| 123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154 |
- ------------------------------------------------------------------------
- CAT12.8.1 r2040: 1/1: ./sub-0025761/ses-1/sub-0025761_ses-1_run-1_T1w.n
- ------------------------------------------------------------------------
- SANLM denoising (medium): 53s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 6s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 37s
- Correct center-of-mass 4s
- Affine registration 9s
- SPM preprocessing 1 (estimate 1 - TPM registration): 73s
- SPM preprocessing 1 (estimate 2): 54s
- SPM preprocessing 2 (write):
- Write Segmentation 17s
- Update Segmentation 19s
- Update Skull-Stripping 42s
- Update probability maps 8s
- 86s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 30s
- Fast Optimized Shooting registration 32s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.11) 15s
- Estimate local tissue thresholds (WM) 19s
- Estimate local tissue thresholds (GM) 26s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 47s
- 116s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 4s
- Ventricle detection 14s
- Blood vessel detection 10s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 27s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 4s
- 71s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 35s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 3s
- 11s
- 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 | 0.0834 0.0000 0.0834 | 32.0000
- 2 | 2.50 | 0.0812 0.0011 0.0823 | 29.4886
- 3 | 2.50 | 0.0805 0.0016 0.0822 | 26.9772
- 4 | 2.50 | 0.0802 0.0018 0.0820 | 24.6107
- 5 | 2.50 | 0.0800 0.0020 0.0819 | 22.6548
- 6 | 2.50 | 0.0797 0.0020 0.0817 | 20.6989
- 7 | 2.50 | 0.0795 0.0021 0.0816 | 18.9688
- 8 | 2.50 | 0.0792 0.0022 0.0814 | 17.4455
- 9 | 2.50 | 0.0790 0.0023 0.0812 | 15.9223
- 10 | 2.50 | 0.0787 0.0024 0.0811 | 14.6627
- 11 | 2.50 | 0.0784 0.0024 0.0809 | 13.4764
- 12 | 2.50 | 0.0782 0.0025 0.0806 | 12.3015
- 13 | 2.50 | 0.0779 0.0026 0.0804 | 11.3776
- 14 | 2.50 | 0.0776 0.0026 0.0802 | 10.4537
- 15 | 2.25 | 0.0777 0.0027 0.0803 | 9.5920
- 16 | 2.25 | 0.0747 0.0041 0.0788 | 8.8725
- 29 | 2.00 | 0.0770 0.0019 0.0788 | 3.3283
- 30 | 2.00 | 0.0706 0.0045 0.0751 | 3.1221
- 31 | 2.00 | 0.0685 0.0055 0.0740 | 2.9160
- 43 | 1.75 | 0.0680 0.0031 0.0711 | 1.5785
- 44 | 1.75 | 0.0631 0.0058 0.0688 | 1.5194
- 45 | 1.75 | 0.0614 0.0067 0.0681 | 1.4626
- 57 | 1.50 | 0.0603 0.0048 0.0651 | 1.0900
- 58 | 1.50 | 0.0567 0.0072 0.0639 | 1.0730
- 59 | 1.50 | 0.0555 0.0079 0.0634 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 165s
- Prepare output 10s
- 176s
- Jacobian determinant (RMS): 0.010 0.034 0.053 0.079 0.105 | 0.111459
- Template Matching: 0.083 0.224 0.206 0.184 0.167 | 0.166612
- Write result maps: 33s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 35s
- CSF distance: 16s
- PBT2x thickness: 48s
- 105s
- Create initial surface 90s
- Topology correction: 103s
- Surface refinement: 82s
- Reduction of surface collisions with optimization: 79s
- Spherical mapping with areal smoothing 88s
- Spherical registration 288s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 31s
- CSF distance: 16s
- PBT2x thickness: 47s
- 101s
- Create initial surface 89s
- Topology correction: 103s
- Surface refinement: 93s
- Reduction of surface collisions with optimization: 80s
- Spherical mapping with areal smoothing 107s
- Spherical registration 329s
- Final surface processing results:
- Average thickness (FS): 2.6136 0.6520 mm
- Surface intensity / position RMSE: 0.0715 / 0.0753
- Euler number / defect number / defect size: 58.0 / 33.5 / 1.08%
- Display thickness: /var/lib/condor/execute/dir_812231/ds/SWU_4/sub-0025761/ses-1/surf/lh.thickness.sub-0025761_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_812231/ds/SWU_4/sub-0025761/ses-1/surf/rh.thickness.sub-0025761_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_812231/ds/SWU_4/sub-0025761/ses-1/sub-0025761_ses-1_run-1_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 1842s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 10s
- ROI estimation of 'neuromorphometrics' atlas 35s
- 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 16s
- ROI estimation of 'mori' atlas 24s
- ROI estimation of 'anatomy3' atlas 37s
- ROI estimation of 'julichbrain' atlas 52s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 20s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 35s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 76s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 95s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s
- Write results 9s
- 462s
- Quality check: 12s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_812231/ds/SWU_4/sub-0025761/ses-1/report/catreport_sub-0025761_ses-1_run-1_T1w.pdf
- ------------------------------------------------------------------------
- CAT preprocessing takes 53 minute(s) and 59 second(s).
- Image Quality Rating (IQR): 82.39% (B-)
- GM volume (GMV): 49.68% (781.30 / 1572.56 ml)
- GM thickness (GMT): 2.61 0.65 mm
- Segmentations are saved in /var/lib/condor/execute/dir_812231/ds/SWU_4/sub-0025761/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_812231/ds/SWU_4/sub-0025761/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_812231/ds/SWU_4/sub-0025761/ses-1/label
- ------------------------------------------------------------------------
|
