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- CAT12.8.1 r2040: 1/1: ./sub-0025514/ses-2/sub-0025514_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 34s
- Internal resampling (1.33x1.00x1.00mm > 1.00x1.00x1.00mm): 1s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 5s
- Initial correction 5s
- Refine background 3s
- Final correction 4s
- Final scaling 4s
- 34s
- Correct center-of-mass 4s
- Affine registration 9s
- SPM preprocessing 1 (estimate 1 - TPM registration): 18s
- Use initial fine affine registration. 63s
- SPM preprocessing 1 (estimate 2): 60s
- SPM preprocessing 2 (write):
- Write Segmentation 16s
- Update Segmentation 18s
- Update Skull-Stripping 40s
- Update probability maps 9s
- 82s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 25s
- Fast Optimized Shooting registration 31s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.15) 13s
- Estimate local tissue thresholds (WM) 17s
- Estimate local tissue thresholds (GM) 24s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 35s
- 98s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 15s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 21s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 3s
- Final corrections 4s
- 63s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 31s
- AMAP peaks: [CSF,GM,WM] = [0.370.05,0.680.07,0.980.05]
- 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 | 0.0806 0.0000 0.0806 | 32.0000
- 2 | 2.50 | 0.0787 0.0010 0.0796 | 29.4886
- 3 | 2.50 | 0.0781 0.0014 0.0796 | 26.9772
- 4 | 2.50 | 0.0779 0.0016 0.0795 | 24.6107
- 5 | 2.50 | 0.0776 0.0017 0.0794 | 22.6548
- 6 | 2.50 | 0.0774 0.0018 0.0792 | 20.6989
- 7 | 2.50 | 0.0772 0.0019 0.0791 | 18.9688
- 8 | 2.50 | 0.0770 0.0019 0.0790 | 17.4455
- 9 | 2.50 | 0.0768 0.0020 0.0788 | 15.9223
- 10 | 2.50 | 0.0766 0.0021 0.0787 | 14.6627
- 11 | 2.50 | 0.0764 0.0021 0.0785 | 13.4764
- 12 | 2.50 | 0.0762 0.0022 0.0783 | 12.3015
- 13 | 2.50 | 0.0759 0.0023 0.0782 | 11.3776
- 14 | 2.50 | 0.0757 0.0023 0.0780 | 10.4537
- 15 | 2.25 | 0.0742 0.0023 0.0765 | 9.5920
- 16 | 2.25 | 0.0717 0.0036 0.0753 | 8.8725
- 29 | 2.00 | 0.0730 0.0016 0.0746 | 3.3283
- 30 | 2.00 | 0.0675 0.0038 0.0713 | 3.1221
- 31 | 2.00 | 0.0657 0.0047 0.0704 | 2.9160
- 43 | 1.75 | 0.0649 0.0027 0.0676 | 1.5785
- 44 | 1.75 | 0.0607 0.0049 0.0656 | 1.5194
- 45 | 1.75 | 0.0593 0.0057 0.0650 | 1.4626
- 57 | 1.50 | 0.0580 0.0041 0.0620 | 1.0900
- 58 | 1.50 | 0.0549 0.0061 0.0609 | 1.0730
- 59 | 1.50 | 0.0538 0.0067 0.0605 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 167s
- Prepare output 10s
- 177s
- Jacobian determinant (RMS): 0.010 0.033 0.048 0.071 0.094 | 0.101081
- Template Matching: 0.081 0.215 0.197 0.178 0.161 | 0.161419
- Write result maps: 68s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 33s
- CSF distance: 15s
- PBT2x thickness: 42s
- 96s
- Create initial surface 78s
- Topology correction: 89s
- Surface refinement: 93s
- Reduction of surface collisions with optimization: 70s
- Spherical mapping with areal smoothing 77s
- Spherical registration 267s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 29s
- CSF distance: 14s
- PBT2x thickness: 42s
- 90s
- Create initial surface 77s
- Topology correction: 89s
- Surface refinement: 98s
- Reduction of surface collisions with optimization: 68s
- Spherical mapping with areal smoothing 77s
- Spherical registration 301s
- Final surface processing results:
- Average thickness (FS): 2.5670 0.6120 mm
- Surface intensity / position RMSE: 0.0690 / 0.0743
- Euler number / defect number / defect size: 14.0 / 10.5 / 0.60%
- Display thickness: /var/lib/condor/execute/dir_2807773/ds/IPCAS_1/sub-0025514/ses-2/surf/lh.thickness.sub-0025514_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2807773/ds/IPCAS_1/sub-0025514/ses-2/surf/rh.thickness.sub-0025514_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2807773/ds/IPCAS_1/sub-0025514/ses-2/sub-0025514_ses-2_run-1_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 1668s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 38s
- ROI estimation of 'lpba40' atlas 11s
- ROI estimation of 'hammers' atlas 34s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 13s
- ROI estimation of 'aal3' atlas 22s
- ROI estimation of 'mori' atlas 33s
- ROI estimation of 'anatomy3' atlas 47s
- ROI estimation of 'julichbrain' atlas 70s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 30s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 58s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 108s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 118s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 9s
- Write results 10s
- 605s
- Quality check: 11s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2807773/ds/IPCAS_1/sub-0025514/ses-2/report/catreport_sub-0025514_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 53 minute(s) and 0 second(s).
- Image Quality Rating (IQR): 80.88% (B-)
- GM volume (GMV): 50.19% (692.98 / 1380.80 ml)
- GM thickness (GMT): 2.57 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2807773/ds/IPCAS_1/sub-0025514/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_2807773/ds/IPCAS_1/sub-0025514/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_2807773/ds/IPCAS_1/sub-0025514/ses-2/label
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