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- CAT12.8.1 r2040: 1/1: ./sub-0025399/ses-1/sub-0025399_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 30s
- APP: Rough bias correction:
- Initialize 4s
- Estimate background 4s
- 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): 47s
- SPM preprocessing 1 (estimate 2): 41s
- SPM preprocessing 2 (write):
- Write Segmentation 12s
- Update Segmentation 14s
- Update Skull-Stripping 29s
- Update probability maps 7s
- 62s
- Global intensity correction: 11s
- SANLM denoising after intensity normalization (medium): 19s
- Fast Optimized Shooting registration 25s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.19) 10s
- Estimate local tissue thresholds (WM) 12s
- Estimate local tissue thresholds (GM) 18s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 32s
- 79s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 2s
- Ventricle detection 10s
- Blood vessel detection 7s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.06) 17s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 3s
- 49s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 25s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- 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
- 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 | 0.0833 0.0000 0.0833 | 32.0000
- 2 | 2.50 | 0.0809 0.0011 0.0820 | 29.4886
- 3 | 2.50 | 0.0802 0.0017 0.0819 | 26.9772
- 4 | 2.50 | 0.0799 0.0019 0.0818 | 24.6107
- 5 | 2.50 | 0.0796 0.0020 0.0816 | 22.6548
- 6 | 2.50 | 0.0793 0.0021 0.0815 | 20.6989
- 7 | 2.50 | 0.0791 0.0022 0.0813 | 18.9688
- 8 | 2.50 | 0.0788 0.0023 0.0811 | 17.4455
- 9 | 2.50 | 0.0785 0.0024 0.0809 | 15.9223
- 10 | 2.50 | 0.0782 0.0025 0.0807 | 14.6627
- 11 | 2.50 | 0.0779 0.0026 0.0805 | 13.4764
- 12 | 2.50 | 0.0776 0.0027 0.0803 | 12.3015
- 13 | 2.50 | 0.0773 0.0028 0.0801 | 11.3776
- 14 | 2.50 | 0.0770 0.0029 0.0799 | 10.4537
- 15 | 2.25 | 0.0767 0.0029 0.0796 | 9.5920
- 16 | 2.25 | 0.0737 0.0044 0.0781 | 8.8725
- 29 | 2.00 | 0.0751 0.0020 0.0771 | 3.3283
- 30 | 2.00 | 0.0687 0.0045 0.0733 | 3.1221
- 31 | 2.00 | 0.0666 0.0056 0.0721 | 2.9160
- 43 | 1.75 | 0.0655 0.0032 0.0687 | 1.5785
- 44 | 1.75 | 0.0611 0.0055 0.0666 | 1.5194
- 45 | 1.75 | 0.0596 0.0063 0.0659 | 1.4626
- 57 | 1.50 | 0.0581 0.0046 0.0627 | 1.0900
- 58 | 1.50 | 0.0549 0.0067 0.0616 | 1.0730
- 59 | 1.50 | 0.0538 0.0073 0.0612 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 138s
- Prepare output 7s
- 146s
- Jacobian determinant (RMS): 0.012 0.043 0.064 0.091 0.116 | 0.124101
- Template Matching: 0.083 0.221 0.200 0.179 0.161 | 0.161454
- Write result maps: 27s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 22s
- CSF distance: 11s
- PBT2x thickness: 32s
- 69s
- Create initial surface 57s
- Topology correction: 57s
- Surface refinement: 72s
- Reduction of surface collisions with optimization: 45s
- Spherical mapping with areal smoothing 60s
- Spherical registration 221s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 19s
- CSF distance: 10s
- PBT2x thickness: 30s
- 63s
- Create initial surface 55s
- Topology correction: 65s
- Surface refinement: 66s
- Reduction of surface collisions with optimization: 45s
- Spherical mapping with areal smoothing 59s
- Spherical registration 223s
- Final surface processing results:
- Average thickness (FS): 2.5857 0.6257 mm
- Surface intensity / position RMSE: 0.0669 / 0.0687
- Euler number / defect number / defect size: 12.0 / 12.0 / 0.27%
- Display thickness: /var/lib/condor/execute/dir_3232778/ds/LMU_2/sub-0025399/ses-1/surf/lh.thickness.sub-0025399_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3232778/ds/LMU_2/sub-0025399/ses-1/surf/rh.thickness.sub-0025399_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3232778/ds/LMU_2/sub-0025399/ses-1/sub-0025399_ses-1_run-1_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1227s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 6s
- ROI estimation of 'neuromorphometrics' atlas 22s
- 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 12s
- ROI estimation of 'anatomy3' atlas 18s
- ROI estimation of 'julichbrain' atlas 25s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 10s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 17s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 40s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 75s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s
- Write results 8s
- 268s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3232778/ds/LMU_2/sub-0025399/ses-1/report/catreport_sub-0025399_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 36 minute(s) and 23 second(s).
- Image Quality Rating (IQR): 80.23% (B-)
- GM volume (GMV): 48.75% (669.08 / 1372.46 ml)
- GM thickness (GMT): 2.59 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3232778/ds/LMU_2/sub-0025399/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_3232778/ds/LMU_2/sub-0025399/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_3232778/ds/LMU_2/sub-0025399/ses-1/label
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