| 123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156 |
- ------------------------------------------------------------------------
- CAT12.8.1 r2040: 1/1: ./sub-0025466/ses-1/sub-0025466_ses-1_run-1_T1w.n
- ------------------------------------------------------------------------
- SANLM denoising (medium): 46s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 8s
- Initial correction 9s
- Refine background 4s
- Final correction 8s
- Final scaling 7s
- 53s
- Correct center-of-mass 4s
- Affine registration 12s
- SPM preprocessing 1 (estimate 1 - TPM registration): 110s
- SPM preprocessing 1 (estimate 2): 104s
- SPM preprocessing 2 (write):
- Write Segmentation 23s
- Update Segmentation 26s
- Update Skull-Stripping 57s
- Update probability maps 11s
- 117s
- Global intensity correction: 21s
- SANLM denoising after intensity normalization (medium): 34s
- Fast Optimized Shooting registration 44s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.00) 19s
- Estimate local tissue thresholds (WM) 26s
- Estimate local tissue thresholds (GM) 39s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 61s
- 158s
- ROI segmentation (partitioning):
- Atlas -> subject space 10s
- Major structures 5s
- Ventricle detection 19s
- Blood vessel detection 14s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.11) 30s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 6s
- 90s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 43s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- 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
- 16s
- 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 | 0.0872 0.0000 0.0872 | 32.0000
- 2 | 2.50 | 0.0844 0.0012 0.0856 | 29.4886
- 3 | 2.50 | 0.0835 0.0019 0.0854 | 26.9772
- 4 | 2.50 | 0.0831 0.0021 0.0852 | 24.6107
- 5 | 2.50 | 0.0828 0.0023 0.0851 | 22.6548
- 6 | 2.50 | 0.0825 0.0024 0.0849 | 20.6989
- 7 | 2.50 | 0.0822 0.0025 0.0847 | 18.9688
- 8 | 2.50 | 0.0818 0.0026 0.0844 | 17.4455
- 9 | 2.50 | 0.0815 0.0027 0.0842 | 15.9223
- 10 | 2.50 | 0.0812 0.0028 0.0840 | 14.6627
- 11 | 2.50 | 0.0808 0.0029 0.0837 | 13.4764
- 12 | 2.50 | 0.0805 0.0030 0.0835 | 12.3015
- 13 | 2.50 | 0.0801 0.0031 0.0832 | 11.3776
- 14 | 2.50 | 0.0798 0.0032 0.0829 | 10.4537
- 15 | 2.25 | 0.0799 0.0033 0.0832 | 9.5920
- 16 | 2.25 | 0.0767 0.0049 0.0816 | 8.8725
- 17 | 2.25 | 0.0753 0.0055 0.0808 | 8.1530
- 18 | 2.25 | 0.0745 0.0058 0.0802 | 7.5234
- 29 | 2.00 | 0.0764 0.0028 0.0792 | 3.3283
- 30 | 2.00 | 0.0708 0.0052 0.0760 | 3.1221
- 31 | 2.00 | 0.0688 0.0062 0.0750 | 2.9160
- 43 | 1.75 | 0.0678 0.0035 0.0713 | 1.5785
- 44 | 1.75 | 0.0633 0.0059 0.0692 | 1.5194
- 45 | 1.75 | 0.0618 0.0067 0.0686 | 1.4626
- 57 | 1.50 | 0.0606 0.0049 0.0655 | 1.0900
- 58 | 1.50 | 0.0573 0.0070 0.0643 | 1.0730
- 59 | 1.50 | 0.0562 0.0077 0.0639 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 207s
- Prepare output 15s
- 221s
- Jacobian determinant (RMS): 0.012 0.043 0.067 0.091 0.114 | 0.121853
- Template Matching: 0.087 0.223 0.206 0.185 0.169 | 0.168617
- Write result maps: 44s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 153s
- CSF distance: 22s
- PBT2x thickness: 65s
- 249s
- Create initial surface 117s
- Topology correction: 130s
- Surface refinement: 152s
- Reduction of surface collisions with optimization: 100s
- Spherical mapping with areal smoothing 120s
- Spherical registration 353s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 71s
- CSF distance: 23s
- PBT2x thickness: 67s
- 170s
- Create initial surface 118s
- Topology correction: 140s
- Surface refinement: 146s
- Reduction of surface collisions with optimization: 106s
- Spherical mapping with areal smoothing 145s
- Spherical registration 361s
- Final surface processing results:
- Average thickness (FS): 2.3494 0.6425 mm
- Surface intensity / position RMSE: 0.0704 / 0.0741
- Euler number / defect number / defect size: 38.0 / 29.0 / 0.91%
- Display thickness: /var/lib/condor/execute/dir_108989/ds/IACAS/sub-0025466/ses-1/surf/lh.thickness.sub-0025466_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_108989/ds/IACAS/sub-0025466/ses-1/surf/rh.thickness.sub-0025466_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_108989/ds/IACAS/sub-0025466/ses-1/sub-0025466_ses-1_run-1_T1w.nii
- Surface ROI estimation: 11s
- Surface and thickness estimation takes: 2537s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 11s
- ROI estimation of 'neuromorphometrics' atlas 42s
- ROI estimation of 'lpba40' atlas 12s
- ROI estimation of 'hammers' atlas 28s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 10s
- ROI estimation of 'aal3' atlas 15s
- ROI estimation of 'mori' atlas 22s
- ROI estimation of 'anatomy3' atlas 32s
- ROI estimation of 'julichbrain' atlas 41s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 16s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 29s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 66s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 100s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s
- Write results 10s
- 437s
- Quality check: 15s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_108989/ds/IACAS/sub-0025466/ses-1/report/catreport_sub-0025466_ses-1_run-1_T1w.pdf
- ------------------------------------------------------------------------
- CAT preprocessing takes 70 minute(s) and 29 second(s).
- Image Quality Rating (IQR): 71.37% (C-)
- GM volume (GMV): 43.38% (744.44 / 1716.02 ml)
- GM thickness (GMT): 2.35 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_108989/ds/IACAS/sub-0025466/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_108989/ds/IACAS/sub-0025466/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_108989/ds/IACAS/sub-0025466/ses-1/label
- ------------------------------------------------------------------------
|
