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- CAT12.8.1 r2040: 1/1: ./sub-0025834/ses-1/sub-0025834_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 38s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 4s
- Initial correction 5s
- Refine background 2s
- Final correction 4s
- Final scaling 4s
- 29s
- Correct center-of-mass 2s
- Affine registration 6s
- SPM preprocessing 1 (estimate 1 - TPM registration): 61s
- SPM preprocessing 1 (estimate 2): 47s
- SPM preprocessing 2 (write):
- Write Segmentation 13s
- Update Segmentation 16s
- Update Skull-Stripping 32s
- Update probability maps 7s
- 67s
- 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 = 1.11) 12s
- Estimate local tissue thresholds (WM) 16s
- Estimate local tissue thresholds (GM) 22s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 38s
- 96s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 3s
- Ventricle detection 12s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.06) 20s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 58s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 29s
- 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) 2s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 9s
- 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 | 0.0832 0.0000 0.0832 | 32.0000
- 2 | 2.50 | 0.0813 0.0010 0.0823 | 29.4886
- 3 | 2.50 | 0.0807 0.0015 0.0822 | 26.9772
- 4 | 2.50 | 0.0805 0.0017 0.0821 | 24.6107
- 5 | 2.50 | 0.0802 0.0018 0.0820 | 22.6548
- 6 | 2.50 | 0.0800 0.0019 0.0819 | 20.6989
- 7 | 2.50 | 0.0798 0.0019 0.0817 | 18.9688
- 8 | 2.50 | 0.0796 0.0020 0.0816 | 17.4455
- 9 | 2.50 | 0.0793 0.0021 0.0814 | 15.9223
- 10 | 2.50 | 0.0791 0.0021 0.0812 | 14.6627
- 11 | 2.50 | 0.0789 0.0022 0.0811 | 13.4764
- 12 | 2.50 | 0.0786 0.0022 0.0809 | 12.3015
- 13 | 2.50 | 0.0783 0.0023 0.0807 | 11.3776
- 14 | 2.50 | 0.0781 0.0024 0.0805 | 10.4537
- 15 | 2.25 | 0.0779 0.0024 0.0803 | 9.5920
- 16 | 2.25 | 0.0751 0.0037 0.0789 | 8.8725
- 17 | 2.25 | 0.0740 0.0042 0.0783 | 8.1530
- 29 | 2.00 | 0.0763 0.0019 0.0782 | 3.3283
- 30 | 2.00 | 0.0707 0.0042 0.0749 | 3.1221
- 31 | 2.00 | 0.0688 0.0051 0.0739 | 2.9160
- 43 | 1.75 | 0.0679 0.0029 0.0709 | 1.5785
- 44 | 1.75 | 0.0635 0.0053 0.0688 | 1.5194
- 45 | 1.75 | 0.0621 0.0061 0.0682 | 1.4626
- 57 | 1.50 | 0.0608 0.0044 0.0652 | 1.0900
- 58 | 1.50 | 0.0575 0.0066 0.0640 | 1.0730
- 59 | 1.50 | 0.0564 0.0072 0.0636 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 138s
- Prepare output 8s
- 146s
- Jacobian determinant (RMS): 0.009 0.031 0.048 0.072 0.097 | 0.103317
- Template Matching: 0.083 0.222 0.206 0.186 0.169 | 0.169182
- Write result maps: 33s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 33s
- CSF distance: 14s
- PBT2x thickness: 38s
- 90s
- Create initial surface 69s
- Topology correction: 90s
- Surface refinement: 83s
- Reduction of surface collisions with optimization: 62s
- Spherical mapping with areal smoothing 73s
- Spherical registration 214s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 27s
- CSF distance: 12s
- PBT2x thickness: 37s
- 82s
- Create initial surface 66s
- Topology correction: 84s
- Surface refinement: 95s
- Reduction of surface collisions with optimization: 64s
- Spherical mapping with areal smoothing 79s
- Spherical registration 206s
- Final surface processing results:
- Average thickness (FS): 2.5041 0.5994 mm
- Surface intensity / position RMSE: 0.0661 / 0.0653
- Euler number / defect number / defect size: 14.0 / 12.0 / 0.33%
- Display thickness: /var/lib/condor/execute/dir_3441304/ds/SWU_4/sub-0025834/ses-1/surf/lh.thickness.sub-0025834_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3441304/ds/SWU_4/sub-0025834/ses-1/surf/rh.thickness.sub-0025834_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3441304/ds/SWU_4/sub-0025834/ses-1/sub-0025834_ses-1_run-1_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1442s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 10s
- ROI estimation of 'neuromorphometrics' atlas 42s
- ROI estimation of 'lpba40' atlas 12s
- ROI estimation of 'hammers' atlas 35s
- ROI estimation of 'thalamus' atlas 4s
- ROI estimation of 'ibsr' atlas 17s
- ROI estimation of 'aal3' atlas 29s
- ROI estimation of 'mori' atlas 47s
- ROI estimation of 'anatomy3' atlas 71s
- ROI estimation of 'julichbrain' atlas 96s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 40s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 79s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 158s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 200s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 13s
- Write results 14s
- 854s
- Quality check: 12s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3441304/ds/SWU_4/sub-0025834/ses-1/report/catreport_sub-0025834_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 51 minute(s) and 37 second(s).
- Image Quality Rating (IQR): 82.31% (B-)
- GM volume (GMV): 46.54% (808.27 / 1736.70 ml)
- GM thickness (GMT): 2.50 0.60 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3441304/ds/SWU_4/sub-0025834/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_3441304/ds/SWU_4/sub-0025834/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_3441304/ds/SWU_4/sub-0025834/ses-1/label
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