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- CAT12.8.1 r2040: 1/1: ./sub-0025421/ses-2/sub-0025421_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 28s
- APP: Rough bias correction:
- Initialize 5s
- Estimate background 4s
- Initial correction 5s
- Refine background 3s
- Final correction 4s
- Final scaling 4s
- 31s
- Correct center-of-mass 3s
- Affine registration 7s
- SPM preprocessing 1 (estimate 1 - TPM registration): 61s
- SPM preprocessing 1 (estimate 2): 58s
- SPM preprocessing 2 (write):
- Write Segmentation 12s
- Update Segmentation 14s
- Update Skull-Stripping 32s
- Update probability maps 7s
- 64s
- Global intensity correction: 11s
- SANLM denoising after intensity normalization (medium): 17s
- Fast Optimized Shooting registration 25s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 2s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.03) 9s
- Estimate local tissue thresholds (WM) 12s
- Estimate local tissue thresholds (GM) 17s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 29s
- 75s
- ROI segmentation (partitioning):
- Atlas -> subject space 5s
- Major structures 2s
- Ventricle detection 7s
- Blood vessel detection 6s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.15) 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): 22s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.05]
- 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
- 7s
- 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 | 0.0856 0.0000 0.0856 | 32.0000
- 2 | 2.50 | 0.0828 0.0013 0.0841 | 29.4886
- 3 | 2.50 | 0.0820 0.0019 0.0839 | 26.9772
- 4 | 2.50 | 0.0816 0.0021 0.0837 | 24.6107
- 5 | 2.50 | 0.0812 0.0023 0.0835 | 22.6548
- 6 | 2.50 | 0.0809 0.0024 0.0833 | 20.6989
- 7 | 2.50 | 0.0807 0.0025 0.0831 | 18.9688
- 8 | 2.50 | 0.0803 0.0026 0.0829 | 17.4455
- 9 | 2.50 | 0.0800 0.0027 0.0827 | 15.9223
- 10 | 2.50 | 0.0797 0.0028 0.0825 | 14.6627
- 11 | 2.50 | 0.0794 0.0029 0.0822 | 13.4764
- 12 | 2.50 | 0.0790 0.0029 0.0820 | 12.3015
- 13 | 2.50 | 0.0787 0.0030 0.0817 | 11.3776
- 14 | 2.50 | 0.0783 0.0031 0.0814 | 10.4537
- 15 | 2.25 | 0.0776 0.0032 0.0808 | 9.5920
- 16 | 2.25 | 0.0743 0.0048 0.0791 | 8.8725
- 29 | 2.00 | 0.0754 0.0021 0.0775 | 3.3283
- 30 | 2.00 | 0.0688 0.0048 0.0736 | 3.1221
- 31 | 2.00 | 0.0665 0.0058 0.0724 | 2.9160
- 43 | 1.75 | 0.0653 0.0034 0.0687 | 1.5785
- 44 | 1.75 | 0.0610 0.0057 0.0666 | 1.5194
- 45 | 1.75 | 0.0595 0.0064 0.0660 | 1.4626
- 57 | 1.50 | 0.0580 0.0047 0.0627 | 1.0900
- 58 | 1.50 | 0.0550 0.0066 0.0616 | 1.0730
- 59 | 1.50 | 0.0540 0.0073 0.0613 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 141s
- Prepare output 7s
- 148s
- Jacobian determinant (RMS): 0.011 0.039 0.061 0.087 0.109 | 0.115200
- Template Matching: 0.086 0.223 0.200 0.179 0.162 | 0.162069
- Write result maps: 29s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 21s
- CSF distance: 10s
- PBT2x thickness: 28s
- 63s
- Create initial surface 51s
- Topology correction: 51s
- Surface refinement: 62s
- Reduction of surface collisions with optimization: 38s
- Spherical mapping with areal smoothing 54s
- Spherical registration 204s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 19s
- CSF distance: 9s
- PBT2x thickness: 27s
- 59s
- Create initial surface 49s
- Topology correction: 52s
- Surface refinement: 48s
- Reduction of surface collisions with optimization: 35s
- Spherical mapping with areal smoothing 51s
- Spherical registration 200s
- Final surface processing results:
- Average thickness (FS): 2.4921 0.6517 mm
- Surface intensity / position RMSE: 0.0650 / 0.0634
- Euler number / defect number / defect size: 6.0 / 7.5 / 0.07%
- Display thickness: /var/lib/condor/execute/dir_2789911/ds/LMU_3/sub-0025421/ses-2/surf/lh.thickness.sub-0025421_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2789911/ds/LMU_3/sub-0025421/ses-2/surf/rh.thickness.sub-0025421_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2789911/ds/LMU_3/sub-0025421/ses-2/sub-0025421_ses-2_run-1_T1w.nii
- Surface ROI estimation: 6s
- Surface and thickness estimation takes: 1079s
- 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 15s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 5s
- ROI estimation of 'aal3' atlas 8s
- ROI estimation of 'mori' atlas 12s
- ROI estimation of 'anatomy3' atlas 19s
- ROI estimation of 'julichbrain' atlas 24s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 10s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 19s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 42s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 60s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s
- Write results 7s
- 254s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2789911/ds/LMU_3/sub-0025421/ses-2/report/catreport_sub-0025421_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 33 minute(s) and 51 second(s).
- Image Quality Rating (IQR): 82.51% (B-)
- GM volume (GMV): 46.56% (597.76 / 1283.98 ml)
- GM thickness (GMT): 2.49 0.65 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2789911/ds/LMU_3/sub-0025421/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_2789911/ds/LMU_3/sub-0025421/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_2789911/ds/LMU_3/sub-0025421/ses-2/label
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