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- CAT12.8.1 r2040: 1/1: ./sub-0027335/ses-1/sub-0027335_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 33s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 5s
- Initial correction 6s
- Refine background 3s
- Final correction 5s
- Final scaling 4s
- 35s
- Correct center-of-mass 3s
- Affine registration 7s
- SPM preprocessing 1 (estimate 1 - TPM registration): 9s
- Use initial fine affine registration. 53s
- SPM preprocessing 1 (estimate 2): 54s
- SPM preprocessing 2 (write):
- Write Segmentation 16s
- Update Segmentation 16s
- Update Skull-Stripping 37s
- Update probability maps 8s
- 76s
- Global intensity correction: 15s
- SANLM denoising after intensity normalization (medium): 18s
- Fast Optimized Shooting registration 27s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.00) 10s
- Estimate local tissue thresholds (WM) 16s
- Estimate local tissue thresholds (GM) 23s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 35s
- 93s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 2s
- Ventricle detection 7s
- Blood vessel detection 6s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 17s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 4s
- 48s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 25s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.04]
- 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
- 8s
- 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 | 0.0824 0.0000 0.0824 | 32.0000
- 2 | 2.50 | 0.0793 0.0013 0.0806 | 29.4886
- 3 | 2.50 | 0.0783 0.0020 0.0803 | 26.9772
- 4 | 2.50 | 0.0779 0.0023 0.0802 | 24.6107
- 5 | 2.50 | 0.0775 0.0025 0.0800 | 22.6548
- 6 | 2.50 | 0.0772 0.0026 0.0798 | 20.6989
- 7 | 2.50 | 0.0769 0.0027 0.0795 | 18.9688
- 8 | 2.50 | 0.0765 0.0028 0.0793 | 17.4455
- 9 | 2.50 | 0.0762 0.0029 0.0791 | 15.9223
- 10 | 2.50 | 0.0758 0.0030 0.0788 | 14.6627
- 11 | 2.50 | 0.0755 0.0031 0.0786 | 13.4764
- 12 | 2.50 | 0.0751 0.0032 0.0783 | 12.3015
- 13 | 2.50 | 0.0747 0.0033 0.0780 | 11.3776
- 14 | 2.50 | 0.0743 0.0034 0.0777 | 10.4537
- 15 | 2.25 | 0.0743 0.0035 0.0778 | 9.5920
- 16 | 2.25 | 0.0712 0.0050 0.0762 | 8.8725
- 29 | 2.00 | 0.0723 0.0023 0.0746 | 3.3283
- 30 | 2.00 | 0.0661 0.0048 0.0709 | 3.1221
- 31 | 2.00 | 0.0638 0.0059 0.0697 | 2.9160
- 43 | 1.75 | 0.0627 0.0034 0.0661 | 1.5785
- 44 | 1.75 | 0.0584 0.0056 0.0640 | 1.5194
- 45 | 1.75 | 0.0569 0.0065 0.0634 | 1.4626
- 57 | 1.50 | 0.0557 0.0047 0.0604 | 1.0900
- 58 | 1.50 | 0.0526 0.0067 0.0593 | 1.0730
- 59 | 1.50 | 0.0516 0.0074 0.0589 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 147s
- Prepare output 8s
- 156s
- Jacobian determinant (RMS): 0.013 0.045 0.067 0.092 0.115 | 0.122781
- Template Matching: 0.082 0.214 0.192 0.171 0.155 | 0.154692
- Write result maps: 39s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 17s
- CSF distance: 10s
- PBT2x thickness: 29s
- 60s
- Create initial surface 53s
- Topology correction: 56s
- Surface refinement: 52s
- Reduction of surface collisions with optimization: 41s
- Spherical mapping with areal smoothing 58s
- Spherical registration 223s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 19s
- CSF distance: 9s
- PBT2x thickness: 28s
- 60s
- Create initial surface 50s
- Topology correction: 55s
- Surface refinement: 43s
- Reduction of surface collisions with optimization: 40s
- Spherical mapping with areal smoothing 54s
- Spherical registration 216s
- Final surface processing results:
- Average thickness (FS): 2.5002 0.6289 mm
- Surface intensity / position RMSE: 0.0713 / 0.0747
- Euler number / defect number / defect size: 38.0 / 21.5 / 1.26%
- Display thickness: /var/lib/condor/execute/dir_2825747/ds/DC_1/sub-0027335/ses-1/surf/lh.thickness.sub-0027335_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2825747/ds/DC_1/sub-0027335/ses-1/surf/rh.thickness.sub-0027335_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2825747/ds/DC_1/sub-0027335/ses-1/sub-0027335_ses-1_run-1_T1w.nii
- Surface ROI estimation: 7s
- Surface and thickness estimation takes: 1134s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 32s
- ROI estimation of 'lpba40' atlas 10s
- ROI estimation of 'hammers' atlas 24s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 8s
- ROI estimation of 'aal3' atlas 13s
- ROI estimation of 'mori' atlas 20s
- ROI estimation of 'anatomy3' atlas 33s
- ROI estimation of 'julichbrain' atlas 45s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 18s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 35s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 77s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 113s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 9s
- Write results 10s
- 450s
- Quality check: 10s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2825747/ds/DC_1/sub-0027335/ses-1/report/catreport_sub-0027335_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 39 minute(s) and 23 second(s).
- Image Quality Rating (IQR): 76.55% (C)
- GM volume (GMV): 51.43% (613.06 / 1191.95 ml)
- GM thickness (GMT): 2.50 0.63 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2825747/ds/DC_1/sub-0027335/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_2825747/ds/DC_1/sub-0027335/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_2825747/ds/DC_1/sub-0027335/ses-1/label
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