123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153 |
- ------------------------------------------------------------------------
- CAT12.8.1 r1980: 1/1: ./execute/dir_375108/ds/sub-43/sub-43_T1w.n
- ------------------------------------------------------------------------
- SANLM denoising (medium): 83s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 8s
- Initial correction 10s
- Refine background 4s
- Final correction 8s
- Final scaling 8s
- 54s
- Correct center-of-mass 6s
- Affine registration 19s
- SPM preprocessing 1 (estimate 1 - TPM registration): 100s
- SPM preprocessing 1 (estimate 2): 95s
- SPM preprocessing 2 (write):
- Write Segmentation 22s
- Update Segmentation 26s
- Update Skull-Stripping 58s
- Update probability maps 11s
- 117s
- Global intensity correction: 20s
- SANLM denoising after intensity normalization (medium): 25s
- Fast Optimized Shooting registration 43s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 6s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.09) 22s
- Estimate local tissue thresholds (WM) 28s
- Estimate local tissue thresholds (GM) 42s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 25s
- 130s
- ROI segmentation (partitioning):
- Atlas -> subject space 11s
- Major structures 5s
- Ventricle detection 32s
- Blood vessel detection 16s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.02) 41s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 5s
- Final corrections 6s
- 121s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 46s
- AMAP peaks: [CSF,GM,WM] = [0.360.07,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 7s
- Level 1 cleanup (brain masking) 5s
- Level 2 cleanup (CSF correction) 3s
- Level 3 cleanup (CSF/WM PVE) 4s
- 18s
- 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 | 0.0845 0.0000 0.0845 | 32.0000
- 2 | 2.50 | 0.0816 0.0013 0.0829 | 29.4886
- 3 | 2.50 | 0.0808 0.0019 0.0827 | 26.9772
- 4 | 2.50 | 0.0804 0.0022 0.0826 | 24.6107
- 5 | 2.50 | 0.0801 0.0023 0.0824 | 22.6548
- 6 | 2.50 | 0.0798 0.0024 0.0822 | 20.6989
- 7 | 2.50 | 0.0795 0.0025 0.0820 | 18.9688
- 8 | 2.50 | 0.0792 0.0026 0.0818 | 17.4455
- 9 | 2.50 | 0.0788 0.0027 0.0815 | 15.9223
- 10 | 2.50 | 0.0785 0.0028 0.0813 | 14.6627
- 11 | 2.50 | 0.0782 0.0029 0.0811 | 13.4764
- 12 | 2.50 | 0.0778 0.0029 0.0808 | 12.3015
- 13 | 2.50 | 0.0775 0.0031 0.0805 | 11.3776
- 14 | 2.50 | 0.0772 0.0031 0.0803 | 10.4537
- 15 | 2.25 | 0.0761 0.0032 0.0792 | 9.5920
- 16 | 2.25 | 0.0729 0.0047 0.0776 | 8.8725
- 29 | 2.00 | 0.0739 0.0021 0.0760 | 3.3283
- 30 | 2.00 | 0.0679 0.0045 0.0724 | 3.1221
- 31 | 2.00 | 0.0659 0.0054 0.0713 | 2.9160
- 43 | 1.75 | 0.0649 0.0031 0.0680 | 1.5785
- 44 | 1.75 | 0.0607 0.0054 0.0661 | 1.5194
- 45 | 1.75 | 0.0593 0.0061 0.0655 | 1.4626
- 57 | 1.50 | 0.0578 0.0044 0.0622 | 1.0900
- 58 | 1.50 | 0.0547 0.0065 0.0612 | 1.0730
- 59 | 1.50 | 0.0537 0.0071 0.0608 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 223s
- Prepare output 15s
- 237s
- Jacobian determinant (RMS): 0.012 0.041 0.060 0.083 0.105 | 0.111058
- Template Matching: 0.085 0.219 0.198 0.178 0.161 | 0.160960
- Write result maps: 76s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 43s
- CSF distance: 21s
- PBT2x thickness: 61s
- 133s
- Create initial surface 99s
- Topology correction: 118s
- Surface refinement: 109s
- Reduction of surface collisions with optimization: 103s
- Spherical mapping with areal smoothing 112s
- Spherical registration 371s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 41s
- CSF distance: 21s
- PBT2x thickness: 63s
- 133s
- Create initial surface 106s
- Topology correction: 124s
- Surface refinement: 115s
- Reduction of surface collisions with optimization: 92s
- Spherical mapping with areal smoothing 112s
- Spherical registration 342s
- Final surface processing results:
- Average thickness (FS): 2.6077 0.5994 mm
- Surface intensity / position RMSE: 0.0623 / 0.0599
- Euler number / defect number / defect size: 10.0 / 8.5 / 0.51%
- Display thickness: /var/lib/condor/execute/dir_375108/ds/sub-43/surf/lh.thickness.sub-43_T1w
- Display thickness: /var/lib/condor/execute/dir_375108/ds/sub-43/surf/rh.thickness.sub-43_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_375108/ds/sub-43/sub-43_T1w.nii
- Surface ROI estimation: 51s
- Surface and thickness estimation takes: 2256s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 11s
- ROI estimation of 'neuromorphometrics' atlas 40s
- ROI estimation of 'lpba40' atlas 13s
- ROI estimation of 'hammers' atlas 31s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 10s
- ROI estimation of 'aal3' atlas 18s
- ROI estimation of 'mori' atlas 27s
- ROI estimation of 'anatomy3' atlas 37s
- ROI estimation of 'julichbrain' atlas 47s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 20s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 37s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 81s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 112s
- Write results 113s
- 489s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_375108/ds/sub-43/report/catreport_sub-43_T1w.pdf
- ------------------------------------------------------------------------
- CAT preprocessing takes 67 minute(s) and 40 second(s).
- Image Quality Rating (IQR): 86.05% (B)
- GM volume (GMV): 49.13% (753.25 / 1533.08 ml)
- GM thickness (GMT): 2.61 0.60 mm
- Segmentations are saved in /var/lib/condor/execute/dir_375108/ds/sub-43/mri
- Reports are saved in /var/lib/condor/execute/dir_375108/ds/sub-43/report
- Labels are saved in /var/lib/condor/execute/dir_375108/ds/sub-43/label
- ------------------------------------------------------------------------
|