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- CAT12.8.1 r2040: 1/1: ./sub-0025250/ses-2/sub-0025250_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 38s
- APP: Rough bias correction:
- Initialize 4s
- Estimate background 3s
- Initial correction 3s
- Refine background 2s
- Final correction 3s
- Final scaling 3s
- 22s
- Correct center-of-mass 3s
- Affine registration 5s
- SPM preprocessing 1 (estimate 1 - TPM registration): 51s
- SPM preprocessing 1 (estimate 2): 39s
- SPM preprocessing 2 (write):
- Write Segmentation 10s
- Update Segmentation 13s
- Update Skull-Stripping 24s
- Update probability maps 5s
- 52s
- Global intensity correction: 9s
- SANLM denoising after intensity normalization (medium): 19s
- Fast Optimized Shooting registration 21s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 2s
- Prepare partitions 1s
- Prepare segments (LASmod = 1.00) 10s
- Estimate local tissue thresholds (WM) 11s
- Estimate local tissue thresholds (GM) 17s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 24s
- 67s
- ROI segmentation (partitioning):
- Atlas -> subject space 4s
- Major structures 2s
- Ventricle detection 8s
- Blood vessel detection 6s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 15s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 3s
- 42s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 24s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- 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 | 0.0850 0.0000 0.0850 | 32.0000
- 2 | 2.50 | 0.0818 0.0013 0.0831 | 29.4886
- 3 | 2.50 | 0.0809 0.0020 0.0829 | 26.9772
- 4 | 2.50 | 0.0805 0.0023 0.0827 | 24.6107
- 5 | 2.50 | 0.0801 0.0025 0.0826 | 22.6548
- 6 | 2.50 | 0.0798 0.0026 0.0824 | 20.6989
- 7 | 2.50 | 0.0795 0.0027 0.0821 | 18.9688
- 8 | 2.50 | 0.0791 0.0028 0.0819 | 17.4455
- 9 | 2.50 | 0.0788 0.0029 0.0817 | 15.9223
- 10 | 2.50 | 0.0785 0.0030 0.0814 | 14.6627
- 11 | 2.50 | 0.0781 0.0031 0.0812 | 13.4764
- 12 | 2.50 | 0.0777 0.0031 0.0809 | 12.3015
- 13 | 2.50 | 0.0774 0.0033 0.0806 | 11.3776
- 14 | 2.50 | 0.0770 0.0033 0.0803 | 10.4537
- 15 | 2.25 | 0.0764 0.0034 0.0798 | 9.5920
- 16 | 2.25 | 0.0731 0.0051 0.0781 | 8.8725
- 29 | 2.00 | 0.0736 0.0023 0.0759 | 3.3283
- 30 | 2.00 | 0.0673 0.0048 0.0722 | 3.1221
- 31 | 2.00 | 0.0652 0.0058 0.0710 | 2.9160
- 43 | 1.75 | 0.0640 0.0034 0.0674 | 1.5785
- 44 | 1.75 | 0.0599 0.0055 0.0654 | 1.5194
- 45 | 1.75 | 0.0586 0.0062 0.0648 | 1.4626
- 57 | 1.50 | 0.0571 0.0046 0.0617 | 1.0900
- 58 | 1.50 | 0.0541 0.0065 0.0606 | 1.0730
- 59 | 1.50 | 0.0532 0.0071 0.0603 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 107s
- Prepare output 7s
- 114s
- Jacobian determinant (RMS): 0.012 0.045 0.068 0.094 0.117 | 0.123272
- Template Matching: 0.085 0.219 0.196 0.176 0.160 | 0.159524
- Write result maps: 20s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 20s
- CSF distance: 10s
- PBT2x thickness: 31s
- 65s
- Create initial surface 54s
- Topology correction: 66s
- Surface refinement: 73s
- Reduction of surface collisions with optimization: 49s
- Spherical mapping with areal smoothing 59s
- Spherical registration 188s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 20s
- CSF distance: 11s
- PBT2x thickness: 30s
- 65s
- Create initial surface 56s
- Topology correction: 67s
- Surface refinement: 50s
- Reduction of surface collisions with optimization: 50s
- Spherical mapping with areal smoothing 66s
- Spherical registration 205s
- Final surface processing results:
- Average thickness (FS): 2.6410 0.6665 mm
- Surface intensity / position RMSE: 0.0723 / 0.0725
- Euler number / defect number / defect size: 32.0 / 16.0 / 0.75%
- Display thickness: /var/lib/condor/execute/dir_2683987/ds/UPSM_1/sub-0025250/ses-2/surf/lh.thickness.sub-0025250_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2683987/ds/UPSM_1/sub-0025250/ses-2/surf/rh.thickness.sub-0025250_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2683987/ds/UPSM_1/sub-0025250/ses-2/sub-0025250_ses-2_run-1_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1180s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 5s
- ROI estimation of 'neuromorphometrics' atlas 19s
- ROI estimation of 'lpba40' atlas 5s
- ROI estimation of 'hammers' atlas 13s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 5s
- ROI estimation of 'aal3' atlas 7s
- ROI estimation of 'mori' atlas 10s
- ROI estimation of 'anatomy3' atlas 15s
- ROI estimation of 'julichbrain' atlas 20s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 8s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 14s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 32s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 49s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 4s
- Write results 5s
- 208s
- Quality check: 7s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2683987/ds/UPSM_1/sub-0025250/ses-2/report/catreport_sub-0025250_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 33 minute(s) and 0 second(s).
- Image Quality Rating (IQR): 80.00% (B-)
- GM volume (GMV): 52.06% (788.96 / 1515.55 ml)
- GM thickness (GMT): 2.64 0.67 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2683987/ds/UPSM_1/sub-0025250/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_2683987/ds/UPSM_1/sub-0025250/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_2683987/ds/UPSM_1/sub-0025250/ses-2/label
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