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- CAT12.8.1 r2040: 1/1: ./sub-0025995/ses-4/sub-0025995_ses-4_run-1_T1w.n
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- SANLM denoising (medium): 30s
- APP: Rough bias correction:
- Initialize 4s
- Estimate background 3s
- Initial correction 3s
- Refine background 2s
- Final correction 3s
- Final scaling 3s
- 22s
- Correct center-of-mass 3s
- Affine registration 5s
- SPM preprocessing 1 (estimate 1 - TPM registration): 5s
- Use initial fine affine registration. 34s
- SPM preprocessing 1 (estimate 2): 35s
- SPM preprocessing 2 (write):
- Write Segmentation 10s
- Update Segmentation 11s
- Update Skull-Stripping 24s
- Update probability maps 5s
- 51s
- Global intensity correction: 10s
- SANLM denoising after intensity normalization (medium): 13s
- Fast Optimized Shooting registration 20s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 2s
- Prepare partitions 1s
- Prepare segments (LASmod = 1.00) 7s
- Estimate local tissue thresholds (WM) 11s
- Estimate local tissue thresholds (GM) 15s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 27s
- 65s
- ROI segmentation (partitioning):
- Atlas -> subject space 4s
- Major structures 2s
- Ventricle detection 5s
- Blood vessel detection 5s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.05) 11s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 3s
- 32s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 19s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 2s
- Level 1 cleanup (brain masking) 1s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 1s
- 6s
- 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 | 0.0808 0.0012 0.0821 | 29.4886
- 3 | 2.50 | 0.0800 0.0019 0.0819 | 26.9772
- 4 | 2.50 | 0.0796 0.0021 0.0817 | 24.6107
- 5 | 2.50 | 0.0792 0.0023 0.0815 | 22.6548
- 6 | 2.50 | 0.0789 0.0024 0.0813 | 20.6989
- 7 | 2.50 | 0.0786 0.0025 0.0811 | 18.9688
- 8 | 2.50 | 0.0783 0.0026 0.0809 | 17.4455
- 9 | 2.50 | 0.0780 0.0027 0.0807 | 15.9223
- 10 | 2.50 | 0.0776 0.0028 0.0804 | 14.6627
- 11 | 2.50 | 0.0772 0.0029 0.0802 | 13.4764
- 12 | 2.50 | 0.0769 0.0030 0.0799 | 12.3015
- 13 | 2.50 | 0.0765 0.0031 0.0796 | 11.3776
- 14 | 2.50 | 0.0761 0.0032 0.0793 | 10.4537
- 15 | 2.25 | 0.0759 0.0033 0.0792 | 9.5920
- 16 | 2.25 | 0.0727 0.0049 0.0776 | 8.8725
- 29 | 2.00 | 0.0736 0.0022 0.0758 | 3.3283
- 30 | 2.00 | 0.0670 0.0048 0.0718 | 3.1221
- 31 | 2.00 | 0.0647 0.0059 0.0706 | 2.9160
- 43 | 1.75 | 0.0634 0.0034 0.0668 | 1.5785
- 44 | 1.75 | 0.0590 0.0057 0.0647 | 1.5194
- 45 | 1.75 | 0.0576 0.0065 0.0641 | 1.4626
- 57 | 1.50 | 0.0562 0.0047 0.0609 | 1.0900
- 58 | 1.50 | 0.0531 0.0067 0.0599 | 1.0730
- 59 | 1.50 | 0.0521 0.0073 0.0595 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 97s
- Prepare output 6s
- 103s
- Jacobian determinant (RMS): 0.011 0.042 0.063 0.087 0.111 | 0.116150
- Template Matching: 0.084 0.218 0.194 0.173 0.156 | 0.156349
- Write result maps: 20s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 21s
- CSF distance: 8s
- PBT2x thickness: 23s
- 55s
- Create initial surface 41s
- Topology correction: 54s
- Surface refinement: 50s
- Reduction of surface collisions with optimization: 34s
- Spherical mapping with areal smoothing 45s
- Spherical registration 164s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 15s
- CSF distance: 8s
- PBT2x thickness: 23s
- 48s
- Create initial surface 41s
- Topology correction: 54s
- Surface refinement: 53s
- Reduction of surface collisions with optimization: 34s
- Spherical mapping with areal smoothing 45s
- Spherical registration 176s
- Final surface processing results:
- Average thickness (FS): 2.3834 0.6297 mm
- Surface intensity / position RMSE: 0.0696 / 0.0742
- Euler number / defect number / defect size: 30.0 / 14.5 / 0.84%
- Display thickness: /var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-4/surf/lh.thickness.sub-0025995_ses-4_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-4/surf/rh.thickness.sub-0025995_ses-4_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-4/sub-0025995_ses-4_run-1_T1w.nii
- Surface ROI estimation: 5s
- Surface and thickness estimation takes: 948s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 6s
- ROI estimation of 'neuromorphometrics' atlas 21s
- ROI estimation of 'lpba40' atlas 6s
- ROI estimation of 'hammers' atlas 15s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 5s
- ROI estimation of 'aal3' atlas 8s
- ROI estimation of 'mori' atlas 11s
- ROI estimation of 'anatomy3' atlas 16s
- ROI estimation of 'julichbrain' atlas 21s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 9s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 15s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 34s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 51s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 4s
- Write results 5s
- 224s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-4/report/catreport_sub-0025995_ses-4_run-1_T1w.pdf
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- CAT preprocessing takes 28 minute(s) and 33 second(s).
- Image Quality Rating (IQR): 81.21% (B-)
- GM volume (GMV): 45.87% (597.31 / 1302.25 ml)
- GM thickness (GMT): 2.38 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-4/mri
- Reports are saved in /var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-4/report
- Labels are saved in /var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-4/label
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