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- CAT12.8.1 r2040: 1/1: ./sub-0025821/ses-2/sub-0025821_ses-2_run-1_T1w.n
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- SANLM denoising (medium): 47s
- APP: Rough bias correction:
- Initialize 6s
- Estimate background 5s
- Initial correction 5s
- Refine background 3s
- Final correction 5s
- Final scaling 5s
- 35s
- Correct center-of-mass 3s
- Affine registration 8s
- SPM preprocessing 1 (estimate 1 - TPM registration): 62s
- SPM preprocessing 1 (estimate 2): 62s
- SPM preprocessing 2 (write):
- Write Segmentation 16s
- Update Segmentation 17s
- Update Skull-Stripping 39s
- Update probability maps 8s
- 80s
- Global intensity correction: 16s
- SANLM denoising after intensity normalization (medium): 24s
- Fast Optimized Shooting registration 31s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 3s
- Prepare partitions 2s
- Prepare segments (LASmod = 1.24) 13s
- Estimate local tissue thresholds (WM) 18s
- Estimate local tissue thresholds (GM) 26s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 44s
- 110s
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 3s
- Ventricle detection 11s
- Blood vessel detection 8s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 21s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 3s
- Final corrections 4s
- 59s
- Blood vessel correction (BVCstr=0.50): 2s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 31s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 4s
- Level 1 cleanup (brain masking) 3s
- Level 2 cleanup (CSF correction) 1s
- Level 3 cleanup (CSF/WM PVE) 3s
- 11s
- 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 | 0.0849 0.0000 0.0849 | 32.0000
- 2 | 2.50 | 0.0808 0.0016 0.0824 | 29.4886
- 3 | 2.50 | 0.0797 0.0024 0.0821 | 26.9772
- 4 | 2.50 | 0.0791 0.0027 0.0818 | 24.6107
- 5 | 2.50 | 0.0787 0.0029 0.0816 | 22.6548
- 6 | 2.50 | 0.0784 0.0029 0.0813 | 20.6989
- 7 | 2.50 | 0.0780 0.0031 0.0811 | 18.9688
- 8 | 2.50 | 0.0776 0.0032 0.0808 | 17.4455
- 9 | 2.50 | 0.0773 0.0032 0.0805 | 15.9223
- 10 | 2.50 | 0.0769 0.0033 0.0802 | 14.6627
- 11 | 2.50 | 0.0765 0.0034 0.0799 | 13.4764
- 12 | 2.50 | 0.0761 0.0035 0.0796 | 12.3015
- 13 | 2.50 | 0.0757 0.0036 0.0793 | 11.3776
- 14 | 2.50 | 0.0753 0.0036 0.0789 | 10.4537
- 15 | 2.25 | 0.0742 0.0037 0.0779 | 9.5920
- 16 | 2.25 | 0.0710 0.0052 0.0762 | 8.8725
- 29 | 2.00 | 0.0719 0.0023 0.0742 | 3.3283
- 30 | 2.00 | 0.0657 0.0048 0.0705 | 3.1221
- 31 | 2.00 | 0.0637 0.0057 0.0694 | 2.9160
- 43 | 1.75 | 0.0625 0.0033 0.0658 | 1.5785
- 44 | 1.75 | 0.0584 0.0054 0.0639 | 1.5194
- 45 | 1.75 | 0.0571 0.0062 0.0633 | 1.4626
- 57 | 1.50 | 0.0556 0.0045 0.0601 | 1.0900
- 58 | 1.50 | 0.0527 0.0064 0.0591 | 1.0730
- 59 | 1.50 | 0.0517 0.0070 0.0588 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 166s
- Prepare output 10s
- 176s
- Jacobian determinant (RMS): 0.011 0.039 0.058 0.083 0.107 | 0.115108
- Template Matching: 0.085 0.213 0.191 0.171 0.155 | 0.155152
- Write result maps: 33s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 27s
- CSF distance: 14s
- PBT2x thickness: 42s
- 89s
- Create initial surface 79s
- Topology correction: 74s
- Surface refinement: 68s
- Reduction of surface collisions with optimization: 63s
- Spherical mapping with areal smoothing 77s
- Spherical registration 291s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 25s
- CSF distance: 14s
- PBT2x thickness: 42s
- 86s
- Create initial surface 79s
- Topology correction: 72s
- Surface refinement: 90s
- Reduction of surface collisions with optimization: 59s
- Spherical mapping with areal smoothing 73s
- Spherical registration 311s
- Final surface processing results:
- Average thickness (FS): 2.6767 0.6352 mm
- Surface intensity / position RMSE: 0.0646 / 0.0616
- Euler number / defect number / defect size: 8.0 / 4.0 / 0.49%
- Display thickness: /var/lib/condor/execute/dir_2900407/ds/SWU_4/sub-0025821/ses-2/surf/lh.thickness.sub-0025821_ses-2_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_2900407/ds/SWU_4/sub-0025821/ses-2/surf/rh.thickness.sub-0025821_ses-2_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_2900407/ds/SWU_4/sub-0025821/ses-2/sub-0025821_ses-2_run-1_T1w.nii
- Surface ROI estimation: 9s
- Surface and thickness estimation takes: 1605s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 9s
- ROI estimation of 'neuromorphometrics' atlas 34s
- ROI estimation of 'lpba40' atlas 11s
- ROI estimation of 'hammers' atlas 23s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 8s
- ROI estimation of 'aal3' atlas 13s
- ROI estimation of 'mori' atlas 19s
- ROI estimation of 'anatomy3' atlas 27s
- ROI estimation of 'julichbrain' atlas 36s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 28s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 56s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 84s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s
- Write results 8s
- 374s
- Quality check: 12s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_2900407/ds/SWU_4/sub-0025821/ses-2/report/catreport_sub-0025821_ses-2_run-1_T1w.pdf
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- CAT preprocessing takes 47 minute(s) and 42 second(s).
- Image Quality Rating (IQR): 82.76% (B-)
- GM volume (GMV): 48.74% (667.81 / 1370.11 ml)
- GM thickness (GMT): 2.68 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_2900407/ds/SWU_4/sub-0025821/ses-2/mri
- Reports are saved in /var/lib/condor/execute/dir_2900407/ds/SWU_4/sub-0025821/ses-2/report
- Labels are saved in /var/lib/condor/execute/dir_2900407/ds/SWU_4/sub-0025821/ses-2/label
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