| 123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154 |
- ------------------------------------------------------------------------
- CAT12.8.1 r2040: 1/1: ./sub-0025294/ses-2/sub-0025294_ses-2_run-1_T1w.n
- ------------------------------------------------------------------------
- SANLM denoising (medium): 58s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 7s
- Initial correction 7s
- Refine background 3s
- Final correction 6s
- Final scaling 5s
- 41s
- Correct center-of-mass 6s
- Affine registration 12s
- SPM preprocessing 1 (estimate 1 - TPM registration): 88s
- SPM preprocessing 1 (estimate 2): 92s
- SPM preprocessing 2 (write):
- Write Segmentation 19s
- Update Segmentation 21s
- Update Skull-Stripping 42s
- Update probability maps 9s
- 91s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 31s
- Fast Optimized Shooting registration 39s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 17s
- Estimate local tissue thresholds (WM) 23s
- Estimate local tissue thresholds (GM) 35s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 45s
- 130s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 15s
- Blood vessel detection 12s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 31s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 4s
- 80s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 39s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.07,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 5s
- Level 1 cleanup (brain masking) 4s
- 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 | 0.0836 0.0000 0.0836 | 32.0000
- 2 | 2.50 | 0.0806 0.0013 0.0818 | 29.4886
- 3 | 2.50 | 0.0797 0.0020 0.0816 | 26.9772
- 4 | 2.50 | 0.0792 0.0022 0.0814 | 24.6107
- 5 | 2.50 | 0.0789 0.0024 0.0813 | 22.6548
- 6 | 2.50 | 0.0786 0.0025 0.0810 | 20.6989
- 7 | 2.50 | 0.0783 0.0026 0.0808 | 18.9688
- 8 | 2.50 | 0.0779 0.0027 0.0806 | 17.4455
- 9 | 2.50 | 0.0776 0.0028 0.0804 | 15.9223
- 10 | 2.50 | 0.0773 0.0029 0.0801 | 14.6627
- 11 | 2.50 | 0.0769 0.0030 0.0799 | 13.4764
- 12 | 2.50 | 0.0766 0.0030 0.0796 | 12.3015
- 13 | 2.50 | 0.0762 0.0031 0.0793 | 11.3776
- 14 | 2.50 | 0.0758 0.0032 0.0790 | 10.4537
- 15 | 2.25 | 0.0766 0.0033 0.0798 | 9.5920
- 16 | 2.25 | 0.0731 0.0049 0.0781 | 8.8725
- 29 | 2.00 | 0.0745 0.0023 0.0767 | 3.3283
- 30 | 2.00 | 0.0682 0.0048 0.0730 | 3.1221
- 31 | 2.00 | 0.0660 0.0058 0.0718 | 2.9160
- 43 | 1.75 | 0.0652 0.0033 0.0686 | 1.5785
- 44 | 1.75 | 0.0609 0.0057 0.0665 | 1.5194
- 45 | 1.75 | 0.0594 0.0065 0.0659 | 1.4626
- 57 | 1.50 | 0.0583 0.0047 0.0630 | 1.0900
- 58 | 1.50 | 0.0551 0.0068 0.0619 | 1.0730
- 59 | 1.50 | 0.0540 0.0075 0.0615 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 196s
- Prepare output 13s
- 209s
- Jacobian determinant (RMS): 0.012 0.042 0.063 0.091 0.118 | 0.126035
- Template Matching: 0.084 0.219 0.198 0.178 0.162 | 0.161917
- Write result maps: 36s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 37s
- CSF distance: 21s
- PBT2x thickness: 61s
- 127s
- Create initial surface 106s
- Topology correction: 123s
- Surface refinement: 113s
- Reduction of surface collisions with optimization: 96s
- Spherical mapping with areal smoothing 116s
- Spherical registration 349s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 35s
- CSF distance: 20s
- PBT2x thickness: 62s
- 124s
- Create initial surface 106s
- Topology correction: 123s
- Surface refinement: 136s
- Reduction of surface collisions with optimization: 95s
- Spherical mapping with areal smoothing 117s
- Spherical registration 350s
- Final surface processing results:
- Average thickness (FS): 2.6315 0.6649 mm
- Surface intensity / position RMSE: 0.0792 / 0.0955
- Euler number / defect number / defect size: 38.0 / 21.5 / 1.96%
- Display thickness: /var/lib/condor/execute/dir_1702050/ds/UPSM_1/sub-0025294/ses-2/surf/lh.thickness.sub-0025294_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1702050/ds/UPSM_1/sub-0025294/ses-2/surf/rh.thickness.sub-0025294_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1702050/ds/UPSM_1/sub-0025294/ses-2/sub-0025294_ses-2_run-1_T1w.nii
- Surface ROI estimation: 11s
- Surface and thickness estimation takes: 2200s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 30s
- ROI estimation of 'lpba40' atlas 9s
- ROI estimation of 'hammers' atlas 21s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 12s
- ROI estimation of 'mori' atlas 18s
- ROI estimation of 'anatomy3' atlas 25s
- ROI estimation of 'julichbrain' atlas 33s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 13s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 23s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 53s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 81s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s
- Write results 8s
- 344s
- Quality check: 13s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1702050/ds/UPSM_1/sub-0025294/ses-2/report/catreport_sub-0025294_ses-2_run-1_T1w.pdf
- ------------------------------------------------------------------------
- CAT preprocessing takes 60 minute(s) and 32 second(s).
- Image Quality Rating (IQR): 83.57% (B)
- GM volume (GMV): 53.85% (788.04 / 1463.44 ml)
- GM thickness (GMT): 2.63 0.67 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1702050/ds/UPSM_1/sub-0025294/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_1702050/ds/UPSM_1/sub-0025294/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_1702050/ds/UPSM_1/sub-0025294/ses-2/label
- ------------------------------------------------------------------------
|
