| 123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161 |
- ------------------------------------------------------------------------
- CAT12.8.1 r1980: 1/1: ./condor/execute/dir_20259/ds/sub-01/sub-01_T1w.n
- ------------------------------------------------------------------------
- SANLM denoising (medium): 75s
- APP: Rough bias correction:
- Initialize 9s
- Estimate background 9s
- Initial correction 8s
- Refine background 5s
- Final correction 6s
- Final scaling 7s
- 52s
- Correct center-of-mass 3s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 78s
- SPM preprocessing 1 (estimate 2): 62s
- SPM preprocessing 2 (write):
- Write Segmentation 21s
- Update Segmentation 22s
- Update Skull-Stripping 57s
- Update probability maps 12s
- 112s
- Global intensity correction: 22s
- SANLM denoising after intensity normalization (medium): 26s
- Fast Optimized Shooting registration 37s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 5s
- Prepare segments (LASmod = 1.07) 17s
- Estimate local tissue thresholds (WM) 23s
- Estimate local tissue thresholds (GM) 31s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 31s
- 118s
- ROI segmentation (partitioning):
- Atlas -> subject space 10s
- Major structures 4s
- Ventricle detection 19s
- Blood vessel detection 12s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.09) 29s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 6s
- 85s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.07): 40s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.09,0.990.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 5s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 3s
- 14s
- 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 | 0.0900 0.0000 0.0900 | 32.0000
- 2 | 2.50 | 0.0869 0.0013 0.0882 | 29.4886
- 3 | 2.50 | 0.0861 0.0019 0.0880 | 26.9772
- 4 | 2.50 | 0.0856 0.0022 0.0878 | 24.6107
- 5 | 2.50 | 0.0853 0.0023 0.0876 | 22.6548
- 6 | 2.50 | 0.0850 0.0024 0.0874 | 20.6989
- 7 | 2.50 | 0.0847 0.0025 0.0872 | 18.9688
- 8 | 2.50 | 0.0844 0.0026 0.0870 | 17.4455
- 9 | 2.50 | 0.0841 0.0026 0.0867 | 15.9223
- 10 | 2.50 | 0.0838 0.0027 0.0865 | 14.6627
- 11 | 2.50 | 0.0835 0.0028 0.0862 | 13.4764
- 12 | 2.50 | 0.0831 0.0028 0.0859 | 12.3015
- 13 | 2.50 | 0.0828 0.0029 0.0857 | 11.3776
- 14 | 2.50 | 0.0825 0.0029 0.0854 | 10.4537
- 15 | 2.25 | 0.0828 0.0030 0.0858 | 9.5920
- 16 | 2.25 | 0.0797 0.0045 0.0842 | 8.8725
- 17 | 2.25 | 0.0786 0.0050 0.0836 | 8.1530
- 18 | 2.25 | 0.0779 0.0052 0.0831 | 7.5234
- 19 | 2.25 | 0.0774 0.0053 0.0826 | 6.9630
- 20 | 2.25 | 0.0769 0.0053 0.0821 | 6.4027
- 21 | 2.25 | 0.0764 0.0053 0.0817 | 5.9447
- 22 | 2.25 | 0.0760 0.0053 0.0813 | 5.5083
- 23 | 2.25 | 0.0756 0.0052 0.0808 | 5.0803
- 24 | 2.25 | 0.0752 0.0053 0.0804 | 4.7404
- 25 | 2.25 | 0.0748 0.0052 0.0800 | 4.4005
- 29 | 2.00 | 0.0769 0.0041 0.0810 | 3.3283
- 30 | 2.00 | 0.0737 0.0056 0.0793 | 3.1221
- 43 | 1.75 | 0.0730 0.0031 0.0760 | 1.5785
- 44 | 1.75 | 0.0678 0.0058 0.0736 | 1.5194
- 45 | 1.75 | 0.0662 0.0067 0.0729 | 1.4626
- 57 | 1.50 | 0.0650 0.0049 0.0698 | 1.0900
- 58 | 1.50 | 0.0613 0.0073 0.0686 | 1.0730
- 59 | 1.50 | 0.0601 0.0080 0.0682 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 180s
- Prepare output 12s
- 192s
- Jacobian determinant (RMS): 0.010 0.035 0.058 0.079 0.106 | 0.113193
- Template Matching: 0.090 0.224 0.221 0.198 0.180 | 0.180437
- Write result maps: 33s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 51s
- CSF distance: 19s
- PBT2x thickness: 54s
- 131s
- Create initial surface 102s
- Topology correction: 115s
- Surface refinement: 106s
- Reduction of surface collisions with optimization: 88s
- Spherical mapping with areal smoothing 93s
- Spherical registration 290s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 32s
- CSF distance: 19s
- PBT2x thickness: 53s
- 111s
- Create initial surface 104s
- Topology correction: 121s
- Surface refinement: 109s
- Reduction of surface collisions with optimization: 91s
- Spherical mapping with areal smoothing 123s
- Spherical registration 329s
- Final surface processing results:
- Average thickness (FS): 2.3639 0.6132 mm
- Surface intensity / position RMSE: 0.0728 / 0.0873
- Euler number / defect number / defect size: 28.0 / 16.0 / 1.42%
- Display thickness: /var/lib/condor/execute/dir_20259/ds/sub-01/surf/lh.thickness.sub-01_T1w
- Display thickness: /var/lib/condor/execute/dir_20259/ds/sub-01/surf/rh.thickness.sub-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_20259/ds/sub-01/sub-01_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 2029s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 12s
- ROI estimation of 'neuromorphometrics' atlas 43s
- ROI estimation of 'lpba40' atlas 12s
- ROI estimation of 'hammers' atlas 30s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 11s
- ROI estimation of 'aal3' atlas 19s
- ROI estimation of 'mori' atlas 26s
- ROI estimation of 'anatomy3' atlas 38s
- ROI estimation of 'julichbrain' atlas 49s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 20s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 35s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 79s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 115s
- Write results 116s
- 493s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_20259/ds/sub-01/report/catreport_sub-01_T1w.pdf
- ------------------------------------------------------------------------
- CAT preprocessing takes 59 minute(s) and 53 second(s).
- Image Quality Rating (IQR): 86.39% (B)
- GM volume (GMV): 44.64% (788.37 / 1766.15 ml)
- GM thickness (GMT): 2.36 0.62 mm
- Segmentations are saved in /var/lib/condor/execute/dir_20259/ds/sub-01/mri
- Reports are saved in /var/lib/condor/execute/dir_20259/ds/sub-01/report
- Labels are saved in /var/lib/condor/execute/dir_20259/ds/sub-01/label
- ------------------------------------------------------------------------
|
