 0.0057 0.0803 | 6.9630
- 29 | 2.00 | 0.0768 0.0029 0.0797 | 3.3283
- 30 | 2.00 | 0.0718 0.0051 0.0769 | 3.1221
- 31 | 2.00 | 0.0701 0.0059 0.0761 | 2.9160
- 43 | 1.75 | 0.0695 0.0033 0.0729 | 1.5785
- 44 | 1.75 | 0.0650 0.0058 0.0708 | 1.5194
- 45 | 1.75 | 0.0635 0.0066 0.0701 | 1.4626
- 57 | 1.50 | 0.0621 0.0048 0.0669 | 1.0900
- 58 | 1.50 | 0.0586 0.0071 0.0657 | 1.0730
- 59 | 1.50 | 0.0575 0.0078 0.0653 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 115s
- Prepare output 11s
- 126s
- Jacobian determinant (RMS): 0.012 0.044 0.065 0.086 0.109 | 0.115663
- Template Matching: 0.089 0.224 0.210 0.191 0.172 | 0.172464
- Write result maps: 157s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 32s
- CSF distance: 14s
- PBT2x thickness: 36s
- 86s
- Create initial surface 65s
- Topology correction: 75s
- Surface refinement: 76s
- Reduction of surface collisions with optimization: 58s
- Spherical mapping with areal smoothing 68s
- Spherical registration 185s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 27s
- CSF distance: 12s
- PBT2x thickness: 34s
- 78s
- Create initial surface 62s
- Topology correction: 74s
- Surface refinement: 68s
- Reduction of surface collisions with optimization: 57s
- Spherical mapping with areal smoothing 84s
- Spherical registration 218s
- Final surface processing results:
- Average thickness (FS): 2.5335 0.6049 mm
- Surface intensity / position RMSE: 0.0642 / 0.0649
- Euler number / defect number / defect size: 16.0 / 13.0 / 0.68%
- Display thickness: /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-1/surf/lh.thickness.sub-0026043_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-1/surf/rh.thickness.sub-0026043_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-1/sub-0026043_ses-1_run-1_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1374s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 13s
- ROI estimation of 'neuromorphometrics' atlas 45s
- ROI estimation of 'lpba40' atlas 13s
- ROI estimation of 'hammers' atlas 32s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 11s
- ROI estimation of 'aal3' atlas 18s
- ROI estimation of 'mori' atlas 27s
- ROI estimation of 'anatomy3' atlas 39s
- ROI estimation of 'julichbrain' atlas 52s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 22s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 38s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 88s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 127s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 10s
- Write results 11s
- 539s
- Quality check: 40s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-1/report/catreport_sub-0026043_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 55 minute(s) and 8 second(s).
- Image Quality Rating (IQR): 84.90% (B)
- GM volume (GMV): 45.47% (818.10 / 1799.22 ml)
- GM thickness (GMT): 2.53 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-1/label
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