123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155 |
- ------------------------------------------------------------------------
- CAT12.8.1 r2040: 1/1: ./sub-0027288/ses-1/sub-0027288_ses-1_run-1_T1w.n
- ------------------------------------------------------------------------
- SANLM denoising (medium): 28s
- Internal resampling (1.33x1.00x1.00mm > 1.00x1.00x1.00mm): 1s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 4s
- Initial correction 4s
- Refine background 2s
- Final correction 4s
- Final scaling 5s
- 30s
- Correct center-of-mass 4s
- Affine registration 8s
- SPM preprocessing 1 (estimate 1 - TPM registration): 77s
- SPM preprocessing 1 (estimate 2): 46s
- SPM preprocessing 2 (write):
- Write Segmentation 14s
- Update Segmentation 17s
- Update Skull-Stripping 36s
- Update probability maps 8s
- 75s
- Global intensity correction: 12s
- SANLM denoising after intensity normalization (medium): 22s
- Fast Optimized Shooting registration 27s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 12s
- Estimate local tissue thresholds (WM) 15s
- Estimate local tissue thresholds (GM) 21s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 30s
- 85s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 11s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.02) 18s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 54s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 29s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.670.08,0.990.04]
- 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
- 9s
- 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 | 0.0806 0.0000 0.0806 | 32.0000
- 2 | 2.50 | 0.0785 0.0010 0.0795 | 29.4886
- 3 | 2.50 | 0.0778 0.0016 0.0794 | 26.9772
- 4 | 2.50 | 0.0775 0.0018 0.0793 | 24.6107
- 5 | 2.50 | 0.0773 0.0019 0.0792 | 22.6548
- 6 | 2.50 | 0.0770 0.0020 0.0790 | 20.6989
- 7 | 2.50 | 0.0768 0.0020 0.0788 | 18.9688
- 8 | 2.50 | 0.0765 0.0021 0.0787 | 17.4455
- 9 | 2.50 | 0.0763 0.0022 0.0785 | 15.9223
- 10 | 2.50 | 0.0760 0.0023 0.0783 | 14.6627
- 11 | 2.50 | 0.0758 0.0024 0.0781 | 13.4764
- 12 | 2.50 | 0.0755 0.0024 0.0779 | 12.3015
- 13 | 2.50 | 0.0752 0.0025 0.0777 | 11.3776
- 14 | 2.50 | 0.0749 0.0026 0.0775 | 10.4537
- 15 | 2.25 | 0.0727 0.0026 0.0754 | 9.5920
- 16 | 2.25 | 0.0702 0.0039 0.0741 | 8.8725
- 29 | 2.00 | 0.0713 0.0018 0.0730 | 3.3283
- 30 | 2.00 | 0.0659 0.0039 0.0698 | 3.1221
- 31 | 2.00 | 0.0641 0.0048 0.0689 | 2.9160
- 43 | 1.75 | 0.0632 0.0027 0.0659 | 1.5785
- 44 | 1.75 | 0.0593 0.0048 0.0641 | 1.5194
- 45 | 1.75 | 0.0580 0.0056 0.0635 | 1.4626
- 57 | 1.50 | 0.0564 0.0040 0.0604 | 1.0900
- 58 | 1.50 | 0.0535 0.0060 0.0594 | 1.0730
- 59 | 1.50 | 0.0525 0.0066 0.0591 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 154s
- Prepare output 8s
- 162s
- Jacobian determinant (RMS): 0.011 0.038 0.055 0.076 0.097 | 0.102778
- Template Matching: 0.081 0.211 0.192 0.174 0.157 | 0.157490
- Write result maps: 74s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 26s
- CSF distance: 13s
- PBT2x thickness: 37s
- 81s
- Create initial surface 66s
- Topology correction: 83s
- Surface refinement: 93s
- Reduction of surface collisions with optimization: 65s
- Spherical mapping with areal smoothing 70s
- Spherical registration 200s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 20s
- CSF distance: 13s
- PBT2x thickness: 37s
- 75s
- Create initial surface 65s
- Topology correction: 82s
- Surface refinement: 68s
- Reduction of surface collisions with optimization: 61s
- Spherical mapping with areal smoothing 73s
- Spherical registration 220s
- Final surface processing results:
- Average thickness (FS): 2.6302 0.6322 mm
- Surface intensity / position RMSE: 0.0650 / 0.0629
- Euler number / defect number / defect size: 14.0 / 11.5 / 0.17%
- Display thickness: /var/lib/condor/execute/dir_2873407/ds/IPCAS_5/sub-0027288/ses-1/surf/lh.thickness.sub-0027288_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2873407/ds/IPCAS_5/sub-0027288/ses-1/surf/rh.thickness.sub-0027288_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2873407/ds/IPCAS_5/sub-0027288/ses-1/sub-0027288_ses-1_run-1_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1388s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 16s
- ROI estimation of 'neuromorphometrics' atlas 68s
- ROI estimation of 'lpba40' atlas 22s
- ROI estimation of 'hammers' atlas 61s
- ROI estimation of 'thalamus' atlas 5s
- ROI estimation of 'ibsr' atlas 23s
- ROI estimation of 'aal3' atlas 40s
- ROI estimation of 'mori' atlas 58s
- ROI estimation of 'anatomy3' atlas 84s
- ROI estimation of 'julichbrain' atlas 110s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 45s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 85s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 165s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 191s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 10s
- Write results 11s
- 983s
- Quality check: 10s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2873407/ds/IPCAS_5/sub-0027288/ses-1/report/catreport_sub-0027288_ses-1_run-1_T1w.pdf
- ------------------------------------------------------------------------
- CAT preprocessing takes 53 minute(s) and 18 second(s).
- Image Quality Rating (IQR): 82.59% (B-)
- GM volume (GMV): 49.98% (810.55 / 1621.85 ml)
- GM thickness (GMT): 2.63 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2873407/ds/IPCAS_5/sub-0027288/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_2873407/ds/IPCAS_5/sub-0027288/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_2873407/ds/IPCAS_5/sub-0027288/ses-1/label
- ------------------------------------------------------------------------
|