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- CAT12.8.1 r2040: 1/1: ./sub-0026043/ses-2/sub-0026043_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 218s
- Internal resampling (1.20x0.50x0.50mm > 0.80x0.50x0.80mm): 3s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 6s
- Initial correction 8s
- Refine background 3s
- Final correction 7s
- Final scaling 11s
- 57s
- Correct center-of-mass 4s
- Affine registration 26s
- SPM preprocessing 1 (estimate 1 - TPM registration): 63s
- SPM preprocessing 1 (estimate 2): 35s
- SPM preprocessing 2 (write):
- Write Segmentation 37s
- Update Segmentation 44s
- Update Skull-Stripping 104s
- Update probability maps 19s
- 205s
- Global intensity correction: 33s
- SANLM denoising after intensity normalization (medium): 154s
- Fast Optimized Shooting registration 39s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 8s
- Prepare partitions 6s
- Prepare segments (LASmod = 1.07) 39s
- Estimate local tissue thresholds (WM) 29s
- Estimate local tissue thresholds (GM) 39s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 137s
- 266s
- ROI segmentation (partitioning):
- Atlas -> subject space 13s
- Major structures 4s
- Ventricle detection 12s
- Blood vessel detection 12s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.19) 24s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 10s
- 82s
- Blood vessel correction (BVCstr=0.50): 4s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 73s
- AMAP peaks: [CSF,GM,WM] = [0.370.05,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 10s
- Level 1 cleanup (brain masking) 6s
- Level 2 cleanup (CSF correction) 3s
- Level 3 cleanup (CSF/WM PVE) 7s
- 27s
- 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 | 0.0903 0.0000 0.0903 | 32.0000
- 2 | 2.50 | 0.0869 0.0014 0.0883 | 29.4886
- 3 | 2.50 | 0.0859 0.0022 0.0880 | 26.9772
- 4 | 2.50 | 0.0853 0.0025 0.0878 | 24.6107
- 5 | 2.50 | 0.0849 0.0027 0.0876 | 22.6548
- 6 | 2.50 | 0.0846 0.0028 0.0874 | 20.6989
- 7 | 2.50 | 0.0842 0.0029 0.0871 | 18.9688
- 8 | 2.50 | 0.0838 0.0030 0.0869 | 17.4455
- 9 | 2.50 | 0.0835 0.0031 0.0866 | 15.9223
- 10 | 2.50 | 0.0830 0.0033 0.0863 | 14.6627
- 11 | 2.50 | 0.0827 0.0034 0.0860 | 13.4764
- 12 | 2.50 | 0.0822 0.0034 0.0857 | 12.3015
- 13 | 2.50 | 0.0818 0.0036 0.0854 | 11.3776
- 14 | 2.50 | 0.0814 0.0036 0.0850 | 10.4537
- 15 | 2.25 | 0.0814 0.0037 0.0852 | 9.5920
- 16 | 2.25 | 0.0780 0.0054 0.0834 | 8.8725
- 17 | 2.25 | 0.0767 0.0060 0.0826 | 8.1530
- 18 | 2.25 | 0.0758 0.0062 0.0820 | 7.5234
- 19 | 2.25 | 0.0752 0.0063 0.0815 | 6.9630
- 20 | 2.25 | 0.0746 0.0062 0.0809 | 6.4027
- 29 | 2.00 | 0.0769 0.0035 0.0803 | 3.3283
- 30 | 2.00 | 0.0720 0.0057 0.0777 | 3.1221
- 31 | 2.00 | 0.0704 0.0064 0.0768 | 2.9160
- 43 | 1.75 | 0.0699 0.0036 0.0735 | 1.5785
- 44 | 1.75 | 0.0652 0.0061 0.0714 | 1.5194
- 45 | 1.75 | 0.0637 0.0070 0.0707 | 1.4626
- 57 | 1.50 | 0.0622 0.0050 0.0672 | 1.0900
- 58 | 1.50 | 0.0586 0.0074 0.0660 | 1.0730
- 59 | 1.50 | 0.0574 0.0082 0.0656 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 115s
- Prepare output 16s
- 131s
- Jacobian determinant (RMS): 0.013 0.047 0.071 0.092 0.116 | 0.122991
- Template Matching: 0.090 0.224 0.211 0.191 0.172 | 0.172219
- Write result maps: 143s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 37s
- CSF distance: 13s
- PBT2x thickness: 36s
- 91s
- Create initial surface 68s
- Topology correction: 75s
- Surface refinement: 72s
- Reduction of surface collisions with optimization: 59s
- Spherical mapping with areal smoothing 69s
- Spherical registration 196s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 36s
- CSF distance: 13s
- PBT2x thickness: 36s
- 91s
- Create initial surface 66s
- Topology correction: 76s
- Surface refinement: 70s
- Reduction of surface collisions with optimization: 58s
- Spherical mapping with areal smoothing 81s
- Spherical registration 196s
- Final surface processing results:
- Average thickness (FS): 2.4824 0.5970 mm
- Surface intensity / position RMSE: 0.0662 / 0.0705
- Euler number / defect number / defect size: 14.0 / 9.0 / 0.60%
- Display thickness: /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-2/surf/lh.thickness.sub-0026043_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-2/surf/rh.thickness.sub-0026043_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-2/sub-0026043_ses-2_run-1_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1395s
- 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 50s
- ROI estimation of 'thalamus' atlas 4s
- ROI estimation of 'ibsr' atlas 17s
- ROI estimation of 'aal3' atlas 29s
- ROI estimation of 'mori' atlas 42s
- ROI estimation of 'anatomy3' atlas 61s
- ROI estimation of 'julichbrain' atlas 79s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 32s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 57s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 124s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 183s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 16s
- Write results 17s
- 807s
- Quality check: 31s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-2/report/catreport_sub-0026043_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 64 minute(s) and 57 second(s).
- Image Quality Rating (IQR): 82.72% (B-)
- GM volume (GMV): 43.84% (798.12 / 1820.48 ml)
- GM thickness (GMT): 2.48 0.60 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-2/label
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