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- CAT12.8.1 r2040: 1/1: ./sub-0025073/ses-1/sub-0025073_ses-1_run-2_T1w.n
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- SANLM denoising (medium): 31s
- 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 7s
- SPM preprocessing 1 (estimate 1 - TPM registration): 54s
- SPM preprocessing 1 (estimate 2): 38s
- SPM preprocessing 2 (write):
- Write Segmentation 11s
- Update Segmentation 13s
- Update Skull-Stripping 28s
- Update probability maps 6s
- 58s
- Global intensity correction: 10s
- SANLM denoising after intensity normalization (medium): 16s
- Fast Optimized Shooting registration 21s
- 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) 18s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 25s
- 70s
- ROI segmentation (partitioning):
- Atlas -> subject space 5s
- Major structures 2s
- Ventricle detection 8s
- Blood vessel detection 6s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 16s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 3s
- 43s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 26s
- 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
- 8s
- 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 | 0.0877 0.0000 0.0877 | 32.0000
- 2 | 2.50 | 0.0851 0.0011 0.0863 | 29.4886
- 3 | 2.50 | 0.0844 0.0017 0.0861 | 26.9772
- 4 | 2.50 | 0.0841 0.0019 0.0860 | 24.6107
- 5 | 2.50 | 0.0838 0.0020 0.0859 | 22.6548
- 6 | 2.50 | 0.0836 0.0021 0.0857 | 20.6989
- 7 | 2.50 | 0.0834 0.0022 0.0855 | 18.9688
- 8 | 2.50 | 0.0831 0.0023 0.0854 | 17.4455
- 9 | 2.50 | 0.0828 0.0023 0.0852 | 15.9223
- 10 | 2.50 | 0.0826 0.0024 0.0850 | 14.6627
- 11 | 2.50 | 0.0823 0.0025 0.0848 | 13.4764
- 12 | 2.50 | 0.0820 0.0025 0.0846 | 12.3015
- 13 | 2.50 | 0.0817 0.0026 0.0844 | 11.3776
- 14 | 2.50 | 0.0815 0.0027 0.0841 | 10.4537
- 15 | 2.25 | 0.0830 0.0027 0.0857 | 9.5920
- 16 | 2.25 | 0.0802 0.0041 0.0843 | 8.8725
- 17 | 2.25 | 0.0791 0.0046 0.0837 | 8.1530
- 18 | 2.25 | 0.0784 0.0048 0.0832 | 7.5234
- 19 | 2.25 | 0.0778 0.0049 0.0827 | 6.9630
- 20 | 2.25 | 0.0774 0.0049 0.0823 | 6.4027
- 21 | 2.25 | 0.0769 0.0050 0.0819 | 5.9447
- 22 | 2.25 | 0.0765 0.0050 0.0815 | 5.5083
- 23 | 2.25 | 0.0761 0.0049 0.0810 | 5.0803
- 24 | 2.25 | 0.0757 0.0050 0.0807 | 4.7404
- 25 | 2.25 | 0.0753 0.0050 0.0803 | 4.4005
- 26 | 2.25 | 0.0749 0.0049 0.0799 | 4.0868
- 29 | 2.00 | 0.0770 0.0041 0.0811 | 3.3283
- 30 | 2.00 | 0.0744 0.0053 0.0797 | 3.1221
- 43 | 1.75 | 0.0740 0.0029 0.0768 | 1.5785
- 44 | 1.75 | 0.0693 0.0054 0.0747 | 1.5194
- 45 | 1.75 | 0.0679 0.0063 0.0741 | 1.4626
- 57 | 1.50 | 0.0679 0.0045 0.0724 | 1.0900
- 58 | 1.50 | 0.0643 0.0069 0.0712 | 1.0730
- 59 | 1.50 | 0.0632 0.0077 0.0709 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 117s
- Prepare output 7s
- 124s
- Jacobian determinant (RMS): 0.010 0.036 0.062 0.082 0.112 | 0.122188
- Template Matching: 0.088 0.225 0.223 0.204 0.190 | 0.189538
- Write result maps: 35s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 18s
- CSF distance: 11s
- PBT2x thickness: 31s
- 63s
- Create initial surface 61s
- Topology correction: 95s
- Surface refinement: 83s
- Reduction of surface collisions with optimization: 99s
- Spherical mapping with areal smoothing 62s
- Spherical registration 187s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 18s
- CSF distance: 11s
- PBT2x thickness: 31s
- 64s
- Create initial surface 63s
- Topology correction: 94s
- Surface refinement: 73s
- Reduction of surface collisions with optimization: 99s
- Spherical mapping with areal smoothing 78s
- Spherical registration 187s
- Final surface processing results:
- Average thickness (FS): 2.1576 0.7255 mm
- Surface intensity / position RMSE: 0.1197 / 0.1912
- Euler number / defect number / defect size: 716.0 / 226.0 / 21.51%
- Display thickness: /var/lib/condor/execute/dir_3356037/ds/NYU_2/sub-0025073/ses-1/surf/lh.thickness.sub-0025073_ses-1_run-2_T1w
- Display thickness: /var/lib/condor/execute/dir_3356037/ds/NYU_2/sub-0025073/ses-1/surf/rh.thickness.sub-0025073_ses-1_run-2_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3356037/ds/NYU_2/sub-0025073/ses-1/sub-0025073_ses-1_run-2_T1w.nii
- Surface ROI estimation: 6s
- Surface and thickness estimation takes: 1377s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 6s
- ROI estimation of 'neuromorphometrics' atlas 21s
- ROI estimation of 'lpba40' atlas 6s
- ROI estimation of 'hammers' atlas 14s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 5s
- ROI estimation of 'aal3' atlas 7s
- ROI estimation of 'mori' atlas 11s
- ROI estimation of 'anatomy3' atlas 16s
- ROI estimation of 'julichbrain' atlas 21s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 9s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 15s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 34s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 51s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 4s
- Write results 5s
- 223s
- Quality check: 7s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3356037/ds/NYU_2/sub-0025073/ses-1/report/catreport_sub-0025073_ses-1_run-2_T1w.pdf
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- CAT preprocessing takes 37 minute(s) and 3 second(s).
- Image Quality Rating (IQR): 46.10% (F)
- GM volume (GMV): 52.47% (816.64 / 1556.29 ml)
- GM thickness (GMT): 2.16 0.73 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3356037/ds/NYU_2/sub-0025073/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_3356037/ds/NYU_2/sub-0025073/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_3356037/ds/NYU_2/sub-0025073/ses-1/label
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