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- CAT12.8.1 r2040: 1/1: ./sub-0027343/ses-1/sub-0027343_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 32s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 7s
- Initial correction 8s
- Refine background 4s
- Final correction 6s
- Final scaling 5s
- 46s
- Correct center-of-mass 3s
- Affine registration 10s
- SPM preprocessing 1 (estimate 1 - TPM registration): 94s
- SPM preprocessing 1 (estimate 2): 73s
- SPM preprocessing 2 (write):
- Write Segmentation 20s
- Update Segmentation 21s
- Update Skull-Stripping 51s
- Update probability maps 12s
- 105s
- Global intensity correction: 20s
- SANLM denoising after intensity normalization (medium): 27s
- Fast Optimized Shooting registration 35s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 4s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.05) 15s
- Estimate local tissue thresholds (WM) 21s
- Estimate local tissue thresholds (GM) 31s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 48s
- 127s
- ROI segmentation (partitioning):
- Atlas -> subject space 8s
- Major structures 4s
- Ventricle detection 19s
- Blood vessel detection 10s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 26s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 4s
- Final corrections 6s
- 77s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 35s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- 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
- 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 | 0.0842 0.0000 0.0842 | 32.0000
- 2 | 2.50 | 0.0815 0.0012 0.0827 | 29.4886
- 3 | 2.50 | 0.0808 0.0018 0.0826 | 26.9772
- 4 | 2.50 | 0.0804 0.0020 0.0824 | 24.6107
- 5 | 2.50 | 0.0801 0.0022 0.0823 | 22.6548
- 6 | 2.50 | 0.0799 0.0022 0.0821 | 20.6989
- 7 | 2.50 | 0.0796 0.0024 0.0819 | 18.9688
- 8 | 2.50 | 0.0793 0.0025 0.0818 | 17.4455
- 9 | 2.50 | 0.0790 0.0025 0.0816 | 15.9223
- 10 | 2.50 | 0.0787 0.0026 0.0814 | 14.6627
- 11 | 2.50 | 0.0784 0.0027 0.0811 | 13.4764
- 12 | 2.50 | 0.0781 0.0028 0.0809 | 12.3015
- 13 | 2.50 | 0.0778 0.0029 0.0807 | 11.3776
- 14 | 2.50 | 0.0775 0.0030 0.0804 | 10.4537
- 15 | 2.25 | 0.0768 0.0030 0.0798 | 9.5920
- 16 | 2.25 | 0.0737 0.0045 0.0782 | 8.8725
- 29 | 2.00 | 0.0751 0.0020 0.0771 | 3.3283
- 30 | 2.00 | 0.0688 0.0046 0.0734 | 3.1221
- 31 | 2.00 | 0.0667 0.0056 0.0722 | 2.9160
- 43 | 1.75 | 0.0656 0.0032 0.0688 | 1.5785
- 44 | 1.75 | 0.0611 0.0056 0.0667 | 1.5194
- 45 | 1.75 | 0.0596 0.0063 0.0660 | 1.4626
- 57 | 1.50 | 0.0581 0.0046 0.0627 | 1.0900
- 58 | 1.50 | 0.0549 0.0067 0.0616 | 1.0730
- 59 | 1.50 | 0.0539 0.0073 0.0612 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 172s
- Prepare output 12s
- 185s
- Jacobian determinant (RMS): 0.012 0.042 0.062 0.086 0.108 | 0.113910
- Template Matching: 0.084 0.221 0.200 0.179 0.162 | 0.161623
- Write result maps: 47s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 27s
- CSF distance: 15s
- PBT2x thickness: 43s
- 92s
- Create initial surface 85s
- Topology correction: 89s
- Surface refinement: 104s
- Reduction of surface collisions with optimization: 67s
- Spherical mapping with areal smoothing 77s
- Spherical registration 282s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 24s
- CSF distance: 15s
- PBT2x thickness: 42s
- 86s
- Create initial surface 82s
- Topology correction: 90s
- Surface refinement: 80s
- Reduction of surface collisions with optimization: 63s
- Spherical mapping with areal smoothing 74s
- Spherical registration 296s
- Final surface processing results:
- Average thickness (FS): 2.5887 0.6350 mm
- Surface intensity / position RMSE: 0.0670 / 0.0742
- Euler number / defect number / defect size: 12.0 / 12.0 / 0.76%
- Display thickness: /var/lib/condor/execute/dir_3675059/ds/DC_1/sub-0027343/ses-1/surf/lh.thickness.sub-0027343_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_3675059/ds/DC_1/sub-0027343/ses-1/surf/rh.thickness.sub-0027343_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_3675059/ds/DC_1/sub-0027343/ses-1/sub-0027343_ses-1_run-1_T1w.nii
- Surface ROI estimation: 11s
- Surface and thickness estimation takes: 1674s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 14s
- ROI estimation of 'neuromorphometrics' atlas 56s
- ROI estimation of 'lpba40' atlas 17s
- ROI estimation of 'hammers' atlas 41s
- ROI estimation of 'thalamus' atlas 3s
- ROI estimation of 'ibsr' atlas 16s
- ROI estimation of 'aal3' atlas 30s
- ROI estimation of 'mori' atlas 49s
- ROI estimation of 'anatomy3' atlas 72s
- ROI estimation of 'julichbrain' atlas 95s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 39s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 77s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 144s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 177s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 12s
- Write results 13s
- 844s
- Quality check: 14s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_3675059/ds/DC_1/sub-0027343/ses-1/report/catreport_sub-0027343_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 59 minute(s) and 6 second(s).
- Image Quality Rating (IQR): 76.25% (C)
- GM volume (GMV): 50.63% (685.42 / 1353.77 ml)
- GM thickness (GMT): 2.59 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_3675059/ds/DC_1/sub-0027343/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_3675059/ds/DC_1/sub-0027343/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_3675059/ds/DC_1/sub-0027343/ses-1/label
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