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- CAT12.8.1 r2040: 1/1: ./sub-0025034/ses-2/sub-0025034_ses-2_run-2_T1w.n
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- SANLM denoising (medium): 28s
- 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 3s
- Affine registration 6s
- SPM preprocessing 1 (estimate 1 - TPM registration): 58s
- SPM preprocessing 1 (estimate 2): 45s
- SPM preprocessing 2 (write):
- Write Segmentation 11s
- Update Segmentation 14s
- Update Skull-Stripping 28s
- Update probability maps 6s
- 59s
- Global intensity correction: 10s
- SANLM denoising after intensity normalization (medium): 18s
- Fast Optimized Shooting registration 22s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 2s
- Prepare partitions 1s
- Prepare segments (LASmod = 1.04) 10s
- Estimate local tissue thresholds (WM) 12s
- Estimate local tissue thresholds (GM) 17s
- 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): 25s
- 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 | 0.0822 0.0000 0.0822 | 32.0000
- 2 | 2.50 | 0.0796 0.0011 0.0808 | 29.4886
- 3 | 2.50 | 0.0789 0.0017 0.0806 | 26.9772
- 4 | 2.50 | 0.0785 0.0020 0.0804 | 24.6107
- 5 | 2.50 | 0.0782 0.0021 0.0803 | 22.6548
- 6 | 2.50 | 0.0779 0.0022 0.0801 | 20.6989
- 7 | 2.50 | 0.0777 0.0023 0.0799 | 18.9688
- 8 | 2.50 | 0.0774 0.0024 0.0798 | 17.4455
- 9 | 2.50 | 0.0771 0.0024 0.0795 | 15.9223
- 10 | 2.50 | 0.0768 0.0025 0.0793 | 14.6627
- 11 | 2.50 | 0.0765 0.0026 0.0791 | 13.4764
- 12 | 2.50 | 0.0762 0.0027 0.0789 | 12.3015
- 13 | 2.50 | 0.0759 0.0028 0.0786 | 11.3776
- 14 | 2.50 | 0.0756 0.0028 0.0784 | 10.4537
- 15 | 2.25 | 0.0748 0.0029 0.0777 | 9.5920
- 16 | 2.25 | 0.0719 0.0043 0.0762 | 8.8725
- 29 | 2.00 | 0.0733 0.0019 0.0753 | 3.3283
- 30 | 2.00 | 0.0675 0.0043 0.0718 | 3.1221
- 31 | 2.00 | 0.0655 0.0053 0.0708 | 2.9160
- 43 | 1.75 | 0.0647 0.0030 0.0678 | 1.5785
- 44 | 1.75 | 0.0605 0.0052 0.0658 | 1.5194
- 45 | 1.75 | 0.0591 0.0060 0.0652 | 1.4626
- 57 | 1.50 | 0.0579 0.0044 0.0623 | 1.0900
- 58 | 1.50 | 0.0548 0.0065 0.0612 | 1.0730
- 59 | 1.50 | 0.0537 0.0071 0.0608 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 105s
- Prepare output 7s
- 112s
- Jacobian determinant (RMS): 0.011 0.038 0.056 0.078 0.101 | 0.106911
- Template Matching: 0.082 0.216 0.197 0.177 0.161 | 0.161195
- Write result maps: 37s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 18s
- CSF distance: 11s
- PBT2x thickness: 31s
- 64s
- Create initial surface 60s
- Topology correction: 71s
- Surface refinement: 69s
- Reduction of surface collisions with optimization: 50s
- Spherical mapping with areal smoothing 59s
- Spherical registration 174s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 18s
- CSF distance: 10s
- PBT2x thickness: 31s
- 63s
- Create initial surface 57s
- Topology correction: 71s
- Surface refinement: 58s
- Reduction of surface collisions with optimization: 50s
- Spherical mapping with areal smoothing 59s
- Spherical registration 184s
- Final surface processing results:
- Average thickness (FS): 2.5485 0.6706 mm
- Surface intensity / position RMSE: 0.0756 / 0.0860
- Euler number / defect number / defect size: 94.0 / 36.5 / 2.51%
- Display thickness: /var/lib/condor/execute/dir_2333949/ds/NYU_2/sub-0025034/ses-2/surf/lh.thickness.sub-0025034_ses-2_run-2_T1w
- Display thickness: /var/lib/condor/execute/dir_2333949/ds/NYU_2/sub-0025034/ses-2/surf/rh.thickness.sub-0025034_ses-2_run-2_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2333949/ds/NYU_2/sub-0025034/ses-2/sub-0025034_ses-2_run-2_T1w.nii
- Surface ROI estimation: 6s
- Surface and thickness estimation takes: 1157s
- 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 15s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 5s
- ROI estimation of 'aal3' atlas 8s
- ROI estimation of 'mori' atlas 12s
- ROI estimation of 'anatomy3' atlas 17s
- ROI estimation of 'julichbrain' atlas 23s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 9s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 16s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 37s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 55s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 5s
- Write results 5s
- 239s
- Quality check: 7s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2333949/ds/NYU_2/sub-0025034/ses-2/report/catreport_sub-0025034_ses-2_run-2_T1w.pdf
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- CAT preprocessing takes 33 minute(s) and 41 second(s).
- Image Quality Rating (IQR): 78.06% (C+)
- GM volume (GMV): 49.52% (761.33 / 1537.46 ml)
- GM thickness (GMT): 2.55 0.67 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2333949/ds/NYU_2/sub-0025034/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_2333949/ds/NYU_2/sub-0025034/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_2333949/ds/NYU_2/sub-0025034/ses-2/label
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