123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153 |
- ------------------------------------------------------------------------
- CAT12.8.1 r1980: 1/1: ./execute/dir_24738/ds/sub-23/sub-23_ses-01_T1w.n
- ------------------------------------------------------------------------
- SANLM denoising (medium): 43s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 7s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 6s
- 38s
- Correct center-of-mass 4s
- Affine registration 14s
- SPM preprocessing 1 (estimate 1 - TPM registration): 65s
- SPM preprocessing 1 (estimate 2): 65s
- SPM preprocessing 2 (write):
- Write Segmentation 17s
- Update Segmentation 19s
- Update Skull-Stripping 38s
- Update probability maps 8s
- 82s
- Global intensity correction: 15s
- SANLM denoising after intensity normalization (medium): 12s
- Fast Optimized Shooting registration 30s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.08) 15s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 26s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 34s
- 101s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 4s
- Ventricle detection 16s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.08) 32s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 4s
- 79s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 36s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.670.08,0.980.04]
- 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 | 0.0829 0.0000 0.0829 | 32.0000
- 2 | 2.50 | 0.0807 0.0011 0.0817 | 29.4886
- 3 | 2.50 | 0.0801 0.0016 0.0816 | 26.9772
- 4 | 2.50 | 0.0797 0.0018 0.0815 | 24.6107
- 5 | 2.50 | 0.0795 0.0019 0.0814 | 22.6548
- 6 | 2.50 | 0.0792 0.0020 0.0812 | 20.6989
- 7 | 2.50 | 0.0790 0.0021 0.0811 | 18.9688
- 8 | 2.50 | 0.0788 0.0021 0.0809 | 17.4455
- 9 | 2.50 | 0.0785 0.0022 0.0807 | 15.9223
- 10 | 2.50 | 0.0782 0.0023 0.0805 | 14.6627
- 11 | 2.50 | 0.0780 0.0024 0.0803 | 13.4764
- 12 | 2.50 | 0.0777 0.0024 0.0801 | 12.3015
- 13 | 2.50 | 0.0774 0.0025 0.0799 | 11.3776
- 14 | 2.50 | 0.0771 0.0025 0.0797 | 10.4537
- 15 | 2.25 | 0.0763 0.0026 0.0789 | 9.5920
- 16 | 2.25 | 0.0737 0.0039 0.0775 | 8.8725
- 29 | 2.00 | 0.0754 0.0017 0.0771 | 3.3283
- 30 | 2.00 | 0.0696 0.0041 0.0737 | 3.1221
- 31 | 2.00 | 0.0676 0.0051 0.0727 | 2.9160
- 43 | 1.75 | 0.0667 0.0029 0.0696 | 1.5785
- 44 | 1.75 | 0.0624 0.0052 0.0676 | 1.5194
- 45 | 1.75 | 0.0609 0.0061 0.0670 | 1.4626
- 57 | 1.50 | 0.0594 0.0044 0.0638 | 1.0900
- 58 | 1.50 | 0.0561 0.0065 0.0627 | 1.0730
- 59 | 1.50 | 0.0551 0.0072 0.0623 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 165s
- Prepare output 11s
- 176s
- Jacobian determinant (RMS): 0.010 0.037 0.055 0.080 0.103 | 0.110129
- Template Matching: 0.083 0.221 0.203 0.183 0.165 | 0.165178
- Write result maps: 24s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 41s
- CSF distance: 18s
- PBT2x thickness: 48s
- 113s
- Create initial surface 86s
- Topology correction: 112s
- Surface refinement: 115s
- Reduction of surface collisions with optimization: 93s
- Spherical mapping with areal smoothing 119s
- Spherical registration 306s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 44s
- CSF distance: 19s
- PBT2x thickness: 50s
- 119s
- Create initial surface 86s
- Topology correction: 108s
- Surface refinement: 81s
- Reduction of surface collisions with optimization: 89s
- Spherical mapping with areal smoothing 101s
- Spherical registration 311s
- Final surface processing results:
- Average thickness (FS): 2.4785 0.5645 mm
- Surface intensity / position RMSE: 0.0657 / 0.0675
- Euler number / defect number / defect size: 20.0 / 14.5 / 0.77%
- Display thickness: /var/lib/condor/execute/dir_24738/ds/sub-23/surf/lh.thickness.sub-23_ses-01_T1w
- Display thickness: /var/lib/condor/execute/dir_24738/ds/sub-23/surf/rh.thickness.sub-23_ses-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_24738/ds/sub-23/sub-23_ses-01_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1942s
- 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 19s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 11s
- ROI estimation of 'mori' atlas 16s
- ROI estimation of 'anatomy3' atlas 23s
- ROI estimation of 'julichbrain' atlas 30s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 47s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 71s
- Write results 71s
- 302s
- Quality check: 5s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_24738/ds/sub-23/report/catreport_sub-23_ses-01_T1w.pdf
- ------------------------------------------------------------------------
- CAT preprocessing takes 52 minute(s) and 13 second(s).
- Image Quality Rating (IQR): 83.46% (B)
- GM volume (GMV): 45.08% (776.31 / 1722.19 ml)
- GM thickness (GMT): 2.48 0.56 mm
- Segmentations are saved in /var/lib/condor/execute/dir_24738/ds/sub-23/mri
- Reports are saved in /var/lib/condor/execute/dir_24738/ds/sub-23/report
- Labels are saved in /var/lib/condor/execute/dir_24738/ds/sub-23/label
- ------------------------------------------------------------------------
|