| 123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156 |
- ------------------------------------------------------------------------
- CAT12.8.1 r2040: 1/1: ./sub-0025378/ses-1/sub-0025378_ses-1_run-1_T1w.n
- ------------------------------------------------------------------------
- SANLM denoising (medium): 48s
- APP: Rough bias correction:
- Initialize 4s
- Estimate background 5s
- Initial correction 5s
- Refine background 2s
- Final correction 4s
- Final scaling 5s
- 29s
- Correct center-of-mass 8s
- Affine registration 9s
- SPM preprocessing 1 (estimate 1 - TPM registration): 56s
- SPM preprocessing 1 (estimate 2): 41s
- SPM preprocessing 2 (write):
- Write Segmentation 12s
- Update Segmentation 14s
- Update Skull-Stripping 30s
- Update probability maps 6s
- 63s
- Global intensity correction: 11s
- SANLM denoising after intensity normalization (medium): 18s
- Fast Optimized Shooting registration 27s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.02) 10s
- Estimate local tissue thresholds (WM) 12s
- Estimate local tissue thresholds (GM) 16s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 29s
- 75s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 2s
- Ventricle detection 7s
- Blood vessel detection 6s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.20) 14s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 3s
- 43s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 24s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 3s
- Level 1 cleanup (brain masking) 2s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 8s
- 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 | 0.0877 0.0000 0.0877 | 32.0000
- 2 | 2.50 | 0.0849 0.0013 0.0861 | 29.4886
- 3 | 2.50 | 0.0840 0.0019 0.0859 | 26.9772
- 4 | 2.50 | 0.0836 0.0022 0.0858 | 24.6107
- 5 | 2.50 | 0.0832 0.0023 0.0856 | 22.6548
- 6 | 2.50 | 0.0829 0.0025 0.0854 | 20.6989
- 7 | 2.50 | 0.0826 0.0026 0.0852 | 18.9688
- 8 | 2.50 | 0.0823 0.0027 0.0850 | 17.4455
- 9 | 2.50 | 0.0819 0.0028 0.0847 | 15.9223
- 10 | 2.50 | 0.0815 0.0029 0.0845 | 14.6627
- 11 | 2.50 | 0.0812 0.0031 0.0842 | 13.4764
- 12 | 2.50 | 0.0808 0.0031 0.0839 | 12.3015
- 13 | 2.50 | 0.0804 0.0033 0.0836 | 11.3776
- 14 | 2.50 | 0.0800 0.0034 0.0833 | 10.4537
- 15 | 2.25 | 0.0804 0.0035 0.0839 | 9.5920
- 16 | 2.25 | 0.0769 0.0052 0.0821 | 8.8725
- 17 | 2.25 | 0.0754 0.0058 0.0813 | 8.1530
- 18 | 2.25 | 0.0745 0.0061 0.0806 | 7.5234
- 29 | 2.00 | 0.0760 0.0030 0.0790 | 3.3283
- 30 | 2.00 | 0.0700 0.0055 0.0755 | 3.1221
- 31 | 2.00 | 0.0678 0.0065 0.0744 | 2.9160
- 43 | 1.75 | 0.0665 0.0038 0.0703 | 1.5785
- 44 | 1.75 | 0.0620 0.0061 0.0681 | 1.5194
- 45 | 1.75 | 0.0606 0.0069 0.0675 | 1.4626
- 57 | 1.50 | 0.0589 0.0051 0.0640 | 1.0900
- 58 | 1.50 | 0.0559 0.0071 0.0629 | 1.0730
- 59 | 1.50 | 0.0549 0.0077 0.0626 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 153s
- Prepare output 7s
- 160s
- Jacobian determinant (RMS): 0.012 0.046 0.074 0.099 0.122 | 0.129588
- Template Matching: 0.088 0.223 0.204 0.182 0.165 | 0.164603
- Write result maps: 35s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 25s
- CSF distance: 11s
- PBT2x thickness: 28s
- 68s
- Create initial surface 52s
- Topology correction: 50s
- Surface refinement: 47s
- Reduction of surface collisions with optimization: 37s
- Spherical mapping with areal smoothing 53s
- Spherical registration 204s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 18s
- CSF distance: 10s
- PBT2x thickness: 26s
- 58s
- Create initial surface 49s
- Topology correction: 51s
- Surface refinement: 44s
- Reduction of surface collisions with optimization: 36s
- Spherical mapping with areal smoothing 53s
- Spherical registration 227s
- Final surface processing results:
- Average thickness (FS): 2.4573 0.6777 mm
- Surface intensity / position RMSE: 0.0660 / 0.0664
- Euler number / defect number / defect size: 14.0 / 8.5 / 0.40%
- Display thickness: /var/lib/condor/execute/dir_1964928/ds/LMU_2/sub-0025378/ses-1/surf/lh.thickness.sub-0025378_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1964928/ds/LMU_2/sub-0025378/ses-1/surf/rh.thickness.sub-0025378_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1964928/ds/LMU_2/sub-0025378/ses-1/sub-0025378_ses-1_run-1_T1w.nii
- Surface ROI estimation: 6s
- Surface and thickness estimation takes: 1092s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 6s
- ROI estimation of 'neuromorphometrics' atlas 22s
- ROI estimation of 'lpba40' atlas 6s
- ROI estimation of 'hammers' atlas 15s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 6s
- ROI estimation of 'aal3' atlas 8s
- ROI estimation of 'mori' atlas 12s
- ROI estimation of 'anatomy3' atlas 18s
- ROI estimation of 'julichbrain' atlas 23s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 10s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 17s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 38s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 82s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 10s
- Write results 11s
- 274s
- Quality check: 9s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1964928/ds/LMU_2/sub-0025378/ses-1/report/catreport_sub-0025378_ses-1_run-1_T1w.pdf
- ------------------------------------------------------------------------
- CAT preprocessing takes 35 minute(s) and 40 second(s).
- Image Quality Rating (IQR): 70.85% (C-)
- GM volume (GMV): 43.85% (543.33 / 1238.93 ml)
- GM thickness (GMT): 2.46 0.68 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1964928/ds/LMU_2/sub-0025378/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_1964928/ds/LMU_2/sub-0025378/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_1964928/ds/LMU_2/sub-0025378/ses-1/label
- ------------------------------------------------------------------------
|
