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- CAT12.8.1 r2040: 1/1: ./sub-0027360/ses-1/sub-0027360_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 48s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 6s
- Initial correction 9s
- Refine background 4s
- Final correction 6s
- Final scaling 5s
- 46s
- Correct center-of-mass 5s
- Affine registration 13s
- SPM preprocessing 1 (estimate 1 - TPM registration): 89s
- SPM preprocessing 1 (estimate 2): 77s
- SPM preprocessing 2 (write):
- Write Segmentation 21s
- Update Segmentation 22s
- Update Skull-Stripping 51s
- Update probability maps 11s
- 104s
- Global intensity correction: 20s
- SANLM denoising after intensity normalization (medium): 29s
- Fast Optimized Shooting registration 36s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 4s
- Prepare segments (LASmod = 1.08) 16s
- Estimate local tissue thresholds (WM) 21s
- Estimate local tissue thresholds (GM) 32s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 50s
- 132s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 17s
- Blood vessel detection 10s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 28s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 5s
- 78s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 40s
- AMAP peaks: [CSF,GM,WM] = [0.370.05,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 5s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 3s
- 13s
- 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 | 0.0841 0.0000 0.0841 | 32.0000
- 2 | 2.50 | 0.0813 0.0013 0.0826 | 29.4886
- 3 | 2.50 | 0.0805 0.0019 0.0824 | 26.9772
- 4 | 2.50 | 0.0801 0.0021 0.0822 | 24.6107
- 5 | 2.50 | 0.0798 0.0023 0.0821 | 22.6548
- 6 | 2.50 | 0.0795 0.0024 0.0819 | 20.6989
- 7 | 2.50 | 0.0792 0.0025 0.0817 | 18.9688
- 8 | 2.50 | 0.0789 0.0026 0.0815 | 17.4455
- 9 | 2.50 | 0.0786 0.0027 0.0813 | 15.9223
- 10 | 2.50 | 0.0782 0.0028 0.0810 | 14.6627
- 11 | 2.50 | 0.0779 0.0029 0.0808 | 13.4764
- 12 | 2.50 | 0.0776 0.0030 0.0805 | 12.3015
- 13 | 2.50 | 0.0772 0.0031 0.0803 | 11.3776
- 14 | 2.50 | 0.0769 0.0032 0.0800 | 10.4537
- 15 | 2.25 | 0.0758 0.0032 0.0790 | 9.5920
- 16 | 2.25 | 0.0727 0.0048 0.0775 | 8.8725
- 29 | 2.00 | 0.0734 0.0022 0.0756 | 3.3283
- 30 | 2.00 | 0.0673 0.0046 0.0719 | 3.1221
- 31 | 2.00 | 0.0652 0.0056 0.0708 | 2.9160
- 43 | 1.75 | 0.0642 0.0032 0.0674 | 1.5785
- 44 | 1.75 | 0.0602 0.0054 0.0655 | 1.5194
- 45 | 1.75 | 0.0588 0.0061 0.0649 | 1.4626
- 57 | 1.50 | 0.0573 0.0045 0.0618 | 1.0900
- 58 | 1.50 | 0.0544 0.0064 0.0608 | 1.0730
- 59 | 1.50 | 0.0534 0.0070 0.0604 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 181s
- Prepare output 12s
- 193s
- Jacobian determinant (RMS): 0.013 0.045 0.067 0.091 0.113 | 0.119413
- Template Matching: 0.084 0.218 0.196 0.177 0.160 | 0.160136
- Write result maps: 43s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 28s
- CSF distance: 16s
- PBT2x thickness: 45s
- 95s
- Create initial surface 86s
- Topology correction: 93s
- Surface refinement: 83s
- Reduction of surface collisions with optimization: 70s
- Spherical mapping with areal smoothing 79s
- Spherical registration 285s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 26s
- CSF distance: 15s
- PBT2x thickness: 45s
- 92s
- Create initial surface 85s
- Topology correction: 94s
- Surface refinement: 101s
- Reduction of surface collisions with optimization: 70s
- Spherical mapping with areal smoothing 88s
- Spherical registration 306s
- Final surface processing results:
- Average thickness (FS): 2.5740 0.6094 mm
- Surface intensity / position RMSE: 0.0654 / 0.0630
- Euler number / defect number / defect size: 28.0 / 18.0 / 0.84%
- Display thickness: /var/lib/condor/execute/dir_671787/ds/DC_1/sub-0027360/ses-1/surf/lh.thickness.sub-0027360_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_671787/ds/DC_1/sub-0027360/ses-1/surf/rh.thickness.sub-0027360_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_671787/ds/DC_1/sub-0027360/ses-1/sub-0027360_ses-1_run-1_T1w.nii
- Surface ROI estimation: 13s
- Surface and thickness estimation takes: 1735s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 13s
- ROI estimation of 'neuromorphometrics' atlas 61s
- ROI estimation of 'lpba40' atlas 16s
- ROI estimation of 'hammers' atlas 41s
- ROI estimation of 'thalamus' atlas 4s
- ROI estimation of 'ibsr' atlas 17s
- ROI estimation of 'aal3' atlas 27s
- ROI estimation of 'mori' atlas 39s
- ROI estimation of 'anatomy3' atlas 56s
- ROI estimation of 'julichbrain' atlas 74s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 31s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 58s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 100s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 137s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 12s
- Write results 13s
- 687s
- Quality check: 15s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_671787/ds/DC_1/sub-0027360/ses-1/report/catreport_sub-0027360_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 58 minute(s) and 19 second(s).
- Image Quality Rating (IQR): 79.04% (C+)
- GM volume (GMV): 51.04% (736.59 / 1443.15 ml)
- GM thickness (GMT): 2.57 0.61 mm
- Segmentations are saved in /var/lib/condor/execute/dir_671787/ds/DC_1/sub-0027360/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_671787/ds/DC_1/sub-0027360/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_671787/ds/DC_1/sub-0027360/ses-1/label
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