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- CAT12.8.1 r1980: 1/1: ./dir_19491/ds/sub-25/sub-25_acq-highres_T1w.n
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- SANLM denoising (medium): 75s
- APP: Rough bias correction:
- Initialize 10s
- Estimate background 10s
- Initial correction 9s
- Refine background 5s
- Final correction 7s
- Final scaling 8s
- 58s
- Correct center-of-mass 8s
- Affine registration 14s
- SPM preprocessing 1 (estimate 1 - TPM registration): 10s
- Use initial fine affine registration. 87s
- SPM preprocessing 1 (estimate 2): 96s
- SPM preprocessing 2 (write):
- Write Segmentation 25s
- Update Segmentation 27s
- Update Skull-Stripping 59s
- Update probability maps 12s
- 124s
- Global intensity correction: 24s
- SANLM denoising after intensity normalization (medium): 15s
- Fast Optimized Shooting registration 51s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 6s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.02) 19s
- Estimate local tissue thresholds (WM) 23s
- Estimate local tissue thresholds (GM) 32s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 29s
- 118s
- ROI segmentation (partitioning):
- Atlas -> subject space 12s
- Major structures 5s
- Ventricle detection 23s
- Blood vessel detection 11s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.04) 32s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 5s
- Final corrections 6s
- 96s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 50s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.08,0.980.04]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 6s
- Level 1 cleanup (brain masking) 4s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 3s
- 15s
- 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 | 0.0853 0.0000 0.0853 | 32.0000
- 2 | 2.50 | 0.0829 0.0011 0.0840 | 29.4886
- 3 | 2.50 | 0.0822 0.0017 0.0839 | 26.9772
- 4 | 2.50 | 0.0818 0.0019 0.0837 | 24.6107
- 5 | 2.50 | 0.0816 0.0020 0.0836 | 22.6548
- 6 | 2.50 | 0.0813 0.0021 0.0834 | 20.6989
- 7 | 2.50 | 0.0811 0.0022 0.0833 | 18.9688
- 8 | 2.50 | 0.0808 0.0023 0.0831 | 17.4455
- 9 | 2.50 | 0.0805 0.0024 0.0829 | 15.9223
- 10 | 2.50 | 0.0802 0.0025 0.0827 | 14.6627
- 11 | 2.50 | 0.0800 0.0025 0.0825 | 13.4764
- 12 | 2.50 | 0.0797 0.0026 0.0823 | 12.3015
- 13 | 2.50 | 0.0794 0.0027 0.0821 | 11.3776
- 14 | 2.50 | 0.0791 0.0027 0.0818 | 10.4537
- 15 | 2.25 | 0.0794 0.0028 0.0822 | 9.5920
- 16 | 2.25 | 0.0765 0.0042 0.0807 | 8.8725
- 17 | 2.25 | 0.0753 0.0047 0.0800 | 8.1530
- 18 | 2.25 | 0.0745 0.0049 0.0795 | 7.5234
- 29 | 2.00 | 0.0771 0.0024 0.0795 | 3.3283
- 30 | 2.00 | 0.0719 0.0047 0.0765 | 3.1221
- 31 | 2.00 | 0.0700 0.0056 0.0756 | 2.9160
- 43 | 1.75 | 0.0694 0.0032 0.0726 | 1.5785
- 44 | 1.75 | 0.0648 0.0056 0.0704 | 1.5194
- 45 | 1.75 | 0.0632 0.0065 0.0697 | 1.4626
- 57 | 1.50 | 0.0621 0.0047 0.0668 | 1.0900
- 58 | 1.50 | 0.0586 0.0070 0.0656 | 1.0730
- 59 | 1.50 | 0.0575 0.0077 0.0652 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 268s
- Prepare output 14s
- 282s
- Jacobian determinant (RMS): 0.011 0.040 0.061 0.085 0.109 | 0.115992
- Template Matching: 0.085 0.224 0.210 0.190 0.172 | 0.172461
- Write result maps: 39s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 43s
- CSF distance: 21s
- PBT2x thickness: 65s
- 138s
- Create initial surface 112s
- Topology correction: 136s
- Surface refinement: 127s
- Reduction of surface collisions with optimization: 114s
- Spherical mapping with areal smoothing 119s
- Spherical registration 309s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 43s
- CSF distance: 22s
- PBT2x thickness: 65s
- 139s
- Create initial surface 111s
- Topology correction: 135s
- Surface refinement: 114s
- Reduction of surface collisions with optimization: 114s
- Spherical mapping with areal smoothing 121s
- Spherical registration 307s
- Final surface processing results:
- Average thickness (FS): 2.4467 0.5804 mm
- Surface intensity / position RMSE: 0.0689 / 0.0758
- Euler number / defect number / defect size: 14.0 / 12.0 / 0.90%
- Display thickness: /var/lib/condor/execute/dir_19491/ds/sub-25/surf/lh.thickness.sub-25_acq-highres_T1w
- Display thickness: /var/lib/condor/execute/dir_19491/ds/sub-25/surf/rh.thickness.sub-25_acq-highres_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_19491/ds/sub-25/sub-25_acq-highres_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 2226s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 20s
- ROI estimation of 'neuromorphometrics' atlas 72s
- ROI estimation of 'lpba40' atlas 21s
- ROI estimation of 'hammers' atlas 49s
- ROI estimation of 'thalamus' atlas 4s
- ROI estimation of 'ibsr' atlas 19s
- ROI estimation of 'aal3' atlas 32s
- ROI estimation of 'mori' atlas 45s
- ROI estimation of 'anatomy3' atlas 64s
- ROI estimation of 'julichbrain' atlas 83s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 28s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 37s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 122s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 182s
- Write results 184s
- 782s
- Quality check: 7s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_19491/ds/sub-25/report/catreport_sub-25_acq-highres_T1w.pdf
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- CAT preprocessing takes 72 minute(s) and 0 second(s).
- Image Quality Rating (IQR): 83.72% (B)
- GM volume (GMV): 48.12% (702.59 / 1459.99 ml)
- GM thickness (GMT): 2.45 0.58 mm
- Segmentations are saved in /var/lib/condor/execute/dir_19491/ds/sub-25/mri
- Reports are saved in /var/lib/condor/execute/dir_19491/ds/sub-25/report
- Labels are saved in /var/lib/condor/execute/dir_19491/ds/sub-25/label
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