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- CAT12.8.1 r2040: 1/1: ./sub-0025405/ses-2/sub-0025405_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 55s
- APP: Rough bias correction:
- Initialize 4s
- Estimate background 5s
- Initial correction 5s
- Refine background 2s
- Final correction 4s
- Final scaling 5s
- 30s
- Correct center-of-mass 7s
- Affine registration 7s
- SPM preprocessing 1 (estimate 1 - TPM registration): 62s
- SPM preprocessing 1 (estimate 2): 53s
- SPM preprocessing 2 (write):
- Write Segmentation 12s
- Update Segmentation 14s
- Update Skull-Stripping 31s
- Update probability maps 7s
- 64s
- Global intensity correction: 11s
- SANLM denoising after intensity normalization (medium): 18s
- Fast Optimized Shooting registration 25s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 2s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 10s
- Estimate local tissue thresholds (WM) 13s
- Estimate local tissue thresholds (GM) 17s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 28s
- 76s
- ROI segmentation (partitioning):
- Atlas -> subject space 6s
- Major structures 2s
- Ventricle detection 9s
- Blood vessel detection 7s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.21) 21s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 4s
- 53s
- 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) 3s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 2s
- 9s
- 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 | 0.0931 0.0000 0.0931 | 32.0000
- 2 | 2.50 | 0.0882 0.0018 0.0900 | 29.4886
- 3 | 2.50 | 0.0868 0.0028 0.0896 | 26.9772
- 4 | 2.50 | 0.0861 0.0032 0.0892 | 24.6107
- 5 | 2.50 | 0.0855 0.0034 0.0889 | 22.6548
- 6 | 2.50 | 0.0851 0.0035 0.0886 | 20.6989
- 7 | 2.50 | 0.0846 0.0037 0.0883 | 18.9688
- 8 | 2.50 | 0.0841 0.0038 0.0879 | 17.4455
- 9 | 2.50 | 0.0837 0.0039 0.0876 | 15.9223
- 10 | 2.50 | 0.0832 0.0040 0.0872 | 14.6627
- 11 | 2.50 | 0.0827 0.0041 0.0868 | 13.4764
- 12 | 2.50 | 0.0822 0.0042 0.0864 | 12.3015
- 13 | 2.50 | 0.0816 0.0044 0.0860 | 11.3776
- 14 | 2.50 | 0.0812 0.0044 0.0856 | 10.4537
- 15 | 2.25 | 0.0818 0.0046 0.0864 | 9.5920
- 16 | 2.25 | 0.0779 0.0065 0.0844 | 8.8725
- 17 | 2.25 | 0.0762 0.0072 0.0834 | 8.1530
- 18 | 2.25 | 0.0752 0.0075 0.0826 | 7.5234
- 19 | 2.25 | 0.0743 0.0076 0.0819 | 6.9630
- 29 | 2.00 | 0.0759 0.0039 0.0798 | 3.3283
- 30 | 2.00 | 0.0701 0.0065 0.0765 | 3.1221
- 31 | 2.00 | 0.0680 0.0074 0.0754 | 2.9160
- 43 | 1.75 | 0.0666 0.0043 0.0709 | 1.5785
- 44 | 1.75 | 0.0621 0.0066 0.0687 | 1.5194
- 45 | 1.75 | 0.0605 0.0075 0.0680 | 1.4626
- 57 | 1.50 | 0.0589 0.0056 0.0644 | 1.0900
- 58 | 1.50 | 0.0557 0.0076 0.0633 | 1.0730
- 59 | 1.50 | 0.0547 0.0082 0.0629 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 186s
- Prepare output 7s
- 193s
- Jacobian determinant (RMS): 0.012 0.047 0.075 0.101 0.127 | 0.133829
- Template Matching: 0.093 0.223 0.204 0.182 0.164 | 0.164118
- Write result maps: 31s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 28s
- CSF distance: 11s
- PBT2x thickness: 28s
- 71s
- Create initial surface 53s
- Topology correction: 52s
- Surface refinement: 52s
- Reduction of surface collisions with optimization: 40s
- Spherical mapping with areal smoothing 53s
- Spherical registration 218s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 26s
- CSF distance: 10s
- PBT2x thickness: 27s
- 67s
- Create initial surface 49s
- Topology correction: 50s
- Surface refinement: 41s
- Reduction of surface collisions with optimization: 37s
- Spherical mapping with areal smoothing 55s
- Spherical registration 207s
- Final surface processing results:
- Average thickness (FS): 2.4875 0.7039 mm
- Surface intensity / position RMSE: 0.0640 / 0.0638
- Euler number / defect number / defect size: 10.0 / 11.5 / 0.44%
- Display thickness: /var/lib/condor/execute/dir_2359706/ds/LMU_3/sub-0025405/ses-2/surf/lh.thickness.sub-0025405_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2359706/ds/LMU_3/sub-0025405/ses-2/surf/rh.thickness.sub-0025405_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2359706/ds/LMU_3/sub-0025405/ses-2/sub-0025405_ses-2_run-1_T1w.nii
- Surface ROI estimation: 6s
- Surface and thickness estimation takes: 1106s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 6s
- ROI estimation of 'neuromorphometrics' atlas 20s
- ROI estimation of 'lpba40' atlas 6s
- ROI estimation of 'hammers' atlas 14s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 5s
- ROI estimation of 'aal3' atlas 8s
- ROI estimation of 'mori' atlas 11s
- ROI estimation of 'anatomy3' atlas 17s
- ROI estimation of 'julichbrain' atlas 22s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 9s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 15s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 35s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 51s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 4s
- Write results 5s
- 226s
- Quality check: 7s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2359706/ds/LMU_3/sub-0025405/ses-2/report/catreport_sub-0025405_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 35 minute(s) and 59 second(s).
- Image Quality Rating (IQR): 80.06% (B-)
- GM volume (GMV): 43.93% (596.64 / 1358.05 ml)
- GM thickness (GMT): 2.49 0.70 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2359706/ds/LMU_3/sub-0025405/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_2359706/ds/LMU_3/sub-0025405/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_2359706/ds/LMU_3/sub-0025405/ses-2/label
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