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- CAT12.8.1 r2040: 1/1: ./sub-0025147/ses-1/sub-0025147_ses-1_run-2_T1w.n
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- SANLM denoising (medium): 25s
- 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
- 25s
- Correct center-of-mass 3s
- Affine registration 6s
- SPM preprocessing 1 (estimate 1 - TPM registration): 24s
- Use previous fine affine registration. 44s
- SPM preprocessing 1 (estimate 2): 50s
- SPM preprocessing 2 (write):
- Write Segmentation 12s
- Update Segmentation 14s
- Update Skull-Stripping 29s
- Update probability maps 6s
- 61s
- Global intensity correction: 11s
- SANLM denoising after intensity normalization (medium): 17s
- Fast Optimized Shooting registration 23s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 2s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 9s
- Estimate local tissue thresholds (WM) 12s
- Estimate local tissue thresholds (GM) 16s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 27s
- 72s
- ROI segmentation (partitioning):
- Atlas -> subject space 5s
- Major structures 2s
- Ventricle detection 7s
- Blood vessel detection 6s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 14s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 3s
- 41s
- 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 | 0.0851 0.0000 0.0851 | 32.0000
- 2 | 2.50 | 0.0821 0.0012 0.0834 | 29.4886
- 3 | 2.50 | 0.0813 0.0019 0.0831 | 26.9772
- 4 | 2.50 | 0.0809 0.0021 0.0830 | 24.6107
- 5 | 2.50 | 0.0805 0.0023 0.0828 | 22.6548
- 6 | 2.50 | 0.0802 0.0023 0.0826 | 20.6989
- 7 | 2.50 | 0.0799 0.0024 0.0824 | 18.9688
- 8 | 2.50 | 0.0796 0.0025 0.0821 | 17.4455
- 9 | 2.50 | 0.0793 0.0026 0.0819 | 15.9223
- 10 | 2.50 | 0.0789 0.0027 0.0816 | 14.6627
- 11 | 2.50 | 0.0786 0.0028 0.0814 | 13.4764
- 12 | 2.50 | 0.0782 0.0029 0.0811 | 12.3015
- 13 | 2.50 | 0.0779 0.0030 0.0808 | 11.3776
- 14 | 2.50 | 0.0775 0.0030 0.0805 | 10.4537
- 15 | 2.25 | 0.0777 0.0031 0.0808 | 9.5920
- 16 | 2.25 | 0.0743 0.0048 0.0791 | 8.8725
- 29 | 2.00 | 0.0759 0.0022 0.0780 | 3.3283
- 30 | 2.00 | 0.0688 0.0050 0.0738 | 3.1221
- 31 | 2.00 | 0.0664 0.0061 0.0726 | 2.9160
- 43 | 1.75 | 0.0653 0.0036 0.0689 | 1.5785
- 44 | 1.75 | 0.0605 0.0061 0.0666 | 1.5194
- 45 | 1.75 | 0.0589 0.0070 0.0658 | 1.4626
- 57 | 1.50 | 0.0573 0.0051 0.0625 | 1.0900
- 58 | 1.50 | 0.0541 0.0072 0.0613 | 1.0730
- 59 | 1.50 | 0.0531 0.0079 0.0610 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 115s
- Prepare output 7s
- 122s
- Jacobian determinant (RMS): 0.010 0.039 0.063 0.094 0.121 | 0.129214
- Template Matching: 0.085 0.223 0.199 0.177 0.159 | 0.159272
- Write result maps: 42s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 20s
- CSF distance: 10s
- PBT2x thickness: 29s
- 63s
- Create initial surface 56s
- Topology correction: 67s
- Surface refinement: 48s
- Reduction of surface collisions with optimization: 43s
- Spherical mapping with areal smoothing 56s
- Spherical registration 183s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 19s
- CSF distance: 9s
- PBT2x thickness: 29s
- 61s
- Create initial surface 54s
- Topology correction: 67s
- Surface refinement: 49s
- Reduction of surface collisions with optimization: 41s
- Spherical mapping with areal smoothing 54s
- Spherical registration 187s
- Final surface processing results:
- Average thickness (FS): 2.4995 0.6600 mm
- Surface intensity / position RMSE: 0.0750 / 0.0854
- Euler number / defect number / defect size: 104.0 / 43.0 / 2.75%
- Display thickness: /var/lib/condor/execute/dir_3588196/ds/NYU_2/sub-0025147/ses-1/surf/lh.thickness.sub-0025147_ses-1_run-2_T1w
- Display thickness: /var/lib/condor/execute/dir_3588196/ds/NYU_2/sub-0025147/ses-1/surf/rh.thickness.sub-0025147_ses-1_run-2_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3588196/ds/NYU_2/sub-0025147/ses-1/sub-0025147_ses-1_run-2_T1w.nii
- Surface ROI estimation: 6s
- Surface and thickness estimation takes: 1096s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 7s
- ROI estimation of 'neuromorphometrics' atlas 23s
- ROI estimation of 'lpba40' atlas 7s
- ROI estimation of 'hammers' atlas 16s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 6s
- ROI estimation of 'aal3' atlas 10s
- ROI estimation of 'mori' atlas 14s
- ROI estimation of 'anatomy3' atlas 20s
- ROI estimation of 'julichbrain' atlas 27s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 19s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 43s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 63s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s
- Write results 7s
- 272s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3588196/ds/NYU_2/sub-0025147/ses-1/report/catreport_sub-0025147_ses-1_run-2_T1w.pdf
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- CAT preprocessing takes 33 minute(s) and 48 second(s).
- Image Quality Rating (IQR): 74.89% (C)
- GM volume (GMV): 47.48% (649.41 / 1367.90 ml)
- GM thickness (GMT): 2.50 0.66 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3588196/ds/NYU_2/sub-0025147/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_3588196/ds/NYU_2/sub-0025147/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_3588196/ds/NYU_2/sub-0025147/ses-1/label
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