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- CAT12.8.1 r2040: 1/1: ./sub-0027153/ses-1/sub-0027153_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 65s
- APP: Rough bias correction:
- Initialize 8s
- Estimate background 8s
- Initial correction 14s
- Refine background 4s
- Final correction 10s
- Final scaling 7s
- 58s
- Correct center-of-mass 4s
- Affine registration 12s
- SPM preprocessing 1 (estimate 1 - TPM registration): 104s
- SPM preprocessing 1 (estimate 2): 76s
- SPM preprocessing 2 (write):
- Write Segmentation 22s
- Update Segmentation 26s
- Update Skull-Stripping 54s
- Update probability maps 10s
- 112s
- Global intensity correction: 20s
- SANLM denoising after intensity normalization (medium): 37s
- Fast Optimized Shooting registration 42s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 5s
- Prepare partitions 3s
- Prepare segments (LASmod = 1.16) 21s
- Estimate local tissue thresholds (WM) 27s
- Estimate local tissue thresholds (GM) 42s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 63s
- 164s
- ROI segmentation (partitioning):
- Atlas -> subject space 9s
- Major structures 5s
- Ventricle detection 26s
- Blood vessel detection 15s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.05) 36s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 5s
- Final corrections 5s
- 105s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 44s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- 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) 4s
- 16s
- 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 | 0.0832 0.0000 0.0832 | 32.0000
- 2 | 2.50 | 0.0813 0.0010 0.0823 | 29.4886
- 3 | 2.50 | 0.0807 0.0015 0.0821 | 26.9772
- 4 | 2.50 | 0.0804 0.0016 0.0820 | 24.6107
- 5 | 2.50 | 0.0801 0.0018 0.0819 | 22.6548
- 6 | 2.50 | 0.0799 0.0018 0.0818 | 20.6989
- 7 | 2.50 | 0.0797 0.0019 0.0816 | 18.9688
- 8 | 2.50 | 0.0795 0.0020 0.0815 | 17.4455
- 9 | 2.50 | 0.0792 0.0021 0.0813 | 15.9223
- 10 | 2.50 | 0.0790 0.0022 0.0811 | 14.6627
- 11 | 2.50 | 0.0787 0.0022 0.0810 | 13.4764
- 12 | 2.50 | 0.0785 0.0023 0.0808 | 12.3015
- 13 | 2.50 | 0.0782 0.0024 0.0806 | 11.3776
- 14 | 2.50 | 0.0780 0.0024 0.0804 | 10.4537
- 15 | 2.25 | 0.0774 0.0025 0.0799 | 9.5920
- 16 | 2.25 | 0.0747 0.0038 0.0786 | 8.8725
- 29 | 2.00 | 0.0769 0.0017 0.0786 | 3.3283
- 30 | 2.00 | 0.0706 0.0043 0.0749 | 3.1221
- 31 | 2.00 | 0.0686 0.0053 0.0739 | 2.9160
- 43 | 1.75 | 0.0680 0.0030 0.0710 | 1.5785
- 44 | 1.75 | 0.0631 0.0056 0.0687 | 1.5194
- 45 | 1.75 | 0.0615 0.0065 0.0680 | 1.4626
- 57 | 1.50 | 0.0601 0.0047 0.0648 | 1.0900
- 58 | 1.50 | 0.0566 0.0069 0.0636 | 1.0730
- 59 | 1.50 | 0.0555 0.0077 0.0632 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 205s
- Prepare output 15s
- 220s
- Jacobian determinant (RMS): 0.009 0.033 0.051 0.078 0.103 | 0.109189
- Template Matching: 0.083 0.224 0.206 0.185 0.166 | 0.166454
- Write result maps: 45s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 89s
- CSF distance: 24s
- PBT2x thickness: 70s
- 191s
- Create initial surface 121s
- Topology correction: 130s
- Surface refinement: 143s
- Reduction of surface collisions with optimization: 107s
- Spherical mapping with areal smoothing 124s
- Spherical registration 334s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 56s
- CSF distance: 25s
- PBT2x thickness: 73s
- 162s
- Create initial surface 124s
- Topology correction: 139s
- Surface refinement: 132s
- Reduction of surface collisions with optimization: 113s
- Spherical mapping with areal smoothing 148s
- Spherical registration 356s
- Final surface processing results:
- Average thickness (FS): 2.6893 0.6526 mm
- Surface intensity / position RMSE: 0.0705 / 0.0692
- Euler number / defect number / defect size: 26.0 / 18.0 / 0.71%
- Display thickness: /var/lib/condor/execute/dir_1728261/ds/SWU_3/sub-0027153/ses-1/surf/lh.thickness.sub-0027153_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1728261/ds/SWU_3/sub-0027153/ses-1/surf/rh.thickness.sub-0027153_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1728261/ds/SWU_3/sub-0027153/ses-1/sub-0027153_ses-1_run-1_T1w.nii
- Surface ROI estimation: 11s
- Surface and thickness estimation takes: 2460s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 11s
- ROI estimation of 'neuromorphometrics' atlas 38s
- ROI estimation of 'lpba40' atlas 11s
- ROI estimation of 'hammers' atlas 27s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 9s
- ROI estimation of 'aal3' atlas 15s
- ROI estimation of 'mori' atlas 22s
- ROI estimation of 'anatomy3' atlas 30s
- ROI estimation of 'julichbrain' atlas 40s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 16s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 27s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 61s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 90s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s
- Write results 9s
- 407s
- Quality check: 15s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1728261/ds/SWU_3/sub-0027153/ses-1/report/catreport_sub-0027153_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 69 minute(s) and 26 second(s).
- Image Quality Rating (IQR): 82.73% (B-)
- GM volume (GMV): 49.36% (855.05 / 1732.42 ml)
- GM thickness (GMT): 2.69 0.65 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1728261/ds/SWU_3/sub-0027153/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_1728261/ds/SWU_3/sub-0027153/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_1728261/ds/SWU_3/sub-0027153/ses-1/label
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