| 123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155 |
- ------------------------------------------------------------------------
- CAT12.8.1 r1980: 1/1: ./execute/dir_40508/ds/sub-14/sub-14_ses-01_T1w.n
- ------------------------------------------------------------------------
- SANLM denoising (medium): 50s
- APP: Rough bias correction:
- Initialize 9s
- Estimate background 10s
- Initial correction 10s
- Refine background 4s
- Final correction 8s
- Final scaling 8s
- 58s
- Correct center-of-mass 4s
- Affine registration 15s
- SPM preprocessing 1 (estimate 1 - TPM registration): 113s
- SPM preprocessing 1 (estimate 2): 110s
- SPM preprocessing 2 (write):
- Write Segmentation 24s
- Update Segmentation 29s
- Update Skull-Stripping 61s
- Update probability maps 12s
- 126s
- Global intensity correction: 22s
- SANLM denoising after intensity normalization (medium): 18s
- Fast Optimized Shooting registration 46s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 6s
- Prepare partitions 4s
- Prepare segments (LASmod = 1.07) 23s
- Estimate local tissue thresholds (WM) 28s
- Estimate local tissue thresholds (GM) 42s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 39s
- 147s
- ROI segmentation (partitioning):
- Atlas -> subject space 12s
- Major structures 5s
- Ventricle detection 21s
- Blood vessel detection 15s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.16) 36s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 5s
- Final corrections 6s
- 102s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 43s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.04]
- 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
- 17s
- 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 | 0.0869 0.0000 0.0869 | 32.0000
- 2 | 2.50 | 0.0843 0.0012 0.0855 | 29.4886
- 3 | 2.50 | 0.0835 0.0018 0.0853 | 26.9772
- 4 | 2.50 | 0.0831 0.0020 0.0852 | 24.6107
- 5 | 2.50 | 0.0828 0.0022 0.0850 | 22.6548
- 6 | 2.50 | 0.0825 0.0023 0.0848 | 20.6989
- 7 | 2.50 | 0.0822 0.0024 0.0846 | 18.9688
- 8 | 2.50 | 0.0819 0.0025 0.0844 | 17.4455
- 9 | 2.50 | 0.0816 0.0026 0.0842 | 15.9223
- 10 | 2.50 | 0.0812 0.0027 0.0839 | 14.6627
- 11 | 2.50 | 0.0809 0.0028 0.0837 | 13.4764
- 12 | 2.50 | 0.0806 0.0029 0.0834 | 12.3015
- 13 | 2.50 | 0.0802 0.0030 0.0832 | 11.3776
- 14 | 2.50 | 0.0799 0.0030 0.0829 | 10.4537
- 15 | 2.25 | 0.0799 0.0031 0.0830 | 9.5920
- 16 | 2.25 | 0.0769 0.0047 0.0816 | 8.8725
- 17 | 2.25 | 0.0756 0.0053 0.0809 | 8.1530
- 18 | 2.25 | 0.0748 0.0055 0.0803 | 7.5234
- 29 | 2.00 | 0.0770 0.0026 0.0796 | 3.3283
- 30 | 2.00 | 0.0715 0.0051 0.0766 | 3.1221
- 31 | 2.00 | 0.0695 0.0061 0.0756 | 2.9160
- 43 | 1.75 | 0.0687 0.0035 0.0721 | 1.5785
- 44 | 1.75 | 0.0641 0.0059 0.0700 | 1.5194
- 45 | 1.75 | 0.0625 0.0068 0.0693 | 1.4626
- 57 | 1.50 | 0.0611 0.0050 0.0661 | 1.0900
- 58 | 1.50 | 0.0576 0.0072 0.0649 | 1.0730
- 59 | 1.50 | 0.0565 0.0080 0.0644 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 203s
- Prepare output 14s
- 217s
- Jacobian determinant (RMS): 0.011 0.043 0.070 0.098 0.125 | 0.132819
- Template Matching: 0.087 0.225 0.209 0.188 0.169 | 0.169441
- Write result maps: 36s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 59s
- CSF distance: 24s
- PBT2x thickness: 69s
- 161s
- Create initial surface 124s
- Topology correction: 138s
- Surface refinement: 111s
- Reduction of surface collisions with optimization: 110s
- Spherical mapping with areal smoothing 124s
- Spherical registration 315s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 58s
- CSF distance: 24s
- PBT2x thickness: 68s
- 158s
- Create initial surface 213s
- Topology correction: 182s
- Surface refinement: 189s
- Reduction of surface collisions with optimization: 109s
- Spherical mapping with areal smoothing 131s
- Spherical registration 349s
- Final surface processing results:
- Average thickness (FS): 2.5844 0.6177 mm
- Surface intensity / position RMSE: 0.0664 / 0.0720
- Euler number / defect number / defect size: 22.0 / 13.0 / 1.08%
- Display thickness: /var/lib/condor/execute/dir_40508/ds/sub-14/surf/lh.thickness.sub-14_ses-01_T1w
- Display thickness: /var/lib/condor/execute/dir_40508/ds/sub-14/surf/rh.thickness.sub-14_ses-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_40508/ds/sub-14/sub-14_ses-01_T1w.nii
- Surface ROI estimation: 11s
- Surface and thickness estimation takes: 2585s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 14s
- ROI estimation of 'neuromorphometrics' atlas 50s
- ROI estimation of 'lpba40' atlas 15s
- ROI estimation of 'hammers' atlas 38s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 13s
- ROI estimation of 'aal3' atlas 21s
- ROI estimation of 'mori' atlas 32s
- ROI estimation of 'anatomy3' atlas 43s
- ROI estimation of 'julichbrain' atlas 62s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 25s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 41s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 88s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 131s
- Write results 132s
- 577s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_40508/ds/sub-14/report/catreport_sub-14_ses-01_T1w.pdf
- ------------------------------------------------------------------------
- CAT preprocessing takes 73 minute(s) and 29 second(s).
- Image Quality Rating (IQR): 85.76% (B)
- GM volume (GMV): 46.54% (841.43 / 1807.98 ml)
- GM thickness (GMT): 2.58 0.62 mm
- Segmentations are saved in /var/lib/condor/execute/dir_40508/ds/sub-14/mri
- Reports are saved in /var/lib/condor/execute/dir_40508/ds/sub-14/report
- Labels are saved in /var/lib/condor/execute/dir_40508/ds/sub-14/label
- ------------------------------------------------------------------------
|
