| 123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154 |
- ------------------------------------------------------------------------
- CAT12.8.1 r1980: 1/1: ./dir_12013/ds/sub-0702/sub-0702_ses-01_T1w.n
- ------------------------------------------------------------------------
- SANLM denoising (medium): 202s
- APP: Rough bias correction:
- Initialize 9s
- Estimate background 9s
- Initial correction 16s
- Refine background 4s
- Final correction 9s
- Final scaling 7s
- 64s
- Correct center-of-mass 6s
- Affine registration 19s
- SPM preprocessing 1 (estimate 1 - TPM registration): 10s
- Use initial fine affine registration. 73s
- SPM preprocessing 1 (estimate 2): 65s
- SPM preprocessing 2 (write):
- Write Segmentation 22s
- Update Segmentation 22s
- Update Skull-Stripping 53s
- Update probability maps 12s
- 108s
- Global intensity correction: 22s
- SANLM denoising after intensity normalization (medium): 14s
- Fast Optimized Shooting registration 36s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 4s
- Prepare segments (LASmod = 1.00) 16s
- Estimate local tissue thresholds (WM) 22s
- Estimate local tissue thresholds (GM) 31s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 43s
- 125s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 4s
- Ventricle detection 14s
- Blood vessel detection 10s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 29s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 6s
- 76s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 33s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.990.04]
- 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
- 12s
- 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 | 0.0805 0.0000 0.0805 | 32.0000
- 2 | 2.50 | 0.0789 0.0009 0.0798 | 29.4886
- 3 | 2.50 | 0.0785 0.0013 0.0798 | 26.9772
- 4 | 2.50 | 0.0783 0.0014 0.0797 | 24.6107
- 5 | 2.50 | 0.0781 0.0015 0.0796 | 22.6548
- 6 | 2.50 | 0.0779 0.0016 0.0795 | 20.6989
- 7 | 2.50 | 0.0777 0.0016 0.0794 | 18.9688
- 8 | 2.50 | 0.0775 0.0017 0.0792 | 17.4455
- 9 | 2.50 | 0.0773 0.0018 0.0791 | 15.9223
- 10 | 2.50 | 0.0771 0.0018 0.0790 | 14.6627
- 11 | 2.50 | 0.0769 0.0019 0.0788 | 13.4764
- 12 | 2.50 | 0.0767 0.0019 0.0786 | 12.3015
- 13 | 2.50 | 0.0765 0.0020 0.0785 | 11.3776
- 14 | 2.50 | 0.0763 0.0021 0.0783 | 10.4537
- 15 | 2.25 | 0.0759 0.0021 0.0780 | 9.5920
- 16 | 2.25 | 0.0733 0.0033 0.0766 | 8.8725
- 29 | 2.00 | 0.0750 0.0015 0.0765 | 3.3283
- 30 | 2.00 | 0.0689 0.0040 0.0728 | 3.1221
- 31 | 2.00 | 0.0669 0.0050 0.0719 | 2.9160
- 43 | 1.75 | 0.0661 0.0028 0.0690 | 1.5785
- 44 | 1.75 | 0.0616 0.0052 0.0669 | 1.5194
- 45 | 1.75 | 0.0602 0.0061 0.0662 | 1.4626
- 57 | 1.50 | 0.0588 0.0044 0.0632 | 1.0900
- 58 | 1.50 | 0.0556 0.0065 0.0621 | 1.0730
- 59 | 1.50 | 0.0545 0.0072 0.0617 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 153s
- Prepare output 12s
- 165s
- Jacobian determinant (RMS): 0.008 0.030 0.049 0.077 0.104 | 0.112869
- Template Matching: 0.080 0.220 0.201 0.180 0.163 | 0.163496
- Write result maps: 32s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 32s
- CSF distance: 13s
- PBT2x thickness: 39s
- 89s
- Create initial surface 78s
- Topology correction: 71s
- Surface refinement: 65s
- Reduction of surface collisions with optimization: 53s
- Spherical mapping with areal smoothing 72s
- Spherical registration 297s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 28s
- CSF distance: 13s
- PBT2x thickness: 37s
- 83s
- Create initial surface 72s
- Topology correction: 70s
- Surface refinement: 77s
- Reduction of surface collisions with optimization: 53s
- Spherical mapping with areal smoothing 65s
- Spherical registration 300s
- Final surface processing results:
- Average thickness (FS): 2.5392 0.6409 mm
- Surface intensity / position RMSE: 0.0757 / 0.0833
- Euler number / defect number / defect size: 34.0 / 24.5 / 1.08%
- Display thickness: /var/lib/condor/execute/dir_12013/ds/sub-0702/surf/lh.thickness.sub-0702_ses-01_T1w
- Display thickness: /var/lib/condor/execute/dir_12013/ds/sub-0702/surf/rh.thickness.sub-0702_ses-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_12013/ds/sub-0702/sub-0702_ses-01_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1542s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 11s
- ROI estimation of 'neuromorphometrics' atlas 41s
- ROI estimation of 'lpba40' atlas 12s
- ROI estimation of 'hammers' atlas 29s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 10s
- ROI estimation of 'aal3' atlas 17s
- ROI estimation of 'mori' atlas 25s
- ROI estimation of 'anatomy3' atlas 36s
- ROI estimation of 'julichbrain' atlas 47s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 19s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 34s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 75s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 113s
- Write results 113s
- 472s
- Quality check: 5s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_12013/ds/sub-0702/report/catreport_sub-0702_ses-01_T1w.pdf
- ------------------------------------------------------------------------
- CAT preprocessing takes 53 minute(s) and 3 second(s).
- Image Quality Rating (IQR): 81.32% (B-)
- GM volume (GMV): 48.56% (626.39 / 1289.86 ml)
- GM thickness (GMT): 2.54 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_12013/ds/sub-0702/mri
- Reports are saved in /var/lib/condor/execute/dir_12013/ds/sub-0702/report
- Labels are saved in /var/lib/condor/execute/dir_12013/ds/sub-0702/label
- ------------------------------------------------------------------------
|
