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- CAT12.8.1 r2040: 1/1: ./sub-0025085/ses-1/sub-0025085_ses-1_run-2_T1w.n
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- SANLM denoising (medium): 26s
- Internal resampling (1.33x1.00x1.00mm > 1.00x1.00x1.00mm): 1s
- APP: Rough bias correction:
- Initialize 4s
- Estimate background 4s
- Initial correction 4s
- Refine background 2s
- Final correction 3s
- Final scaling 3s
- 24s
- Correct center-of-mass 2s
- Affine registration 6s
- SPM preprocessing 1 (estimate 1 - TPM registration): 10s
- Use initial fine affine registration. 41s
- SPM preprocessing 1 (estimate 2): 42s
- SPM preprocessing 2 (write):
- Write Segmentation 12s
- Update Segmentation 12s
- Update Skull-Stripping 28s
- Update probability maps 6s
- 58s
- Global intensity correction: 11s
- SANLM denoising after intensity normalization (medium): 16s
- Fast Optimized Shooting registration 23s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 2s
- Prepare partitions 1s
- Prepare segments (LASmod = 1.00) 9s
- Estimate local tissue thresholds (WM) 12s
- Estimate local tissue thresholds (GM) 17s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 26s
- 70s
- ROI segmentation (partitioning):
- Atlas -> subject space 5s
- Major structures 2s
- Ventricle detection 6s
- Blood vessel detection 5s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 13s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 3s
- 38s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 24s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- 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
- 7s
- 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 | 0.0796 0.0000 0.0796 | 32.0000
- 2 | 2.50 | 0.0783 0.0007 0.0790 | 29.4886
- 3 | 2.50 | 0.0779 0.0011 0.0790 | 26.9772
- 4 | 2.50 | 0.0777 0.0012 0.0790 | 24.6107
- 5 | 2.50 | 0.0776 0.0013 0.0789 | 22.6548
- 6 | 2.50 | 0.0774 0.0014 0.0788 | 20.6989
- 7 | 2.50 | 0.0773 0.0014 0.0787 | 18.9688
- 8 | 2.50 | 0.0772 0.0015 0.0786 | 17.4455
- 9 | 2.50 | 0.0770 0.0015 0.0785 | 15.9223
- 10 | 2.50 | 0.0768 0.0016 0.0784 | 14.6627
- 11 | 2.50 | 0.0767 0.0016 0.0783 | 13.4764
- 12 | 2.50 | 0.0765 0.0017 0.0782 | 12.3015
- 13 | 2.50 | 0.0764 0.0017 0.0781 | 11.3776
- 14 | 2.50 | 0.0762 0.0018 0.0780 | 10.4537
- 15 | 2.25 | 0.0757 0.0018 0.0775 | 9.5920
- 16 | 2.25 | 0.0736 0.0028 0.0765 | 8.8725
- 29 | 2.00 | 0.0765 0.0013 0.0778 | 3.3283
- 30 | 2.00 | 0.0712 0.0035 0.0747 | 3.1221
- 31 | 2.00 | 0.0695 0.0044 0.0739 | 2.9160
- 43 | 1.75 | 0.0693 0.0025 0.0718 | 1.5785
- 44 | 1.75 | 0.0647 0.0050 0.0697 | 1.5194
- 45 | 1.75 | 0.0632 0.0058 0.0691 | 1.4626
- 57 | 1.50 | 0.0626 0.0041 0.0667 | 1.0900
- 58 | 1.50 | 0.0591 0.0065 0.0655 | 1.0730
- 59 | 1.50 | 0.0579 0.0072 0.0651 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 118s
- Prepare output 7s
- 125s
- Jacobian determinant (RMS): 0.008 0.027 0.043 0.069 0.096 | 0.102963
- Template Matching: 0.080 0.221 0.208 0.190 0.174 | 0.173754
- Write result maps: 45s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 15s
- CSF distance: 9s
- PBT2x thickness: 28s
- 56s
- Create initial surface 52s
- Topology correction: 82s
- Surface refinement: 73s
- Reduction of surface collisions with optimization: 81s
- Spherical mapping with areal smoothing 56s
- Spherical registration 208s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 16s
- CSF distance: 10s
- PBT2x thickness: 29s
- 59s
- Create initial surface 53s
- Topology correction: 73s
- Surface refinement: 64s
- Reduction of surface collisions with optimization: 46s
- Spherical mapping with areal smoothing 55s
- Spherical registration 193s
- Final surface processing results:
- Average thickness (FS): 2.3846 0.7340 mm
- Surface intensity / position RMSE: 0.0988 / 0.1376
- Euler number / defect number / defect size: 204.0 / 61.5 / 8.27%
- Display thickness: /var/lib/condor/execute/dir_3648061/ds/NYU_2/sub-0025085/ses-1/surf/lh.thickness.sub-0025085_ses-1_run-2_T1w
- Display thickness: /var/lib/condor/execute/dir_3648061/ds/NYU_2/sub-0025085/ses-1/surf/rh.thickness.sub-0025085_ses-1_run-2_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3648061/ds/NYU_2/sub-0025085/ses-1/sub-0025085_ses-1_run-2_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1219s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 25s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 18s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 11s
- ROI estimation of 'mori' atlas 16s
- ROI estimation of 'anatomy3' atlas 23s
- ROI estimation of 'julichbrain' atlas 30s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 45s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 67s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s
- Write results 6s
- 297s
- Quality check: 7s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3648061/ds/NYU_2/sub-0025085/ses-1/report/catreport_sub-0025085_ses-1_run-2_T1w.pdf
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- CAT preprocessing takes 35 minute(s) and 43 second(s).
- Image Quality Rating (IQR): 69.30% (D+)
- GM volume (GMV): 54.61% (672.30 / 1231.08 ml)
- GM thickness (GMT): 2.38 0.74 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3648061/ds/NYU_2/sub-0025085/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_3648061/ds/NYU_2/sub-0025085/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_3648061/ds/NYU_2/sub-0025085/ses-1/label
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