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- CAT12.8.1 r2040: 1/1: ./sub-0026131/ses-2/sub-0026131_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 36s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 4s
- Initial correction 4s
- Refine background 2s
- Final correction 3s
- Final scaling 4s
- 26s
- Correct center-of-mass 3s
- Affine registration 6s
- SPM preprocessing 1 (estimate 1 - TPM registration): 58s
- SPM preprocessing 1 (estimate 2): 49s
- SPM preprocessing 2 (write):
- Write Segmentation 12s
- Update Segmentation 14s
- Update Skull-Stripping 30s
- Update probability maps 7s
- 63s
- Global intensity correction: 11s
- SANLM denoising after intensity normalization (medium): 18s
- Fast Optimized Shooting registration 27s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 2s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.01) 9s
- Estimate local tissue thresholds (WM) 12s
- Estimate local tissue thresholds (GM) 18s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 33s
- 79s
- ROI segmentation (partitioning):
- Atlas -> subject space 5s
- Major structures 2s
- Ventricle detection 7s
- Blood vessel detection 6s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.34) 13s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 3s
- 40s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 24s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- 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 | 0.0940 0.0000 0.0940 | 32.0000
- 2 | 2.50 | 0.0909 0.0014 0.0923 | 29.4886
- 3 | 2.50 | 0.0899 0.0021 0.0920 | 26.9772
- 4 | 2.50 | 0.0894 0.0024 0.0918 | 24.6107
- 5 | 2.50 | 0.0891 0.0026 0.0916 | 22.6548
- 6 | 2.50 | 0.0887 0.0027 0.0914 | 20.6989
- 7 | 2.50 | 0.0883 0.0029 0.0912 | 18.9688
- 8 | 2.50 | 0.0880 0.0030 0.0910 | 17.4455
- 9 | 2.50 | 0.0876 0.0031 0.0907 | 15.9223
- 10 | 2.50 | 0.0872 0.0033 0.0904 | 14.6627
- 11 | 2.50 | 0.0868 0.0034 0.0902 | 13.4764
- 12 | 2.50 | 0.0863 0.0035 0.0898 | 12.3015
- 13 | 2.50 | 0.0859 0.0037 0.0896 | 11.3776
- 14 | 2.50 | 0.0855 0.0038 0.0892 | 10.4537
- 15 | 2.25 | 0.0865 0.0039 0.0904 | 9.5920
- 16 | 2.25 | 0.0826 0.0059 0.0885 | 8.8725
- 17 | 2.25 | 0.0810 0.0066 0.0876 | 8.1530
- 18 | 2.25 | 0.0800 0.0069 0.0869 | 7.5234
- 19 | 2.25 | 0.0792 0.0071 0.0863 | 6.9630
- 20 | 2.25 | 0.0784 0.0072 0.0856 | 6.4027
- 21 | 2.25 | 0.0777 0.0073 0.0850 | 5.9447
- 22 | 2.25 | 0.0771 0.0073 0.0844 | 5.5083
- 23 | 2.25 | 0.0764 0.0073 0.0837 | 5.0803
- 24 | 2.25 | 0.0758 0.0074 0.0832 | 4.7404
- 25 | 2.25 | 0.0752 0.0073 0.0826 | 4.4005
- 26 | 2.25 | 0.0747 0.0073 0.0820 | 4.0868
- 29 | 2.00 | 0.0763 0.0062 0.0824 | 3.3283
- 30 | 2.00 | 0.0729 0.0077 0.0805 | 3.1221
- 43 | 1.75 | 0.0714 0.0042 0.0756 | 1.5785
- 44 | 1.75 | 0.0657 0.0072 0.0729 | 1.5194
- 45 | 1.75 | 0.0638 0.0082 0.0720 | 1.4626
- 57 | 1.50 | 0.0620 0.0061 0.0681 | 1.0900
- 58 | 1.50 | 0.0584 0.0085 0.0669 | 1.0730
- 59 | 1.50 | 0.0572 0.0092 0.0664 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 153s
- Prepare output 7s
- 160s
- Jacobian determinant (RMS): 0.013 0.051 0.091 0.120 0.155 | 0.164985
- Template Matching: 0.094 0.224 0.219 0.191 0.172 | 0.171538
- Write result maps: 30s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 25s
- CSF distance: 9s
- PBT2x thickness: 27s
- 65s
- Create initial surface 50s
- Topology correction: 48s
- Surface refinement: 42s
- Reduction of surface collisions with optimization: 32s
- Spherical mapping with areal smoothing 50s
- Spherical registration 213s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 18s
- CSF distance: 10s
- PBT2x thickness: 27s
- 59s
- Create initial surface 52s
- Topology correction: 50s
- Surface refinement: 44s
- Reduction of surface collisions with optimization: 35s
- Spherical mapping with areal smoothing 75s
- Spherical registration 236s
- Final surface processing results:
- Average thickness (FS): 2.3841 0.6609 mm
- Surface intensity / position RMSE: 0.0568 / 0.0526
- Euler number / defect number / defect size: 8.0 / 8.5 / 0.13%
- Display thickness: /var/lib/condor/execute/dir_3631435/ds/UM/sub-0026131/ses-2/surf/lh.thickness.sub-0026131_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3631435/ds/UM/sub-0026131/ses-2/surf/rh.thickness.sub-0026131_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3631435/ds/UM/sub-0026131/ses-2/sub-0026131_ses-2_run-1_T1w.nii
- Surface ROI estimation: 8s
- Surface and thickness estimation takes: 1117s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 11s
- ROI estimation of 'neuromorphometrics' atlas 43s
- ROI estimation of 'lpba40' atlas 12s
- ROI estimation of 'hammers' atlas 28s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 10s
- ROI estimation of 'aal3' atlas 18s
- ROI estimation of 'mori' atlas 26s
- ROI estimation of 'anatomy3' atlas 35s
- ROI estimation of 'julichbrain' atlas 44s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 20s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 36s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 61s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 82s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s
- Write results 8s
- 436s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3631435/ds/UM/sub-0026131/ses-2/report/catreport_sub-0026131_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 38 minute(s) and 36 second(s).
- Image Quality Rating (IQR): 81.95% (B-)
- GM volume (GMV): 43.46% (541.99 / 1247.09 ml)
- GM thickness (GMT): 2.38 0.66 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3631435/ds/UM/sub-0026131/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_3631435/ds/UM/sub-0026131/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_3631435/ds/UM/sub-0026131/ses-2/label
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