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- CAT12.8.1 r2040: 1/1: ./sub-0025038/ses-1/sub-0025038_ses-1_run-2_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 6s
- 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): 13s
- Use initial fine affine registration. 61s
- SPM preprocessing 1 (estimate 2): 54s
- SPM preprocessing 2 (write):
- Write Segmentation 15s
- Update Segmentation 17s
- Update Skull-Stripping 37s
- Update probability maps 8s
- 76s
- Global intensity correction: 15s
- SANLM denoising after intensity normalization (medium): 23s
- Fast Optimized Shooting registration 29s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.10) 12s
- Estimate local tissue thresholds (WM) 16s
- Estimate local tissue thresholds (GM) 24s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 38s
- 99s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 10s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 21s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 58s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 28s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.990.05]
- 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 | 0.0812 0.0000 0.0812 | 32.0000
- 2 | 2.50 | 0.0788 0.0011 0.0799 | 29.4886
- 3 | 2.50 | 0.0780 0.0017 0.0797 | 26.9772
- 4 | 2.50 | 0.0777 0.0019 0.0796 | 24.6107
- 5 | 2.50 | 0.0774 0.0021 0.0794 | 22.6548
- 6 | 2.50 | 0.0771 0.0022 0.0793 | 20.6989
- 7 | 2.50 | 0.0769 0.0023 0.0791 | 18.9688
- 8 | 2.50 | 0.0766 0.0024 0.0789 | 17.4455
- 9 | 2.50 | 0.0763 0.0024 0.0787 | 15.9223
- 10 | 2.50 | 0.0760 0.0025 0.0785 | 14.6627
- 11 | 2.50 | 0.0757 0.0026 0.0783 | 13.4764
- 12 | 2.50 | 0.0754 0.0027 0.0781 | 12.3015
- 13 | 2.50 | 0.0751 0.0028 0.0779 | 11.3776
- 14 | 2.50 | 0.0748 0.0028 0.0776 | 10.4537
- 15 | 2.25 | 0.0732 0.0029 0.0761 | 9.5920
- 16 | 2.25 | 0.0704 0.0043 0.0747 | 8.8725
- 29 | 2.00 | 0.0714 0.0019 0.0733 | 3.3283
- 30 | 2.00 | 0.0656 0.0043 0.0699 | 3.1221
- 31 | 2.00 | 0.0637 0.0052 0.0689 | 2.9160
- 43 | 1.75 | 0.0628 0.0030 0.0657 | 1.5785
- 44 | 1.75 | 0.0588 0.0051 0.0639 | 1.5194
- 45 | 1.75 | 0.0575 0.0058 0.0633 | 1.4626
- 57 | 1.50 | 0.0561 0.0042 0.0603 | 1.0900
- 58 | 1.50 | 0.0532 0.0061 0.0593 | 1.0730
- Shooting registration with 2.50:-0.25:1.50 mm takes: 124s
- Prepare output 8s
- 133s
- Jacobian determinant (RMS): 0.011 0.039 0.059 0.083 0.105 | 0.109661
- Template Matching: 0.081 0.211 0.191 0.173 0.160 | 0.159713
- Write result maps: 48s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 20s
- CSF distance: 11s
- PBT2x thickness: 34s
- 69s
- Create initial surface 65s
- Topology correction: 71s
- Surface refinement: 62s
- Reduction of surface collisions with optimization: 53s
- Spherical mapping with areal smoothing 62s
- Spherical registration 247s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 22s
- CSF distance: 12s
- PBT2x thickness: 35s
- 74s
- Create initial surface 68s
- Topology correction: 74s
- Surface refinement: 61s
- Reduction of surface collisions with optimization: 51s
- Spherical mapping with areal smoothing 61s
- Spherical registration 248s
- Final surface processing results:
- Average thickness (FS): 2.5544 0.6960 mm
- Surface intensity / position RMSE: 0.0802 / 0.0952
- Euler number / defect number / defect size: 92.0 / 42.0 / 2.66%
- Display thickness: /var/lib/condor/execute/dir_1362078/ds/NYU_2/sub-0025038/ses-1/surf/lh.thickness.sub-0025038_ses-1_run-2_T1w
- Display thickness: /var/lib/condor/execute/dir_1362078/ds/NYU_2/sub-0025038/ses-1/surf/rh.thickness.sub-0025038_ses-1_run-2_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1362078/ds/NYU_2/sub-0025038/ses-1/sub-0025038_ses-1_run-2_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1344s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 25s
- ROI estimation of 'lpba40' atlas 7s
- ROI estimation of 'hammers' atlas 18s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 6s
- ROI estimation of 'aal3' atlas 10s
- ROI estimation of 'mori' atlas 15s
- ROI estimation of 'anatomy3' atlas 21s
- ROI estimation of 'julichbrain' atlas 28s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 20s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 46s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 68s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s
- Write results 7s
- 291s
- Quality check: 9s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1362078/ds/NYU_2/sub-0025038/ses-1/report/catreport_sub-0025038_ses-1_run-2_T1w.pdf
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- CAT preprocessing takes 40 minute(s) and 34 second(s).
- Image Quality Rating (IQR): 79.38% (C+)
- GM volume (GMV): 51.89% (661.45 / 1274.73 ml)
- GM thickness (GMT): 2.55 0.70 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1362078/ds/NYU_2/sub-0025038/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_1362078/ds/NYU_2/sub-0025038/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_1362078/ds/NYU_2/sub-0025038/ses-1/label
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