| 123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153 |
- ------------------------------------------------------------------------
- CAT12.8.1 r2040: 1/1: ./sub-0025689/ses-2/sub-0025689_ses-2_run-1_T1w.n
- ------------------------------------------------------------------------
- SANLM denoising (medium): 56s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 6s
- Initial correction 6s
- Refine background 4s
- Final correction 5s
- Final scaling 6s
- 39s
- Correct center-of-mass 10s
- Affine registration 12s
- SPM preprocessing 1 (estimate 1 - TPM registration): 76s
- SPM preprocessing 1 (estimate 2): 70s
- SPM preprocessing 2 (write):
- Write Segmentation 14s
- Update Segmentation 14s
- Update Skull-Stripping 35s
- Update probability maps 8s
- 72s
- Global intensity correction: 13s
- SANLM denoising after intensity normalization (medium): 18s
- Fast Optimized Shooting registration 28s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.16) 10s
- Estimate local tissue thresholds (WM) 14s
- Estimate local tissue thresholds (GM) 19s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 34s
- 85s
- ROI segmentation (partitioning):
- Atlas -> subject space 5s
- Major structures 2s
- Ventricle detection 10s
- Blood vessel detection 6s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 16s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 4s
- 47s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 24s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- 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 | 0.0828 0.0000 0.0828 | 32.0000
- 2 | 2.50 | 0.0798 0.0013 0.0811 | 29.4886
- 3 | 2.50 | 0.0790 0.0020 0.0809 | 26.9772
- 4 | 2.50 | 0.0786 0.0022 0.0808 | 24.6107
- 5 | 2.50 | 0.0782 0.0023 0.0806 | 22.6548
- 6 | 2.50 | 0.0780 0.0024 0.0804 | 20.6989
- 7 | 2.50 | 0.0777 0.0025 0.0802 | 18.9688
- 8 | 2.50 | 0.0773 0.0026 0.0799 | 17.4455
- 9 | 2.50 | 0.0770 0.0027 0.0797 | 15.9223
- 10 | 2.50 | 0.0767 0.0028 0.0795 | 14.6627
- 11 | 2.50 | 0.0764 0.0028 0.0792 | 13.4764
- 12 | 2.50 | 0.0761 0.0029 0.0789 | 12.3015
- 13 | 2.50 | 0.0757 0.0030 0.0787 | 11.3776
- 14 | 2.50 | 0.0754 0.0030 0.0784 | 10.4537
- 15 | 2.25 | 0.0738 0.0031 0.0769 | 9.5920
- 16 | 2.25 | 0.0707 0.0046 0.0753 | 8.8725
- 29 | 2.00 | 0.0713 0.0021 0.0734 | 3.3283
- 30 | 2.00 | 0.0657 0.0043 0.0700 | 3.1221
- 31 | 2.00 | 0.0638 0.0052 0.0690 | 2.9160
- 43 | 1.75 | 0.0626 0.0030 0.0656 | 1.5785
- 44 | 1.75 | 0.0587 0.0050 0.0637 | 1.5194
- 45 | 1.75 | 0.0574 0.0057 0.0631 | 1.4626
- 57 | 1.50 | 0.0557 0.0041 0.0599 | 1.0900
- 58 | 1.50 | 0.0530 0.0059 0.0589 | 1.0730
- Shooting registration with 2.50:-0.25:1.50 mm takes: 109s
- Prepare output 7s
- 117s
- Jacobian determinant (RMS): 0.010 0.037 0.054 0.075 0.096 | 0.100619
- Template Matching: 0.083 0.212 0.192 0.172 0.159 | 0.158951
- Write result maps: 27s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 18s
- CSF distance: 10s
- PBT2x thickness: 30s
- 63s
- Create initial surface 62s
- Topology correction: 67s
- Surface refinement: 44s
- Reduction of surface collisions with optimization: 47s
- Spherical mapping with areal smoothing 83s
- Spherical registration 229s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 18s
- CSF distance: 10s
- PBT2x thickness: 30s
- 62s
- Create initial surface 57s
- Topology correction: 68s
- Surface refinement: 62s
- Reduction of surface collisions with optimization: 44s
- Spherical mapping with areal smoothing 91s
- Spherical registration 230s
- Final surface processing results:
- Average thickness (FS): 2.5191 0.6603 mm
- Surface intensity / position RMSE: 0.0685 / 0.0786
- Euler number / defect number / defect size: 44.0 / 16.5 / 1.57%
- Display thickness: /var/lib/condor/execute/dir_2158312/ds/SWU_4/sub-0025689/ses-2/surf/lh.thickness.sub-0025689_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2158312/ds/SWU_4/sub-0025689/ses-2/surf/rh.thickness.sub-0025689_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2158312/ds/SWU_4/sub-0025689/ses-2/sub-0025689_ses-2_run-1_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1282s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 8s
- ROI estimation of 'neuromorphometrics' atlas 28s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 19s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 6s
- ROI estimation of 'aal3' atlas 10s
- ROI estimation of 'mori' atlas 14s
- ROI estimation of 'anatomy3' atlas 21s
- ROI estimation of 'julichbrain' atlas 29s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 50s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 74s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s
- Write results 7s
- 307s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2158312/ds/SWU_4/sub-0025689/ses-2/report/catreport_sub-0025689_ses-2_run-1_T1w.pdf
- ------------------------------------------------------------------------
- CAT preprocessing takes 39 minute(s) and 33 second(s).
- Image Quality Rating (IQR): 82.75% (B-)
- GM volume (GMV): 49.13% (631.12 / 1284.60 ml)
- GM thickness (GMT): 2.52 0.66 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2158312/ds/SWU_4/sub-0025689/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_2158312/ds/SWU_4/sub-0025689/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_2158312/ds/SWU_4/sub-0025689/ses-2/label
- ------------------------------------------------------------------------
|
