| 123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162 |
- ------------------------------------------------------------------------
- CAT12.8.1 r1980: 1/1: ./condor/execute/dir_9290/ds/sub-76/sub-76_T1w.n
- ------------------------------------------------------------------------
- SANLM denoising (medium): 82s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 15s
- Initial correction 12s
- Refine background 5s
- Final correction 8s
- Final scaling 11s
- 66s
- Correct center-of-mass 10s
- Affine registration 10s
- ------------------------------------------------------------------------------
- WARNING 01: cat_run_job1639:StrokeLesionButNoCorrection
- There are 2.29 cm of zeros within the brain but Stroke Lesion
- Correction (SLC) inactive (available in the expert mode).
- ------------------------------------------------------------------------------
- SPM preprocessing 1 (estimate 1 - TPM registration): 81s
- SPM preprocessing 1 (estimate 2): 90s
- SPM preprocessing 2 (write):
- Write Segmentation 20s
- Update Segmentation 24s
- Update Skull-Stripping 50s
- Update probability maps 12s
- 106s
- Global intensity correction: 19s
- SANLM denoising after intensity normalization (medium): 11s
- Fast Optimized Shooting registration 43s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 17s
- Estimate local tissue thresholds (WM) 27s
- Estimate local tissue thresholds (GM) 37s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 35s
- 126s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 17s
- Blood vessel detection 12s
- WMH detection (WMHCstr=0.48 > WMHCstr'=0.00) 33s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 85s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 35s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.07,0.980.05]
- Final cleanup (gcutstr=0.24):
- 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 | 0.0934 0.0000 0.0934 | 32.0000
- 2 | 2.50 | 0.0886 0.0018 0.0904 | 29.4886
- 3 | 2.50 | 0.0872 0.0028 0.0900 | 26.9772
- 4 | 2.50 | 0.0865 0.0032 0.0897 | 24.6107
- 5 | 2.50 | 0.0860 0.0034 0.0894 | 22.6548
- 6 | 2.50 | 0.0855 0.0036 0.0890 | 20.6989
- 7 | 2.50 | 0.0850 0.0037 0.0887 | 18.9688
- 8 | 2.50 | 0.0845 0.0039 0.0884 | 17.4455
- 9 | 2.50 | 0.0840 0.0040 0.0880 | 15.9223
- 10 | 2.50 | 0.0834 0.0042 0.0876 | 14.6627
- 11 | 2.50 | 0.0829 0.0043 0.0872 | 13.4764
- 12 | 2.50 | 0.0824 0.0044 0.0868 | 12.3015
- 13 | 2.50 | 0.0818 0.0046 0.0864 | 11.3776
- 14 | 2.50 | 0.0813 0.0047 0.0860 | 10.4537
- 15 | 2.25 | 0.0842 0.0048 0.0890 | 9.5920
- 16 | 2.25 | 0.0797 0.0072 0.0868 | 8.8725
- 17 | 2.25 | 0.0779 0.0080 0.0858 | 8.1530
- 18 | 2.25 | 0.0767 0.0083 0.0850 | 7.5234
- 19 | 2.25 | 0.0758 0.0085 0.0842 | 6.9630
- 20 | 2.25 | 0.0749 0.0085 0.0834 | 6.4027
- 29 | 2.00 | 0.0763 0.0047 0.0810 | 3.3283
- 30 | 2.00 | 0.0708 0.0073 0.0781 | 3.1221
- 31 | 2.00 | 0.0687 0.0082 0.0770 | 2.9160
- 43 | 1.75 | 0.0679 0.0047 0.0726 | 1.5785
- 44 | 1.75 | 0.0628 0.0074 0.0702 | 1.5194
- 45 | 1.75 | 0.0609 0.0084 0.0694 | 1.4626
- 57 | 1.50 | 0.0598 0.0063 0.0661 | 1.0900
- 58 | 1.50 | 0.0561 0.0087 0.0648 | 1.0730
- 59 | 1.50 | 0.0548 0.0095 0.0643 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 217s
- Prepare output 14s
- 231s
- Jacobian determinant (RMS): 0.014 0.054 0.092 0.138 0.195 | 0.205664
- Template Matching: 0.093 0.225 0.206 0.183 0.164 | 0.164354
- Write result maps: 29s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 47s
- CSF distance: 24s
- PBT2x thickness: 69s
- 148s
- Create initial surface 131s
- Topology correction: 133s
- Surface refinement: 104s
- Reduction of surface collisions with optimization: 98s
- Spherical mapping with areal smoothing 123s
- Spherical registration 376s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 48s
- CSF distance: 22s
- PBT2x thickness: 68s
- 145s
- Create initial surface 113s
- Topology correction: 129s
- Surface refinement: 151s
- Reduction of surface collisions with optimization: 99s
- Spherical mapping with areal smoothing 117s
- Spherical registration 327s
- Final surface processing results:
- Average thickness (FS): 2.6321 0.6096 mm
- Surface intensity / position RMSE: 0.0691 / 0.0700
- Euler number / defect number / defect size: 20.0 / 15.5 / 0.65%
- Display thickness: /var/lib/condor/execute/dir_9290/ds/sub-76/surf/lh.thickness.sub-76_T1w
- Display thickness: /var/lib/condor/execute/dir_9290/ds/sub-76/surf/rh.thickness.sub-76_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_9290/ds/sub-76/sub-76_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 2319s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- 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 28s
- ROI estimation of 'julichbrain' atlas 37s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 26s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 61s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 92s
- Write results 93s
- 374s
- Quality check: 7s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_9290/ds/sub-76/report/catreport_sub-76_T1w.pdf
- ------------------------------------------------------------------------
- CAT preprocessing takes 64 minute(s) and 3 second(s).
- Image Quality Rating (IQR): 81.66% (B-)
- GM volume (GMV): 50.02% (795.74 / 1590.98 ml)
- GM thickness (GMT): 2.63 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_9290/ds/sub-76/mri
- Reports are saved in /var/lib/condor/execute/dir_9290/ds/sub-76/report
- Labels are saved in /var/lib/condor/execute/dir_9290/ds/sub-76/label
- ------------------------------------------------------------------------
|
