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- CAT12.8.1 r2040: 1/1: ./sub-0027250/ses-2/sub-0027250_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 51s
- APP: Rough bias correction:
- Initialize 7s
- Estimate background 7s
- Initial correction 7s
- Refine background 3s
- Final correction 6s
- Final scaling 5s
- 43s
- Correct center-of-mass 7s
- Affine registration 11s
- SPM preprocessing 1 (estimate 1 - TPM registration): 17s
- Use initial fine affine registration. 7s
- Use previous fine affine registration. 64s
- SPM preprocessing 1 (estimate 2): 65s
- SPM preprocessing 2 (write):
- Write Segmentation 20s
- Update Segmentation 21s
- Update Skull-Stripping 49s
- Update probability maps 10s
- 101s
- Global intensity correction: 20s
- SANLM denoising after intensity normalization (medium): 29s
- Fast Optimized Shooting registration 41s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 16s
- Estimate local tissue thresholds (WM) 22s
- Estimate local tissue thresholds (GM) 33s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 50s
- 132s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 14s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.07) 26s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 72s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 37s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.670.08,0.990.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 5s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 3s
- 13s
- 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 | 0.0859 0.0000 0.0859 | 32.0000
- 2 | 2.50 | 0.0833 0.0012 0.0844 | 29.4886
- 3 | 2.50 | 0.0825 0.0018 0.0843 | 26.9772
- 4 | 2.50 | 0.0821 0.0020 0.0841 | 24.6107
- 5 | 2.50 | 0.0818 0.0021 0.0839 | 22.6548
- 6 | 2.50 | 0.0815 0.0022 0.0837 | 20.6989
- 7 | 2.50 | 0.0812 0.0023 0.0836 | 18.9688
- 8 | 2.50 | 0.0809 0.0024 0.0834 | 17.4455
- 9 | 2.50 | 0.0807 0.0025 0.0832 | 15.9223
- 10 | 2.50 | 0.0803 0.0026 0.0829 | 14.6627
- 11 | 2.50 | 0.0800 0.0027 0.0827 | 13.4764
- 12 | 2.50 | 0.0797 0.0027 0.0825 | 12.3015
- 13 | 2.50 | 0.0794 0.0028 0.0822 | 11.3776
- 14 | 2.50 | 0.0791 0.0029 0.0820 | 10.4537
- 15 | 2.25 | 0.0785 0.0030 0.0815 | 9.5920
- 16 | 2.25 | 0.0754 0.0045 0.0799 | 8.8725
- 17 | 2.25 | 0.0742 0.0051 0.0793 | 8.1530
- 29 | 2.00 | 0.0762 0.0023 0.0785 | 3.3283
- 30 | 2.00 | 0.0700 0.0049 0.0749 | 3.1221
- 31 | 2.00 | 0.0678 0.0060 0.0738 | 2.9160
- 43 | 1.75 | 0.0667 0.0034 0.0701 | 1.5785
- 44 | 1.75 | 0.0618 0.0060 0.0678 | 1.5194
- 45 | 1.75 | 0.0602 0.0068 0.0671 | 1.4626
- 57 | 1.50 | 0.0586 0.0050 0.0635 | 1.0900
- 58 | 1.50 | 0.0553 0.0071 0.0624 | 1.0730
- 59 | 1.50 | 0.0543 0.0077 0.0620 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 210s
- Prepare output 13s
- 224s
- Jacobian determinant (RMS): 0.010 0.037 0.059 0.085 0.109 | 0.115155
- Template Matching: 0.086 0.223 0.203 0.181 0.163 | 0.162781
- Write result maps: 46s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 29s
- CSF distance: 17s
- PBT2x thickness: 50s
- 102s
- Create initial surface 87s
- Topology correction: 83s
- Surface refinement: 100s
- Reduction of surface collisions with optimization: 62s
- Spherical mapping with areal smoothing 88s
- Spherical registration 323s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 33s
- CSF distance: 16s
- PBT2x thickness: 49s
- 105s
- Create initial surface 85s
- Topology correction: 82s
- Surface refinement: 75s
- Reduction of surface collisions with optimization: 61s
- Spherical mapping with areal smoothing 89s
- Spherical registration 319s
- Final surface processing results:
- Average thickness (FS): 2.5714 0.6644 mm
- Surface intensity / position RMSE: 0.0605 / 0.0623
- Euler number / defect number / defect size: 16.0 / 7.0 / 0.39%
- Display thickness: /var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-2/surf/lh.thickness.sub-0027250_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-2/surf/rh.thickness.sub-0027250_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-2/sub-0027250_ses-2_run-1_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 1764s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 34s
- ROI estimation of 'lpba40' atlas 10s
- ROI estimation of 'hammers' atlas 25s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 9s
- ROI estimation of 'aal3' atlas 15s
- ROI estimation of 'mori' atlas 22s
- ROI estimation of 'anatomy3' atlas 31s
- ROI estimation of 'julichbrain' atlas 42s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 31s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 76s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 123s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 11s
- Write results 13s
- 460s
- Quality check: 16s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-2/report/catreport_sub-0027250_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 55 minute(s) and 21 second(s).
- Image Quality Rating (IQR): 84.40% (B)
- GM volume (GMV): 47.21% (604.75 / 1280.88 ml)
- GM thickness (GMT): 2.57 0.66 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-2/label
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