| 123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176 |
- ------------------------------------------------------------------------
- CAT12.8.1 r1980: 1/1: ./dir_730/ds/sub-349/sub-349_ses-20121111_T1w.n
- ------------------------------------------------------------------------
- SANLM denoising (medium): 17s
- Internal resampling (3.30x0.78x0.78mm > 1.00x0.78x0.78mm): 1s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 10s
- Initial correction 14s
- Refine background 4s
- Final correction 11s
- Final scaling 10s
- 62s
- Correct center-of-mass 2s
- Affine registration 16s
- SPM preprocessing 1 (estimate 1 - TPM registration): 94s
- SPM preprocessing 1 (estimate 2): 59s
- SPM preprocessing 2 (write):
- Write Segmentation 19s
- Update Segmentation 27s
- Update Skull-Stripping 54s
- Update probability maps 18s
- 116s
- Global intensity correction: 19s
- SANLM denoising after intensity normalization (medium): 22s
- Fast Optimized Shooting registration 36s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 6s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.61) 22s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 21s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 40s
- 112s
- ROI segmentation (partitioning):
- Atlas -> subject space 10s
- Major structures 5s
- Ventricle detection 17s
- Blood vessel detection 16s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.43) 45s
- Manual stroke lesion detection 0s
- Closing of deep structures 3s
- Side alignment 6s
- Final corrections 5s
- 107s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 50s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.970.06]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 6s
- Level 1 cleanup (brain masking) 4s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 4s
- 16s
- 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 | 0.1013 0.0000 0.1013 | 32.0000
- 2 | 2.50 | 0.0980 0.0014 0.0994 | 29.4886
- 3 | 2.50 | 0.0970 0.0022 0.0991 | 26.9772
- 4 | 2.50 | 0.0964 0.0024 0.0989 | 24.6107
- 5 | 2.50 | 0.0960 0.0026 0.0987 | 22.6548
- 6 | 2.50 | 0.0957 0.0028 0.0984 | 20.6989
- 7 | 2.50 | 0.0953 0.0029 0.0982 | 18.9688
- 8 | 2.50 | 0.0949 0.0030 0.0979 | 17.4455
- 9 | 2.50 | 0.0945 0.0031 0.0976 | 15.9223
- 10 | 2.50 | 0.0941 0.0033 0.0974 | 14.6627
- 11 | 2.50 | 0.0937 0.0034 0.0971 | 13.4764
- 12 | 2.50 | 0.0933 0.0035 0.0967 | 12.3015
- 13 | 2.50 | 0.0928 0.0036 0.0964 | 11.3776
- 14 | 2.50 | 0.0924 0.0037 0.0961 | 10.4537
- 15 | 2.25 | 0.0959 0.0038 0.0997 | 9.5920
- 16 | 2.25 | 0.0921 0.0057 0.0979 | 8.8725
- 17 | 2.25 | 0.0906 0.0064 0.0971 | 8.1530
- 18 | 2.25 | 0.0897 0.0067 0.0964 | 7.5234
- 19 | 2.25 | 0.0889 0.0069 0.0958 | 6.9630
- 20 | 2.25 | 0.0882 0.0069 0.0951 | 6.4027
- 21 | 2.25 | 0.0875 0.0070 0.0946 | 5.9447
- 22 | 2.25 | 0.0869 0.0071 0.0940 | 5.5083
- 23 | 2.25 | 0.0863 0.0071 0.0934 | 5.0803
- 24 | 2.25 | 0.0857 0.0071 0.0928 | 4.7404
- 25 | 2.25 | 0.0852 0.0071 0.0923 | 4.4005
- 26 | 2.25 | 0.0846 0.0071 0.0917 | 4.0868
- 27 | 2.25 | 0.0841 0.0072 0.0912 | 3.8221
- 28 | 2.25 | 0.0836 0.0071 0.0907 | 3.5574
- 29 | 2.00 | 0.0867 0.0068 0.0935 | 3.3283
- 30 | 2.00 | 0.0837 0.0081 0.0918 | 3.1221
- 31 | 2.00 | 0.0826 0.0085 0.0911 | 2.9160
- 32 | 2.00 | 0.0817 0.0087 0.0905 | 2.7495
- 33 | 2.00 | 0.0811 0.0088 0.0899 | 2.5890
