| 123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155 |
- ------------------------------------------------------------------------
- CAT12.8.1 r2040: 1/1: ./sub-0026004/ses-1/sub-0026004_ses-1_run-1_T1w.n
- ------------------------------------------------------------------------
- SANLM denoising (medium): 51s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 6s
- Initial correction 5s
- Refine background 3s
- Final correction 5s
- Final scaling 4s
- 34s
- Correct center-of-mass 4s
- Affine registration 9s
- SPM preprocessing 1 (estimate 1 - TPM registration): 75s
- SPM preprocessing 1 (estimate 2): 67s
- SPM preprocessing 2 (write):
- Write Segmentation 17s
- Update Segmentation 20s
- Update Skull-Stripping 40s
- Update probability maps 8s
- 85s
- Global intensity correction: 17s
- SANLM denoising after intensity normalization (medium): 27s
- Fast Optimized Shooting registration 31s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 14s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 27s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 48s
- 117s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 15s
- Blood vessel detection 10s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.05) 27s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 4s
- 73s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 37s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 1s
- 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 | 0.0871 0.0000 0.0871 | 32.0000
- 2 | 2.50 | 0.0836 0.0014 0.0850 | 29.4886
- 3 | 2.50 | 0.0826 0.0021 0.0848 | 26.9772
- 4 | 2.50 | 0.0821 0.0024 0.0845 | 24.6107
- 5 | 2.50 | 0.0817 0.0026 0.0843 | 22.6548
- 6 | 2.50 | 0.0814 0.0027 0.0841 | 20.6989
- 7 | 2.50 | 0.0810 0.0028 0.0838 | 18.9688
- 8 | 2.50 | 0.0806 0.0030 0.0836 | 17.4455
- 9 | 2.50 | 0.0802 0.0030 0.0833 | 15.9223
- 10 | 2.50 | 0.0798 0.0032 0.0830 | 14.6627
- 11 | 2.50 | 0.0794 0.0033 0.0827 | 13.4764
- 12 | 2.50 | 0.0790 0.0033 0.0824 | 12.3015
- 13 | 2.50 | 0.0786 0.0035 0.0821 | 11.3776
- 14 | 2.50 | 0.0782 0.0035 0.0818 | 10.4537
- 15 | 2.25 | 0.0792 0.0036 0.0829 | 9.5920
- 16 | 2.25 | 0.0758 0.0054 0.0812 | 8.8725
- 17 | 2.25 | 0.0744 0.0060 0.0804 | 8.1530
- 29 | 2.00 | 0.0769 0.0027 0.0796 | 3.3283
- 30 | 2.00 | 0.0705 0.0054 0.0760 | 3.1221
- 31 | 2.00 | 0.0683 0.0065 0.0748 | 2.9160
- 43 | 1.75 | 0.0674 0.0037 0.0711 | 1.5785
- 44 | 1.75 | 0.0626 0.0063 0.0689 | 1.5194
- 45 | 1.75 | 0.0609 0.0072 0.0681 | 1.4626
- 57 | 1.50 | 0.0596 0.0053 0.0649 | 1.0900
- 58 | 1.50 | 0.0560 0.0076 0.0637 | 1.0730
- 59 | 1.50 | 0.0548 0.0083 0.0631 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 170s
- Prepare output 11s
- 181s
- Jacobian determinant (RMS): 0.011 0.041 0.062 0.088 0.136 | 0.123913
- Template Matching: 0.087 0.223 0.205 0.183 0.164 | 0.164357
- Write result maps: 33s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 43s
- CSF distance: 17s
- PBT2x thickness: 48s
- 114s
- Create initial surface 91s
- Topology correction: 104s
- Surface refinement: 96s
- Reduction of surface collisions with optimization: 80s
- Spherical mapping with areal smoothing 88s
- Spherical registration 304s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 48s
- CSF distance: 16s
- PBT2x thickness: 46s
- 116s
- Create initial surface 88s
- Topology correction: 105s
- Surface refinement: 127s
- Reduction of surface collisions with optimization: 84s
- Spherical mapping with areal smoothing 94s
- Spherical registration 321s
- Final surface processing results:
- Average thickness (FS): 2.4616 0.6221 mm
- Surface intensity / position RMSE: 0.0654 / 0.0686
- Euler number / defect number / defect size: 32.0 / 16.5 / 0.99%
- Display thickness: /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-1/surf/lh.thickness.sub-0026004_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-1/surf/rh.thickness.sub-0026004_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-1/sub-0026004_ses-1_run-1_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1914s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 8s
- ROI estimation of 'neuromorphometrics' atlas 31s
- ROI estimation of 'lpba40' atlas 9s
- ROI estimation of 'hammers' atlas 22s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 8s
- ROI estimation of 'aal3' atlas 13s
- ROI estimation of 'mori' atlas 19s
- ROI estimation of 'anatomy3' atlas 27s
- ROI estimation of 'julichbrain' atlas 36s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 28s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 62s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 95s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 9s
- Write results 10s
- 385s
- Quality check: 13s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-1/report/catreport_sub-0026004_ses-1_run-1_T1w.pdf
- ------------------------------------------------------------------------
- CAT preprocessing takes 54 minute(s) and 53 second(s).
- Image Quality Rating (IQR): 82.45% (B-)
- GM volume (GMV): 45.06% (758.56 / 1683.60 ml)
- GM thickness (GMT): 2.46 0.62 mm
- Segmentations are saved in /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_359021/ds/XHCUMS/sub-0026004/ses-1/label
- ------------------------------------------------------------------------
|
