| 123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152 |
- ------------------------------------------------------------------------
- CAT12.8.1 r1980: 1/1: ./sub-season127_ses-3_acq-MPrageHiRes_T1w.n
- ------------------------------------------------------------------------
- SANLM denoising (medium): 38s
- APP: Rough bias correction:
- Initialize 10s
- Estimate background 11s
- Initial correction 32s
- Refine background 5s
- Final correction 22s
- Final scaling 14s
- 104s
- Correct center-of-mass 6s
- Affine registration 17s
- SPM preprocessing 1 (estimate 1 - TPM registration): 139s
- SPM preprocessing 1 (estimate 2): 111s
- SPM preprocessing 2 (write):
- Write Segmentation 26s
- Update Segmentation 32s
- Update Skull-Stripping 69s
- Update probability maps 13s
- 141s
- Global intensity correction: 24s
- SANLM denoising after intensity normalization (medium): 15s
- Fast Optimized Shooting registration 43s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 7s
- Prepare partitions 4s
- Prepare segments (LASmod = 1.00) 28s
- Estimate local tissue thresholds (WM) 33s
- Estimate local tissue thresholds (GM) 48s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 38s
- 164s
- ROI segmentation (partitioning):
- Atlas -> subject space 13s
- Major structures 7s
- Ventricle detection 24s
- Blood vessel detection 20s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 50s
- Manual stroke lesion detection 0s
- Closing of deep structures 3s
- Side alignment 6s
- Final corrections 7s
- 130s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 57s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 8s
- Level 1 cleanup (brain masking) 5s
- Level 2 cleanup (CSF correction) 3s
- Level 3 cleanup (CSF/WM PVE) 5s
- 21s
- 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 | 0.0824 0.0000 0.0824 | 32.0000
- 2 | 2.50 | 0.0792 0.0013 0.0805 | 29.4886
- 3 | 2.50 | 0.0783 0.0020 0.0803 | 26.9772
- 4 | 2.50 | 0.0779 0.0022 0.0801 | 24.6107
- 5 | 2.50 | 0.0775 0.0024 0.0799 | 22.6548
- 6 | 2.50 | 0.0772 0.0025 0.0797 | 20.6989
- 7 | 2.50 | 0.0769 0.0026 0.0794 | 18.9688
- 8 | 2.50 | 0.0765 0.0027 0.0792 | 17.4455
- 9 | 2.50 | 0.0762 0.0027 0.0790 | 15.9223
- 10 | 2.50 | 0.0759 0.0029 0.0787 | 14.6627
- 11 | 2.50 | 0.0755 0.0029 0.0785 | 13.4764
- 12 | 2.50 | 0.0752 0.0030 0.0782 | 12.3015
- 13 | 2.50 | 0.0748 0.0031 0.0779 | 11.3776
- 14 | 2.50 | 0.0745 0.0032 0.0776 | 10.4537
- 15 | 2.25 | 0.0727 0.0032 0.0760 | 9.5920
- 16 | 2.25 | 0.0699 0.0047 0.0746 | 8.8725
- 29 | 2.00 | 0.0705 0.0021 0.0726 | 3.3283
- 30 | 2.00 | 0.0648 0.0044 0.0692 | 3.1221
- 31 | 2.00 | 0.0629 0.0053 0.0682 | 2.9160
- 43 | 1.75 | 0.0618 0.0031 0.0648 | 1.5785
- 44 | 1.75 | 0.0579 0.0051 0.0630 | 1.5194
- 45 | 1.75 | 0.0567 0.0058 0.0625 | 1.4626
- 57 | 1.50 | 0.0552 0.0042 0.0594 | 1.0900
- 58 | 1.50 | 0.0523 0.0061 0.0584 | 1.0730
- Shooting registration with 2.50:-0.25:1.50 mm takes: 162s
- Prepare output 16s
- 178s
- Jacobian determinant (RMS): 0.012 0.044 0.064 0.088 0.110 | 0.114850
- Template Matching: 0.082 0.210 0.189 0.170 0.157 | 0.157038
- Write result maps: 40s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 67s
- CSF distance: 20s
- PBT2x thickness: 59s
- 153s
- Create initial surface 103s
- Topology correction: 114s
- Surface refinement: 98s
- Reduction of surface collisions with optimization: 89s
- Spherical mapping with areal smoothing 99s
- Spherical registration 322s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 48s
- CSF distance: 20s
- PBT2x thickness: 60s
- 136s
- Create initial surface 103s
- Topology correction: 107s
- Surface refinement: 119s
- Reduction of surface collisions with optimization: 82s
- Spherical mapping with areal smoothing 97s
- Spherical registration 290s
- Final surface processing results:
- Average thickness (FS): 2.5723 0.5909 mm
- Surface intensity / position RMSE: 0.0678 / 0.0662
- Euler number / defect number / defect size: 12.0 / 18.0 / 0.29%
- Display thickness: /var/lib/condor/execute/dir_377798/ds/sub-season127/surf/lh.thickness.sub-season127_ses-3_acq-MPrageHiRes_T1w
- Display thickness: /var/lib/condor/execute/dir_377798/ds/sub-season127/surf/rh.thickness.sub-season127_ses-3_acq-MPrageHiRes_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_377798/ds/sub-season127/sub-season127_ses-3_acq-MPrageHiRes_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 2033s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 12s
- ROI estimation of 'neuromorphometrics' atlas 42s
- ROI estimation of 'lpba40' atlas 12s
- ROI estimation of 'hammers' atlas 30s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 10s
- ROI estimation of 'aal3' atlas 18s
- ROI estimation of 'mori' atlas 26s
- ROI estimation of 'anatomy3' atlas 31s
- ROI estimation of 'julichbrain' atlas 41s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 16s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 27s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 64s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 95s
- Write results 96s
- 427s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_377798/ds/sub-season127/report/catreport_sub-season127_ses-3_acq-MPrageHiRes_T1w.pdf
- ------------------------------------------------------------------------
- CAT preprocessing takes 64 minute(s) and 1 second(s).
- Image Quality Rating (IQR): 86.72% (B+)
- GM volume (GMV): 49.12% (770.40 / 1568.46 ml)
- GM thickness (GMT): 2.57 0.59 mm
- Segmentations are saved in /var/lib/condor/execute/dir_377798/ds/sub-season127/mri
- Reports are saved in /var/lib/condor/execute/dir_377798/ds/sub-season127/report
- Labels are saved in /var/lib/condor/execute/dir_377798/ds/sub-season127/label
- ------------------------------------------------------------------------
|
