| 123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154 |
- ------------------------------------------------------------------------
- CAT12.8.1 r2040: 1/1: ./sub-0025840/ses-1/sub-0025840_ses-1_run-1_T1w.n
- ------------------------------------------------------------------------
- SANLM denoising (medium): 46s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 5s
- Initial correction 5s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 35s
- Correct center-of-mass 3s
- Affine registration 9s
- SPM preprocessing 1 (estimate 1 - TPM registration): 68s
- SPM preprocessing 1 (estimate 2): 58s
- SPM preprocessing 2 (write):
- Write Segmentation 16s
- Update Segmentation 17s
- Update Skull-Stripping 39s
- Update probability maps 9s
- 82s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 24s
- Fast Optimized Shooting registration 32s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.20) 13s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 26s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 48s
- 114s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 12s
- Blood vessel detection 9s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.02) 21s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 61s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 31s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- 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
- 10s
- 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 | 0.0808 0.0000 0.0808 | 32.0000
- 2 | 2.50 | 0.0786 0.0011 0.0797 | 29.4886
- 3 | 2.50 | 0.0780 0.0016 0.0796 | 26.9772
- 4 | 2.50 | 0.0777 0.0018 0.0794 | 24.6107
- 5 | 2.50 | 0.0774 0.0019 0.0793 | 22.6548
- 6 | 2.50 | 0.0772 0.0019 0.0792 | 20.6989
- 7 | 2.50 | 0.0770 0.0020 0.0790 | 18.9688
- 8 | 2.50 | 0.0768 0.0021 0.0789 | 17.4455
- 9 | 2.50 | 0.0765 0.0021 0.0787 | 15.9223
- 10 | 2.50 | 0.0763 0.0022 0.0785 | 14.6627
- 11 | 2.50 | 0.0760 0.0023 0.0783 | 13.4764
- 12 | 2.50 | 0.0758 0.0023 0.0781 | 12.3015
- 13 | 2.50 | 0.0755 0.0024 0.0779 | 11.3776
- 14 | 2.50 | 0.0753 0.0024 0.0777 | 10.4537
- 15 | 2.25 | 0.0737 0.0025 0.0762 | 9.5920
- 16 | 2.25 | 0.0709 0.0038 0.0747 | 8.8725
- 29 | 2.00 | 0.0728 0.0017 0.0745 | 3.3283
- 30 | 2.00 | 0.0668 0.0041 0.0709 | 3.1221
- 31 | 2.00 | 0.0649 0.0050 0.0699 | 2.9160
- 43 | 1.75 | 0.0640 0.0029 0.0669 | 1.5785
- 44 | 1.75 | 0.0596 0.0052 0.0648 | 1.5194
- 45 | 1.75 | 0.0582 0.0060 0.0642 | 1.4626
- 57 | 1.50 | 0.0567 0.0043 0.0610 | 1.0900
- 58 | 1.50 | 0.0536 0.0063 0.0599 | 1.0730
- 59 | 1.50 | 0.0525 0.0069 0.0595 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 168s
- Prepare output 10s
- 178s
- Jacobian determinant (RMS): 0.009 0.030 0.046 0.068 0.091 | 0.098575
- Template Matching: 0.081 0.213 0.195 0.175 0.158 | 0.157617
- Write result maps: 32s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 38s
- CSF distance: 14s
- PBT2x thickness: 41s
- 98s
- Create initial surface 78s
- Topology correction: 72s
- Surface refinement: 59s
- Reduction of surface collisions with optimization: 57s
- Spherical mapping with areal smoothing 69s
- Spherical registration 296s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 37s
- CSF distance: 14s
- PBT2x thickness: 42s
- 98s
- Create initial surface 80s
- Topology correction: 72s
- Surface refinement: 68s
- Reduction of surface collisions with optimization: 58s
- Spherical mapping with areal smoothing 73s
- Spherical registration 293s
- Final surface processing results:
- Average thickness (FS): 2.7107 0.6247 mm
- Surface intensity / position RMSE: 0.0658 / 0.0655
- Euler number / defect number / defect size: 20.0 / 10.5 / 0.52%
- Display thickness: /var/lib/condor/execute/dir_797063/ds/SWU_4/sub-0025840/ses-1/surf/lh.thickness.sub-0025840_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_797063/ds/SWU_4/sub-0025840/ses-1/surf/rh.thickness.sub-0025840_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_797063/ds/SWU_4/sub-0025840/ses-1/sub-0025840_ses-1_run-1_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1562s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 8s
- ROI estimation of 'neuromorphometrics' atlas 29s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 20s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 13s
- ROI estimation of 'mori' atlas 18s
- ROI estimation of 'anatomy3' atlas 27s
- ROI estimation of 'julichbrain' atlas 35s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 27s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 61s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 100s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 9s
- Write results 11s
- 381s
- Quality check: 12s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_797063/ds/SWU_4/sub-0025840/ses-1/report/catreport_sub-0025840_ses-1_run-1_T1w.pdf
- ------------------------------------------------------------------------
- CAT preprocessing takes 48 minute(s) and 4 second(s).
- Image Quality Rating (IQR): 84.15% (B)
- GM volume (GMV): 49.17% (668.66 / 1359.98 ml)
- GM thickness (GMT): 2.71 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_797063/ds/SWU_4/sub-0025840/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_797063/ds/SWU_4/sub-0025840/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_797063/ds/SWU_4/sub-0025840/ses-1/label
- ------------------------------------------------------------------------
|