- 34 | 2.00 | 0.0805 0.0088 0.0893 | 2.4330
- 35 | 2.00 | 0.0800 0.0089 0.0888 | 2.3080
- 36 | 2.00 | 0.0795 0.0088 0.0883 | 2.1830
- 37 | 2.00 | 0.0790 0.0088 0.0878 | 2.0688
- 38 | 2.00 | 0.0785 0.0089 0.0874 | 1.9714
- 39 | 2.00 | 0.0781 0.0088 0.0869 | 1.8740
- 40 | 2.00 | 0.0776 0.0089 0.0865 | 1.7907
- 41 | 2.00 | 0.0772 0.0089 0.0861 | 1.7148
- 42 | 2.00 | 0.0769 0.0088 0.0857 | 1.6390
- 43 | 1.75 | 0.0768 0.0080 0.0848 | 1.5785
- 44 | 1.75 | 0.0746 0.0093 0.0839 | 1.5194
- 57 | 1.50 | 0.0742 0.0066 0.0807 | 1.0900
- 58 | 1.50 | 0.0696 0.0097 0.0793 | 1.0730
- 59 | 1.50 | 0.0682 0.0106 0.0788 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 235s
- Prepare output 12s
- 247s
- Jacobian determinant (RMS): 0.012 0.047 0.089 0.128 0.157 | 0.166354
- Template Matching: 0.101 0.096 0.087 0.224 0.205 | 0.204586
- Write result maps: 45s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 53s
- CSF distance: 15s
- PBT2x thickness: 41s
- 115s
- Create initial surface 89s
- Topology correction: 105s
- Surface refinement: 93s
- Reduction of surface collisions with optimization: 69s
- Spherical mapping with areal smoothing 96s
- Spherical registration 303s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 55s
- CSF distance: 16s
- PBT2x thickness: 42s
- 118s
- Create initial surface 84s
- Topology correction: 97s
- Surface refinement: 103s
- Reduction of surface collisions with optimization: 65s
- Spherical mapping with areal smoothing 88s
- Spherical registration 298s
- Final surface processing results:
- Average thickness (FS): 1.8150 0.5397 mm
- Surface intensity / position RMSE: 0.0763 / 0.0976
- Euler number / defect number / defect size: 122.0 / 77.0 / 2.43%
- Display thickness: /var/lib/condor/execute/dir_730/ds/sub-349/surf/lh.thickness.sub-349_ses-20121111_T1w
- Display thickness: /var/lib/condor/execute/dir_730/ds/sub-349/surf/rh.thickness.sub-349_ses-20121111_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_730/ds/sub-349/sub-349_ses-20121111_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1819s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 10s
- ROI estimation of 'neuromorphometrics' atlas 34s
- ROI estimation of 'lpba40' atlas 10s
- ROI estimation of 'hammers' atlas 23s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 8s
- ROI estimation of 'aal3' atlas 14s
- ROI estimation of 'mori' atlas 20s
- ROI estimation of 'anatomy3' atlas 29s
- ROI estimation of 'julichbrain' atlas 38s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 27s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 61s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 89s
- Write results 90s
- 380s
- Quality check: 4s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_730/ds/sub-349/report/catreport_sub-349_ses-20121111_T1w.pdf
- ------------------------------------------------------------------------
- CAT preprocessing takes 55 minute(s) and 25 second(s).
- Image Quality Rating (IQR): 58.13% (E+)
- GM volume (GMV): 33.71% (536.34 / 1591.00 ml)
- GM thickness (GMT): 1.81 0.54 mm
- Segmentations are saved in /var/lib/condor/execute/dir_730/ds/sub-349/mri
- Reports are saved in /var/lib/condor/execute/dir_730/ds/sub-349/report
- Labels are saved in /var/lib/condor/execute/dir_730/ds/sub-349/label
- ------------------------------------------------------------------------
|
