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- CAT12.8.1 r2040: 1/1: ./sub-0025148/ses-1/sub-0025148_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 43s
- Internal resampling (1.33x1.00x1.00mm > 1.00x1.00x1.00mm): 1s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 6s
- Initial correction 6s
- Refine background 3s
- Final correction 4s
- Final scaling 4s
- 34s
- Correct center-of-mass 3s
- Affine registration 9s
- SPM preprocessing 1 (estimate 1 - TPM registration): 84s
- SPM preprocessing 1 (estimate 2): 62s
- SPM preprocessing 2 (write):
- Write Segmentation 15s
- Update Segmentation 18s
- Update Skull-Stripping 36s
- Update probability maps 8s
- 76s
- Global intensity correction: 14s
- SANLM denoising after intensity normalization (medium): 25s
- Fast Optimized Shooting registration 28s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 13s
- Estimate local tissue thresholds (WM) 16s
- Estimate local tissue thresholds (GM) 23s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 35s
- 95s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 3s
- Ventricle detection 14s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 22s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 61s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 30s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 2s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 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 | 0.0809 0.0000 0.0809 | 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 0.0795 | 24.6107
- 5 | 2.50 | 0.0775 0.0019 0.0793 | 22.6548
- 6 | 2.50 | 0.0773 0.0019 0.0792 | 20.6989
- 7 | 2.50 | 0.0771 0.0020 0.0790 | 18.9688
- 8 | 2.50 | 0.0768 0.0020 0.0789 | 17.4455
- 9 | 2.50 | 0.0766 0.0021 0.0787 | 15.9223
- 10 | 2.50 | 0.0764 0.0021 0.0785 | 14.6627
- 11 | 2.50 | 0.0762 0.0022 0.0783 | 13.4764
- 12 | 2.50 | 0.0759 0.0022 0.0781 | 12.3015
- 13 | 2.50 | 0.0757 0.0023 0.0779 | 11.3776
- 14 | 2.50 | 0.0754 0.0023 0.0777 | 10.4537
- 15 | 2.25 | 0.0746 0.0024 0.0770 | 9.5920
- 16 | 2.25 | 0.0721 0.0035 0.0756 | 8.8725
- 29 | 2.00 | 0.0743 0.0016 0.0758 | 3.3283
- 30 | 2.00 | 0.0687 0.0038 0.0725 | 3.1221
- 31 | 2.00 | 0.0668 0.0048 0.0715 | 2.9160
- 43 | 1.75 | 0.0660 0.0027 0.0688 | 1.5785
- 44 | 1.75 | 0.0616 0.0051 0.0667 | 1.5194
- 45 | 1.75 | 0.0601 0.0059 0.0660 | 1.4626
- 57 | 1.50 | 0.0589 0.0043 0.0632 | 1.0900
- 58 | 1.50 | 0.0556 0.0064 0.0621 | 1.0730
- 59 | 1.50 | 0.0545 0.0071 0.0616 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 138s
- Prepare output 9s
- 147s
- Jacobian determinant (RMS): 0.009 0.030 0.047 0.071 0.131 | 0.103661
- Template Matching: 0.081 0.216 0.200 0.180 0.164 | 0.163586
- Write result maps: 46s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 26s
- CSF distance: 14s
- PBT2x thickness: 40s
- 86s
- Create initial surface 78s
- Topology correction: 94s
- Surface refinement: 82s
- Reduction of surface collisions with optimization: 69s
- Spherical mapping with areal smoothing 73s
- Spherical registration 245s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 24s
- CSF distance: 13s
- PBT2x thickness: 40s
- 83s
- Create initial surface 77s
- Topology correction: 98s
- Surface refinement: 109s
- Reduction of surface collisions with optimization: 71s
- Spherical mapping with areal smoothing 85s
- Spherical registration 245s
- Final surface processing results:
- Average thickness (FS): 2.4464 0.6637 mm
- Surface intensity / position RMSE: 0.0808 / 0.1001
- Euler number / defect number / defect size: 170.0 / 56.5 / 4.72%
- Display thickness: /var/lib/condor/execute/dir_1362075/ds/NYU_2/sub-0025148/ses-1/surf/lh.thickness.sub-0025148_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1362075/ds/NYU_2/sub-0025148/ses-1/surf/rh.thickness.sub-0025148_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1362075/ds/NYU_2/sub-0025148/ses-1/sub-0025148_ses-1_run-1_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1582s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 24s
- ROI estimation of 'lpba40' atlas 7s
- ROI estimation of 'hammers' atlas 17s
- 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 44s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 67s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s
- Write results 7s
- 285s
- Quality check: 9s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1362075/ds/NYU_2/sub-0025148/ses-1/report/catreport_sub-0025148_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 45 minute(s) and 11 second(s).
- Image Quality Rating (IQR): 75.49% (C)
- GM volume (GMV): 49.38% (756.04 / 1531.16 ml)
- GM thickness (GMT): 2.45 0.66 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1362075/ds/NYU_2/sub-0025148/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_1362075/ds/NYU_2/sub-0025148/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_1362075/ds/NYU_2/sub-0025148/ses-1/label
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