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- CAT12.8.1 r2040: 1/1: ./sub-0003062/ses-1/sub-0003062_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 78s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 6s
- Initial correction 5s
- Refine background 3s
- Final correction 4s
- Final scaling 5s
- 33s
- Correct center-of-mass 2s
- Affine registration 7s
- SPM preprocessing 1 (estimate 1 - TPM registration): 55s
- SPM preprocessing 1 (estimate 2): 48s
- SPM preprocessing 2 (write):
- Write Segmentation 14s
- Update Segmentation 17s
- Update Skull-Stripping 37s
- Update probability maps 8s
- 75s
- Global intensity correction: 14s
- SANLM denoising after intensity normalization (medium): 21s
- Fast Optimized Shooting registration 27s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.01) 12s
- Estimate local tissue thresholds (WM) 14s
- Estimate local tissue thresholds (GM) 20s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 33s
- 87s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 10s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.12) 20s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 55s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 31s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 3s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 10s
- 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 | 0.0864 0.0000 0.0864 | 32.0000
- 2 | 2.50 | 0.0842 0.0011 0.0853 | 29.4886
- 3 | 2.50 | 0.0836 0.0016 0.0852 | 26.9772
- 4 | 2.50 | 0.0832 0.0018 0.0850 | 24.6107
- 5 | 2.50 | 0.0830 0.0019 0.0849 | 22.6548
- 6 | 2.50 | 0.0828 0.0020 0.0848 | 20.6989
- 7 | 2.50 | 0.0825 0.0021 0.0846 | 18.9688
- 8 | 2.50 | 0.0823 0.0022 0.0845 | 17.4455
- 9 | 2.50 | 0.0821 0.0022 0.0843 | 15.9223
- 10 | 2.50 | 0.0818 0.0023 0.0841 | 14.6627
- 11 | 2.50 | 0.0815 0.0024 0.0839 | 13.4764
- 12 | 2.50 | 0.0813 0.0024 0.0837 | 12.3015
- 13 | 2.50 | 0.0810 0.0025 0.0835 | 11.3776
- 14 | 2.50 | 0.0807 0.0026 0.0833 | 10.4537
- 15 | 2.25 | 0.0802 0.0026 0.0828 | 9.5920
- 16 | 2.25 | 0.0775 0.0039 0.0815 | 8.8725
- 17 | 2.25 | 0.0765 0.0044 0.0809 | 8.1530
- 18 | 2.25 | 0.0758 0.0046 0.0804 | 7.5234
- 19 | 2.25 | 0.0753 0.0047 0.0800 | 6.9630
- 20 | 2.25 | 0.0749 0.0047 0.0796 | 6.4027
- 29 | 2.00 | 0.0766 0.0026 0.0792 | 3.3283
- 30 | 2.00 | 0.0721 0.0046 0.0767 | 3.1221
- 31 | 2.00 | 0.0705 0.0054 0.0759 | 2.9160
- 43 | 1.75 | 0.0696 0.0030 0.0726 | 1.5785
- 44 | 1.75 | 0.0652 0.0054 0.0706 | 1.5194
- 45 | 1.75 | 0.0638 0.0062 0.0700 | 1.4626
- 57 | 1.50 | 0.0625 0.0044 0.0669 | 1.0900
- 58 | 1.50 | 0.0592 0.0066 0.0658 | 1.0730
- 59 | 1.50 | 0.0582 0.0073 0.0655 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 170s
- Prepare output 8s
- 178s
- Jacobian determinant (RMS): 0.010 0.035 0.055 0.076 0.099 | 0.105716
- Template Matching: 0.086 0.225 0.211 0.191 0.175 | 0.174550
- Write result maps: 37s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 31s
- CSF distance: 12s
- PBT2x thickness: 36s
- 84s
- Create initial surface 65s
- Topology correction: 74s
- Surface refinement: 54s
- Reduction of surface collisions with optimization: 52s
- Spherical mapping with areal smoothing 64s
- Spherical registration 202s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 29s
- CSF distance: 12s
- PBT2x thickness: 36s
- 82s
- Create initial surface 67s
- Topology correction: 75s
- Surface refinement: 59s
- Reduction of surface collisions with optimization: 56s
- Spherical mapping with areal smoothing 65s
- Spherical registration 226s
- Final surface processing results:
- Average thickness (FS): 2.4410 0.6204 mm
- Surface intensity / position RMSE: 0.0673 / 0.0705
- Euler number / defect number / defect size: 26.0 / 10.5 / 0.78%
- Display thickness: /var/lib/condor/execute/dir_2389396/ds/BMB_1/sub-0003062/ses-1/surf/lh.thickness.sub-0003062_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2389396/ds/BMB_1/sub-0003062/ses-1/surf/rh.thickness.sub-0003062_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2389396/ds/BMB_1/sub-0003062/ses-1/sub-0003062_ses-1_run-1_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1308s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 18s
- ROI estimation of 'neuromorphometrics' atlas 72s
- ROI estimation of 'lpba40' atlas 26s
- ROI estimation of 'hammers' atlas 65s
- ROI estimation of 'thalamus' atlas 5s
- ROI estimation of 'ibsr' atlas 23s
- ROI estimation of 'aal3' atlas 40s
- ROI estimation of 'mori' atlas 60s
- ROI estimation of 'anatomy3' atlas 85s
- ROI estimation of 'julichbrain' atlas 108s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 43s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 79s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 154s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 200s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 15s
- Write results 16s
- 997s
- Quality check: 11s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2389396/ds/BMB_1/sub-0003062/ses-1/report/catreport_sub-0003062_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 53 minute(s) and 48 second(s).
- Image Quality Rating (IQR): 82.24% (B-)
- GM volume (GMV): 44.39% (709.87 / 1599.32 ml)
- GM thickness (GMT): 2.44 0.62 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2389396/ds/BMB_1/sub-0003062/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_2389396/ds/BMB_1/sub-0003062/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_2389396/ds/BMB_1/sub-0003062/ses-1/label
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