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- CAT12.8.1 r1980: 1/1: ./dir_12661/ds/sub-040/sub-040_ses-t0_T1w.n
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- SANLM denoising (medium): 25s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 8s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 7s
- 41s
- Correct center-of-mass 4s
- Affine registration 16s
- SPM preprocessing 1 (estimate 1 - TPM registration): 69s
- SPM preprocessing 1 (estimate 2): 65s
- SPM preprocessing 2 (write):
- Write Segmentation 16s
- Update Segmentation 18s
- Update Skull-Stripping 39s
- Update probability maps 8s
- 81s
- Global intensity correction: 15s
- SANLM denoising after intensity normalization (medium): 21s
- Fast Optimized Shooting registration 31s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.22) 14s
- Estimate local tissue thresholds (WM) 17s
- Estimate local tissue thresholds (GM) 21s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 30s
- 91s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 14s
- Blood vessel detection 9s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.10) 26s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 4s
- 69s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 34s
- 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) 2s
- Level 3 cleanup (CSF/WM PVE) 3s
- 12s
- 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 | 0.0868 0.0000 0.0868 | 32.0000
- 2 | 2.50 | 0.0836 0.0014 0.0850 | 29.4886
- 3 | 2.50 | 0.0826 0.0021 0.0847 | 26.9772
- 4 | 2.50 | 0.0822 0.0023 0.0845 | 24.6107
- 5 | 2.50 | 0.0818 0.0025 0.0843 | 22.6548
- 6 | 2.50 | 0.0815 0.0026 0.0841 | 20.6989
- 7 | 2.50 | 0.0812 0.0027 0.0839 | 18.9688
- 8 | 2.50 | 0.0808 0.0028 0.0837 | 17.4455
- 9 | 2.50 | 0.0805 0.0029 0.0834 | 15.9223
- 10 | 2.50 | 0.0801 0.0030 0.0831 | 14.6627
- 11 | 2.50 | 0.0797 0.0031 0.0829 | 13.4764
- 12 | 2.50 | 0.0794 0.0032 0.0826 | 12.3015
- 13 | 2.50 | 0.0790 0.0033 0.0823 | 11.3776
- 14 | 2.50 | 0.0786 0.0034 0.0820 | 10.4537
- 15 | 2.25 | 0.0789 0.0035 0.0823 | 9.5920
- 16 | 2.25 | 0.0755 0.0051 0.0806 | 8.8725
- 17 | 2.25 | 0.0741 0.0057 0.0798 | 8.1530
- 29 | 2.00 | 0.0761 0.0026 0.0787 | 3.3283
- 30 | 2.00 | 0.0700 0.0052 0.0752 | 3.1221
- 31 | 2.00 | 0.0680 0.0062 0.0741 | 2.9160
- 43 | 1.75 | 0.0670 0.0035 0.0706 | 1.5785
- 44 | 1.75 | 0.0624 0.0060 0.0684 | 1.5194
- 45 | 1.75 | 0.0609 0.0068 0.0677 | 1.4626
- 57 | 1.50 | 0.0595 0.0050 0.0645 | 1.0900
- 58 | 1.50 | 0.0561 0.0072 0.0633 | 1.0730
- 59 | 1.50 | 0.0550 0.0079 0.0629 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 170s
- Prepare output 10s
- 180s
- Jacobian determinant (RMS): 0.012 0.043 0.066 0.093 0.119 | 0.126772
- Template Matching: 0.087 0.222 0.204 0.183 0.165 | 0.164995
- Write result maps: 24s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 57s
- CSF distance: 15s
- PBT2x thickness: 42s
- 120s
- Create initial surface 81s
- Topology correction: 92s
- Surface refinement: 97s
- Reduction of surface collisions with optimization: 68s
- Spherical mapping with areal smoothing 77s
- Spherical registration 269s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 37s
- CSF distance: 15s
- PBT2x thickness: 42s
- 100s
- Create initial surface 82s
- Topology correction: 90s
- Surface refinement: 87s
- Reduction of surface collisions with optimization: 65s
- Spherical mapping with areal smoothing 78s
- Spherical registration 304s
- Final surface processing results:
- Average thickness (FS): 2.4192 0.6304 mm
- Surface intensity / position RMSE: 0.0618 / 0.0641
- Euler number / defect number / defect size: 10.0 / 8.5 / 0.64%
- Display thickness: /var/lib/condor/execute/dir_12661/ds/sub-040/surf/lh.thickness.sub-040_ses-t0_T1w
- Display thickness: /var/lib/condor/execute/dir_12661/ds/sub-040/surf/rh.thickness.sub-040_ses-t0_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_12661/ds/sub-040/sub-040_ses-t0_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 1701s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 36s
- ROI estimation of 'lpba40' atlas 14s
- ROI estimation of 'hammers' atlas 27s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 9s
- ROI estimation of 'aal3' atlas 19s
- ROI estimation of 'mori' atlas 29s
- ROI estimation of 'anatomy3' atlas 43s
- ROI estimation of 'julichbrain' atlas 64s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 20s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 40s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 77s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 113s
- Write results 114s
- 503s
- Quality check: 6s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_12661/ds/sub-040/report/catreport_sub-040_ses-t0_T1w.pdf
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- CAT preprocessing takes 51 minute(s) and 26 second(s).
- Image Quality Rating (IQR): 83.78% (B)
- GM volume (GMV): 42.99% (638.68 / 1485.52 ml)
- GM thickness (GMT): 2.42 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_12661/ds/sub-040/mri
- Reports are saved in /var/lib/condor/execute/dir_12661/ds/sub-040/report
- Labels are saved in /var/lib/condor/execute/dir_12661/ds/sub-040/label
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