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- CAT12.8.1 r2040: 1/1: ./sub-0026068/ses-1/sub-0026068_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 37s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 5s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 7s
- 40s
- Correct center-of-mass 4s
- Affine registration 11s
- SPM preprocessing 1 (estimate 1 - TPM registration): 116s
- SPM preprocessing 1 (estimate 2): 74s
- SPM preprocessing 2 (write):
- Write Segmentation 18s
- Update Segmentation 21s
- Update Skull-Stripping 49s
- Update probability maps 12s
- 99s
- Global intensity correction: 17s
- SANLM denoising after intensity normalization (medium): 21s
- Fast Optimized Shooting registration 34s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 4s
- Prepare segments (LASmod = 1.00) 14s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 24s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 30s
- 99s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 3s
- Ventricle detection 24s
- Blood vessel detection 9s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.03) 26s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 5s
- 81s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 29s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.670.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 3s
- 11s
- 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 | 0.0846 0.0000 0.0846 | 32.0000
- 2 | 2.50 | 0.0823 0.0011 0.0834 | 29.4886
- 3 | 2.50 | 0.0817 0.0016 0.0833 | 26.9772
- 4 | 2.50 | 0.0814 0.0018 0.0832 | 24.6107
- 5 | 2.50 | 0.0811 0.0019 0.0830 | 22.6548
- 6 | 2.50 | 0.0809 0.0019 0.0829 | 20.6989
- 7 | 2.50 | 0.0807 0.0020 0.0827 | 18.9688
- 8 | 2.50 | 0.0805 0.0021 0.0826 | 17.4455
- 9 | 2.50 | 0.0802 0.0021 0.0824 | 15.9223
- 10 | 2.50 | 0.0800 0.0022 0.0822 | 14.6627
- 11 | 2.50 | 0.0797 0.0023 0.0820 | 13.4764
- 12 | 2.50 | 0.0795 0.0023 0.0818 | 12.3015
- 13 | 2.50 | 0.0792 0.0024 0.0816 | 11.3776
- 14 | 2.50 | 0.0790 0.0024 0.0814 | 10.4537
- 15 | 2.25 | 0.0801 0.0025 0.0826 | 9.5920
- 16 | 2.25 | 0.0770 0.0040 0.0810 | 8.8725
- 17 | 2.25 | 0.0759 0.0045 0.0804 | 8.1530
- 18 | 2.25 | 0.0752 0.0047 0.0799 | 7.5234
- 19 | 2.25 | 0.0746 0.0048 0.0795 | 6.9630
- 29 | 2.00 | 0.0777 0.0024 0.0802 | 3.3283
- 30 | 2.00 | 0.0722 0.0050 0.0772 | 3.1221
- 31 | 2.00 | 0.0704 0.0059 0.0763 | 2.9160
- 43 | 1.75 | 0.0700 0.0033 0.0733 | 1.5785
- 44 | 1.75 | 0.0648 0.0062 0.0710 | 1.5194
- 45 | 1.75 | 0.0632 0.0071 0.0703 | 1.4626
- 57 | 1.50 | 0.0623 0.0051 0.0674 | 1.0900
- 58 | 1.50 | 0.0584 0.0076 0.0661 | 1.0730
- 59 | 1.50 | 0.0572 0.0084 0.0656 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 180s
- Prepare output 7s
- 187s
- Jacobian determinant (RMS): 0.008 0.028 0.048 0.075 0.104 | 0.111426
- Template Matching: 0.085 0.224 0.211 0.190 0.172 | 0.171744
- Write result maps: 34s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 28s
- CSF distance: 13s
- PBT2x thickness: 35s
- 80s
- Create initial surface 61s
- Topology correction: 74s
- Surface refinement: 61s
- Reduction of surface collisions with optimization: 57s
- Spherical mapping with areal smoothing 68s
- Spherical registration 204s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 25s
- CSF distance: 12s
- PBT2x thickness: 36s
- 78s
- Create initial surface 62s
- Topology correction: 87s
- Surface refinement: 71s
- Reduction of surface collisions with optimization: 60s
- Spherical mapping with areal smoothing 80s
- Spherical registration 224s
- Final surface processing results:
- Average thickness (FS): 2.6040 0.7119 mm
- Surface intensity / position RMSE: 0.0804 / 0.0994
- Euler number / defect number / defect size: 24.0 / 15.5 / 1.15%
- Display thickness: /var/lib/condor/execute/dir_2247569/ds/IPCAS_7/sub-0026068/ses-1/surf/lh.thickness.sub-0026068_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2247569/ds/IPCAS_7/sub-0026068/ses-1/surf/rh.thickness.sub-0026068_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2247569/ds/IPCAS_7/sub-0026068/ses-1/sub-0026068_ses-1_run-1_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1346s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 8s
- ROI estimation of 'neuromorphometrics' atlas 28s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 20s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 12s
- ROI estimation of 'mori' atlas 17s
- ROI estimation of 'anatomy3' atlas 27s
- ROI estimation of 'julichbrain' atlas 34s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 24s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 52s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 77s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s
- Write results 7s
- 335s
- Quality check: 9s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2247569/ds/IPCAS_7/sub-0026068/ses-1/report/catreport_sub-0026068_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 44 minute(s) and 13 second(s).
- Image Quality Rating (IQR): 83.82% (B)
- GM volume (GMV): 50.31% (777.04 / 1544.48 ml)
- GM thickness (GMT): 2.60 0.72 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2247569/ds/IPCAS_7/sub-0026068/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_2247569/ds/IPCAS_7/sub-0026068/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_2247569/ds/IPCAS_7/sub-0026068/ses-1/label
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