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- CAT12.8.1 r2040: 1/1: ./sub-0025665/ses-2/sub-0025665_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 41s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 5s
- Initial correction 5s
- Refine background 3s
- Final correction 4s
- Final scaling 4s
- 33s
- Correct center-of-mass 3s
- Affine registration 8s
- SPM preprocessing 1 (estimate 1 - TPM registration): 69s
- SPM preprocessing 1 (estimate 2): 63s
- SPM preprocessing 2 (write):
- Write Segmentation 16s
- Update Segmentation 17s
- Update Skull-Stripping 39s
- Update probability maps 8s
- 79s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 22s
- Fast Optimized Shooting registration 32s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.16) 12s
- Estimate local tissue thresholds (WM) 17s
- Estimate local tissue thresholds (GM) 25s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 44s
- 107s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 10s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.19) 21s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 57s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 31s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 3s
- 10s
- 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 | 0.0913 0.0000 0.0913 | 32.0000
- 2 | 2.50 | 0.0878 0.0014 0.0893 | 29.4886
- 3 | 2.50 | 0.0868 0.0022 0.0890 | 26.9772
- 4 | 2.50 | 0.0862 0.0025 0.0888 | 24.6107
- 5 | 2.50 | 0.0858 0.0027 0.0885 | 22.6548
- 6 | 2.50 | 0.0854 0.0029 0.0883 | 20.6989
- 7 | 2.50 | 0.0850 0.0030 0.0880 | 18.9688
- 8 | 2.50 | 0.0846 0.0032 0.0878 | 17.4455
- 9 | 2.50 | 0.0842 0.0033 0.0875 | 15.9223
- 10 | 2.50 | 0.0838 0.0034 0.0872 | 14.6627
- 11 | 2.50 | 0.0833 0.0036 0.0869 | 13.4764
- 12 | 2.50 | 0.0829 0.0037 0.0866 | 12.3015
- 13 | 2.50 | 0.0824 0.0038 0.0862 | 11.3776
- 14 | 2.50 | 0.0820 0.0039 0.0859 | 10.4537
- 15 | 2.25 | 0.0837 0.0040 0.0878 | 9.5920
- 16 | 2.25 | 0.0798 0.0060 0.0858 | 8.8725
- 17 | 2.25 | 0.0781 0.0068 0.0849 | 8.1530
- 18 | 2.25 | 0.0770 0.0072 0.0842 | 7.5234
- 19 | 2.25 | 0.0761 0.0074 0.0835 | 6.9630
- 20 | 2.25 | 0.0753 0.0074 0.0827 | 6.4027
- 21 | 2.25 | 0.0746 0.0076 0.0821 | 5.9447
- 29 | 2.00 | 0.0768 0.0045 0.0812 | 3.3283
- 30 | 2.00 | 0.0712 0.0070 0.0783 | 3.1221
- 31 | 2.00 | 0.0692 0.0080 0.0772 | 2.9160
- 43 | 1.75 | 0.0681 0.0045 0.0726 | 1.5785
- 44 | 1.75 | 0.0629 0.0073 0.0702 | 1.5194
- 45 | 1.75 | 0.0612 0.0082 0.0694 | 1.4626
- 57 | 1.50 | 0.0595 0.0060 0.0656 | 1.0900
- 58 | 1.50 | 0.0560 0.0083 0.0644 | 1.0730
- 59 | 1.50 | 0.0549 0.0090 0.0639 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 177s
- Prepare output 10s
- 187s
- Jacobian determinant (RMS): 0.012 0.047 0.079 0.108 0.137 | 0.141272
- Template Matching: 0.091 0.224 0.208 0.184 0.165 | 0.164611
- Write result maps: 33s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 33s
- CSF distance: 14s
- PBT2x thickness: 40s
- 93s
- Create initial surface 77s
- Topology correction: 87s
- Surface refinement: 94s
- Reduction of surface collisions with optimization: 62s
- Spherical mapping with areal smoothing 78s
- Spherical registration 300s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 29s
- CSF distance: 13s
- PBT2x thickness: 39s
- 87s
- Create initial surface 73s
- Topology correction: 82s
- Surface refinement: 71s
- Reduction of surface collisions with optimization: 58s
- Spherical mapping with areal smoothing 72s
- Spherical registration 304s
- Final surface processing results:
- Average thickness (FS): 2.4744 0.6934 mm
- Surface intensity / position RMSE: 0.0686 / 0.0846
- Euler number / defect number / defect size: 28.0 / 10.0 / 1.25%
- Display thickness: /var/lib/condor/execute/dir_3026467/ds/SWU_4/sub-0025665/ses-2/surf/lh.thickness.sub-0025665_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3026467/ds/SWU_4/sub-0025665/ses-2/surf/rh.thickness.sub-0025665_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3026467/ds/SWU_4/sub-0025665/ses-2/sub-0025665_ses-2_run-1_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1627s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 8s
- ROI estimation of 'neuromorphometrics' atlas 29s
- ROI estimation of 'lpba40' atlas 8s
- ROI estimation of 'hammers' atlas 20s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 7s
- ROI estimation of 'aal3' atlas 12s
- ROI estimation of 'mori' atlas 18s
- ROI estimation of 'anatomy3' atlas 25s
- ROI estimation of 'julichbrain' atlas 34s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 14s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 24s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 55s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 80s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s
- Write results 8s
- 344s
- Quality check: 11s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3026467/ds/SWU_4/sub-0025665/ses-2/report/catreport_sub-0025665_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 48 minute(s) and 34 second(s).
- Image Quality Rating (IQR): 81.51% (B-)
- GM volume (GMV): 45.21% (620.67 / 1372.75 ml)
- GM thickness (GMT): 2.47 0.70 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3026467/ds/SWU_4/sub-0025665/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_3026467/ds/SWU_4/sub-0025665/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_3026467/ds/SWU_4/sub-0025665/ses-2/label
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