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- CAT12.8.1 r2040: 1/1: ./sub-0025326/ses-1/sub-0025326_ses-1_run-1_T1w.n
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- SANLM denoising (medium): 34s
- APP: Rough bias correction:
- Initialize 3s
- Estimate background 3s
- Initial correction 3s
- Refine background 2s
- Final correction 3s
- Final scaling 3s
- 21s
- Correct center-of-mass 2s
- Affine registration 5s
- SPM preprocessing 1 (estimate 1 - TPM registration): 48s
- SPM preprocessing 1 (estimate 2): 42s
- SPM preprocessing 2 (write):
- Write Segmentation 10s
- Update Segmentation 12s
- Update Skull-Stripping 24s
- Update probability maps 5s
- 51s
- Global intensity correction: 9s
- SANLM denoising after intensity normalization (medium): 18s
- Fast Optimized Shooting registration 21s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 2s
- Prepare partitions 1s
- Prepare segments (LASmod = 1.00) 9s
- Estimate local tissue thresholds (WM) 11s
- Estimate local tissue thresholds (GM) 16s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 28s
- 71s
- ROI segmentation (partitioning):
- Atlas -> subject space 4s
- Major structures 2s
- Ventricle detection 8s
- Blood vessel detection 6s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 14s
- Manual stroke lesion detection 0s
- Closing of deep structures 1s
- Side alignment 2s
- Final corrections 3s
- 41s
- Blood vessel correction (BVCstr=0.50): 1s
- Amap using initial SPM12 segmentations (MRF filter strength 0.05): 24s
- AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05]
- 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 | 0.0827 0.0000 0.0827 | 32.0000
- 2 | 2.50 | 0.0799 0.0013 0.0812 | 29.4886
- 3 | 2.50 | 0.0791 0.0019 0.0810 | 26.9772
- 4 | 2.50 | 0.0787 0.0021 0.0808 | 24.6107
- 5 | 2.50 | 0.0784 0.0023 0.0807 | 22.6548
- 6 | 2.50 | 0.0781 0.0024 0.0805 | 20.6989
- 7 | 2.50 | 0.0778 0.0025 0.0803 | 18.9688
- 8 | 2.50 | 0.0775 0.0026 0.0801 | 17.4455
- 9 | 2.50 | 0.0772 0.0027 0.0798 | 15.9223
- 10 | 2.50 | 0.0768 0.0028 0.0796 | 14.6627
- 11 | 2.50 | 0.0765 0.0029 0.0794 | 13.4764
- 12 | 2.50 | 0.0762 0.0029 0.0791 | 12.3015
- 13 | 2.50 | 0.0758 0.0030 0.0788 | 11.3776
- 14 | 2.50 | 0.0755 0.0031 0.0786 | 10.4537
- 15 | 2.25 | 0.0745 0.0032 0.0776 | 9.5920
- 16 | 2.25 | 0.0711 0.0048 0.0759 | 8.8725
- 29 | 2.00 | 0.0717 0.0022 0.0739 | 3.3283
- 30 | 2.00 | 0.0654 0.0047 0.0701 | 3.1221
- 31 | 2.00 | 0.0633 0.0056 0.0689 | 2.9160
- 43 | 1.75 | 0.0619 0.0033 0.0651 | 1.5785
- 44 | 1.75 | 0.0578 0.0054 0.0632 | 1.5194
- 45 | 1.75 | 0.0564 0.0061 0.0625 | 1.4626
- 57 | 1.50 | 0.0547 0.0045 0.0592 | 1.0900
- 58 | 1.50 | 0.0519 0.0063 0.0582 | 1.0730
- 59 | 1.50 | 0.0509 0.0068 0.0578 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 110s
- Prepare output 7s
- 116s
- Jacobian determinant (RMS): 0.012 0.042 0.063 0.089 0.111 | 0.117231
- Template Matching: 0.083 0.213 0.190 0.169 0.153 | 0.152838
- Write result maps: 20s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 19s
- CSF distance: 10s
- PBT2x thickness: 30s
- 63s
- Create initial surface 53s
- Topology correction: 65s
- Surface refinement: 54s
- Reduction of surface collisions with optimization: 48s
- Spherical mapping with areal smoothing 59s
- Spherical registration 191s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 18s
- CSF distance: 10s
- PBT2x thickness: 28s
- 61s
- Create initial surface 51s
- Topology correction: 61s
- Surface refinement: 67s
- Reduction of surface collisions with optimization: 45s
- Spherical mapping with areal smoothing 57s
- Spherical registration 185s
- Final surface processing results:
- Average thickness (FS): 2.7043 0.6424 mm
- Surface intensity / position RMSE: 0.0695 / 0.0656
- Euler number / defect number / defect size: 16.0 / 10.0 / 0.42%
- Display thickness: /var/lib/condor/execute/dir_1958205/ds/UPSM_1/sub-0025326/ses-1/surf/lh.thickness.sub-0025326_ses-1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_1958205/ds/UPSM_1/sub-0025326/ses-1/surf/rh.thickness.sub-0025326_ses-1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1958205/ds/UPSM_1/sub-0025326/ses-1/sub-0025326_ses-1_run-1_T1w.nii
- Surface ROI estimation: 6s
- Surface and thickness estimation takes: 1124s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 5s
- ROI estimation of 'neuromorphometrics' atlas 19s
- ROI estimation of 'lpba40' atlas 5s
- ROI estimation of 'hammers' atlas 13s
- ROI estimation of 'thalamus' atlas 1s
- ROI estimation of 'ibsr' atlas 5s
- ROI estimation of 'aal3' atlas 7s
- ROI estimation of 'mori' atlas 11s
- ROI estimation of 'anatomy3' atlas 15s
- ROI estimation of 'julichbrain' atlas 20s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 8s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 14s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 32s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 48s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 4s
- Write results 5s
- 208s
- Quality check: 7s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1958205/ds/UPSM_1/sub-0025326/ses-1/report/catreport_sub-0025326_ses-1_run-1_T1w.pdf
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- CAT preprocessing takes 32 minute(s) and 19 second(s).
- Image Quality Rating (IQR): 81.16% (B-)
- GM volume (GMV): 51.33% (737.02 / 1435.91 ml)
- GM thickness (GMT): 2.70 0.64 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1958205/ds/UPSM_1/sub-0025326/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_1958205/ds/UPSM_1/sub-0025326/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_1958205/ds/UPSM_1/sub-0025326/ses-1/label
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