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- CAT12.8.1 r2040: 1/1: ./sub-0025605/ses-1/sub-0025605_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 35s
- APP: Rough bias correction:
- Initialize 4s
- Estimate background 4s
- Initial correction 4s
- Refine background 2s
- Final correction 3s
- Final scaling 3s
- 24s
- Correct center-of-mass 3s
- Affine registration 5s
- SPM preprocessing 1 (estimate 1 - TPM registration): 59s
- SPM preprocessing 1 (estimate 2): 43s
- SPM preprocessing 2 (write):
- Write Segmentation 13s
- Update Segmentation 14s
- Update Skull-Stripping 29s
- Update probability maps 7s
- 63s
- Global intensity correction: 12s
- SANLM denoising after intensity normalization (medium): 23s
- Fast Optimized Shooting registration 26s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.05) 11s
- Estimate local tissue thresholds (WM) 13s
- Estimate local tissue thresholds (GM) 20s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 29s
- 80s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 3s
- Ventricle detection 8s
- Blood vessel detection 7s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.15) 15s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 3s
- 45s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 26s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 3s
- Level 1 cleanup (brain masking) 2s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 8s
- 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 | 0.0884 0.0000 0.0884 | 32.0000
- 2 | 2.50 | 0.0852 0.0014 0.0866 | 29.4886
- 3 | 2.50 | 0.0843 0.0021 0.0864 | 26.9772
- 4 | 2.50 | 0.0838 0.0024 0.0862 | 24.6107
- 5 | 2.50 | 0.0834 0.0025 0.0860 | 22.6548
- 6 | 2.50 | 0.0831 0.0027 0.0858 | 20.6989
- 7 | 2.50 | 0.0828 0.0028 0.0855 | 18.9688
- 8 | 2.50 | 0.0824 0.0029 0.0853 | 17.4455
- 9 | 2.50 | 0.0820 0.0030 0.0850 | 15.9223
- 10 | 2.50 | 0.0816 0.0031 0.0848 | 14.6627
- 11 | 2.50 | 0.0812 0.0032 0.0845 | 13.4764
- 12 | 2.50 | 0.0808 0.0033 0.0841 | 12.3015
- 13 | 2.50 | 0.0804 0.0035 0.0839 | 11.3776
- 14 | 2.50 | 0.0800 0.0035 0.0835 | 10.4537
- 15 | 2.25 | 0.0807 0.0036 0.0843 | 9.5920
- 16 | 2.25 | 0.0772 0.0054 0.0825 | 8.8725
- 17 | 2.25 | 0.0757 0.0060 0.0817 | 8.1530
- 18 | 2.25 | 0.0747 0.0063 0.0810 | 7.5234
- 29 | 2.00 | 0.0766 0.0030 0.0796 | 3.3283
- 30 | 2.00 | 0.0705 0.0057 0.0762 | 3.1221
- 31 | 2.00 | 0.0683 0.0067 0.0750 | 2.9160
- 43 | 1.75 | 0.0671 0.0038 0.0710 | 1.5785
- 44 | 1.75 | 0.0624 0.0063 0.0688 | 1.5194
- 45 | 1.75 | 0.0609 0.0072 0.0680 | 1.4626
- 57 | 1.50 | 0.0593 0.0052 0.0646 | 1.0900
- 58 | 1.50 | 0.0559 0.0075 0.0634 | 1.0730
- 59 | 1.50 | 0.0548 0.0081 0.0630 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 132s
- Prepare output 7s
- 139s
- Jacobian determinant (RMS): 0.011 0.043 0.067 0.092 0.117 | 0.123611
- Template Matching: 0.088 0.224 0.205 0.183 0.164 | 0.164472
- Write result maps: 28s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 46s
- CSF distance: 11s
- PBT2x thickness: 33s
- 95s
- Create initial surface 59s
- Topology correction: 68s
- Surface refinement: 48s
- Reduction of surface collisions with optimization: 43s
- Spherical mapping with areal smoothing 57s
- Spherical registration 209s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 33s
- CSF distance: 11s
- PBT2x thickness: 32s
- 80s
- Create initial surface 59s
- Topology correction: 69s
- Surface refinement: 66s
- Reduction of surface collisions with optimization: 45s
- Spherical mapping with areal smoothing 64s
- Spherical registration 217s
- Final surface processing results:
- Average thickness (FS): 2.5425 0.6233 mm
- Surface intensity / position RMSE: 0.0595 / 0.0559
- Euler number / defect number / defect size: 12.0 / 11.5 / 0.29%
- Display thickness: /var/lib/condor/execute/dir_541944/ds/JHNU/sub-0025605/ses-1/surf/lh.thickness.sub-0025605_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_541944/ds/JHNU/sub-0025605/ses-1/surf/rh.thickness.sub-0025605_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_541944/ds/JHNU/sub-0025605/ses-1/sub-0025605_ses-1_run-1_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1249s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 26s
- ROI estimation of 'lpba40' atlas 7s
- ROI estimation of 'hammers' atlas 19s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 11s
- ROI estimation of 'mori' atlas 18s
- ROI estimation of 'anatomy3' atlas 30s
- ROI estimation of 'julichbrain' atlas 40s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 37s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 79s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 115s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 9s
- Write results 10s
- 424s
- Quality check: 10s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_541944/ds/JHNU/sub-0025605/ses-1/report/catreport_sub-0025605_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 39 minute(s) and 31 second(s).
- Image Quality Rating (IQR): 82.05% (B-)
- GM volume (GMV): 44.14% (666.98 / 1511.10 ml)
- GM thickness (GMT): 2.54 0.62 mm
- Segmentations are saved in /var/lib/condor/execute/dir_541944/ds/JHNU/sub-0025605/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_541944/ds/JHNU/sub-0025605/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_541944/ds/JHNU/sub-0025605/ses-1/label
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